PACN Stream Monitoring Protocol

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National Park Service
U.S. Department of the Interior

Natural Resource Stewardship and Science

Pacific Islands Stream Monitoring Protocol:
Fish, Shrimp, Snails, and Habitat Characterization
Pacific Island Network
Natural Resource Report NPS/PACN/NRR—2011/468

ON THE COVER
NPS Photos – clockwise from upper left: Macrobrachium latimanus in the National Park of American Samoa, Lentipes concolor in
Kalaupapa National Historical Park, Neritina granosa in Kalaupapa National Historical Park, Waikolu stream in Kalaupapa National
Historical Park.

Pacific Islands Stream Monitoring Protocol:
Fish, Shrimp, Snails, and Habitat Characterization
Pacific Island Network
Natural Resource Report NPS/PACN/NRR—2011/468
Anne Brasher1, Tahzay Jones2, Anne Farahi3, Matt Miller1 and Kelly Kozar3
1

U.S. Geological Survey
Utah Water Science Center
121 West 200 South
Moab, UT 84532
2

National Park Service
Ocean Stewardship Program
240 West 5th Ave.
Anchorage, AK 99501
3

National Park Service
Pacific Island Inventory and Monitoring Network
Hawaii Volcanoes National Park
P.O. Box 52
Hawaii National Park, Hawaii 96718

December 2011
U.S. Department of the Interior
National Park Service
Natural Resource Stewardship and Science
Fort Collins, Colorado

The National Park Service, Natural Resource Stewardship and Science office in Fort Collins,
Colorado publishes a range of reports that address natural resource topics of interest and
applicability to a broad audience in the National Park Service and others in natural resource
management, including scientists, conservation and environmental constituencies, and the public.
The Natural Resource Report Series is used to disseminate high-priority, current natural resource
management information with managerial application. The series targets a general, diverse
audience, and may contain NPS policy considerations or address sensitive issues of management
applicability.
All manuscripts in the series receive the appropriate level of peer review to ensure that the
information is scientifically credible, technically accurate, appropriately written for the intended
audience, and designed and published in a professional manner. This report received formal peer
review by subject-matter experts who were not directly involved in the collection, analysis, or
reporting of the data, and whose background and expertise put them on par technically and
scientifically with the authors of the information.
Views, statements, findings, conclusions, recommendations, and data in this report do not
necessarily reflect views and policies of the National Park Service, U.S. Department of the
Interior. Mention of trade names or commercial products does not constitute endorsement or
recommendation for use by the U.S. Government.
This report is available from Pacific Island I&M Network website
(http://www.nature.nps.gov/im/units/PACN) and on the Natural Resource Publications
Management website (http://www.nature.nps.gov/publications/NRPM).
Please cite this publication as:
Brasher, A. M. D., T. Jones, A. C. Farahi, M. P. Miller, and K. Kozar. 2011. Stream monitoring
protocol: fish, shrimp, and snails; Pacific Island Network. Natural Resource Report
NPS/PACN/NRR—2011/468. National Park Service, Fort Collins, Colorado.

NPS 988/111725, December 2011
ii

Contents
Page
Figures............................................................................................................................................ ix
Tables ............................................................................................................................................. xi
Appendices ................................................................................................................................... xiii
Standard Operating Procedures..................................................................................................... xv
Abstract ........................................................................................................................................ xix
Chapter 1: Background and Objectives .......................................................................................... 1
Overview.................................................................................................................................. 1
Stream Fauna of Tropical Pacific Islands ................................................................................ 5
Life History Characteristics ................................................................................................ 5
Fauna of Hawaii, American Samoa, and Guam .................................................................. 6
American Samoa ...................................................................................................................... 7
Fish ...................................................................................................................................... 7
Crustaceans ......................................................................................................................... 8
Snails ................................................................................................................................... 9
Guam...................................................................................................................................... 10
Fish .................................................................................................................................... 10
Crustaceans ....................................................................................................................... 11
Hawaii .................................................................................................................................... 12
Fish .................................................................................................................................... 12
Crustaceans ....................................................................................................................... 13
Natural Drivers and Anthropogenic Stressors ....................................................................... 14
Channelization .................................................................................................................. 15
Sedimentation ................................................................................................................... 15
iii

Contents continued
Page
Riparian Cover and Temperature ...................................................................................... 16
Contaminants .................................................................................................................... 16
Stream Flow Alteration ..................................................................................................... 17
Invasive Species ................................................................................................................ 18
Measurable Objectives........................................................................................................... 19
Management Implications ..................................................................................................... 21
Parks and Streams Where Protocol Will Be Implemented .................................................... 21
Chapter 2: Sampling Design ......................................................................................................... 25
Background ............................................................................................................................ 25
Important Considerations....................................................................................................... 25
Maximizing Personnel Safety ................................................................................................ 25
Logistical and Fiscal Constraints ........................................................................................... 26
Integration with Other Vital Signs ......................................................................................... 26
Sampling ................................................................................................................................ 27
Stream Selection ............................................................................................................... 27
Station Selection ............................................................................................................... 27
Sampling Units.................................................................................................................. 27
Target Population .............................................................................................................. 28
Rationale for Sampling Design ......................................................................................... 28
Establishing Sampling Stations (Spatial Design) ............................................................. 29
Temporal Design and Sampling Frequency...................................................................... 30
Sampling Methodology ......................................................................................................... 30

iv

Contents continued
Page
Statistical Evaluation of Existing Data Sets .......................................................................... 30
Annual Precision Calculations .......................................................................................... 31
Quality Assurance of Data ..................................................................................................... 41
Chapter 3: Field Methods.............................................................................................................. 43
Field Season Preparations ...................................................................................................... 43
Training ............................................................................................................................. 43
Field Schedule ................................................................................................................... 43
Supplies and Equipment ................................................................................................... 43
Permits .............................................................................................................................. 44
Logistics ............................................................................................................................ 44
Overview of Sampling Methods for Pacific Island Streams ................................................. 44
Conducting Field Surveys—Fish, Shrimp, and Snails .......................................................... 44
Conducting Surveys on Tau, American Samoa ................................................................ 45
Conducting Surveys on Tutuila, American Samoa ........................................................... 45
Conducting Surveys on Guam .......................................................................................... 45
Conducting Surveys in Hawaii ......................................................................................... 46
Electrofishing for Fish and Crustaceans ................................................................................ 46
Conducting Field Surveys—Habitat ...................................................................................... 46
Conducting Field Surveys—Water Quality and Discharge ................................................... 47
After Field Activities ............................................................................................................. 47
Chapter 4: Data Handling, Analysis, and Reporting..................................................................... 49
Project Information Management Overview ......................................................................... 49

v

Contents continued
Page
Pre-season Preparations for Information Management ......................................................... 50
Set up Project Workspace ................................................................................................. 50
GPS Loading and Preparation........................................................................................... 50
Implement Working Database Copy................................................................................. 50
Overview of Database Design ............................................................................................... 51
Data Entry and Processing ..................................................................................................... 52
Regular Data Backups....................................................................................................... 52
Data Verification ............................................................................................................... 52
Field Form Handling Procedures ...................................................................................... 53
Image Handling Procedures .............................................................................................. 53
GPS Data Procedures ........................................................................................................ 53
Data Quality Review.............................................................................................................. 53
Data edits after certification .............................................................................................. 53
Geospatial Data ................................................................................................................. 54
Metadata Procedures .............................................................................................................. 54
Data Certification and Delivery ............................................................................................. 54
Data Analysis ......................................................................................................................... 55
Analytical Approach ......................................................................................................... 55
Status and Trend Analyses ................................................................................................ 55
Reporting and Product Development..................................................................................... 56
Report Content .................................................................................................................. 56
Standard Report Format ......................................................................................................... 57
Review Products for Sensitive Information ...................................................................... 57
vi

Contents continued
Page
Product Delivery, Posting, and Distribution .......................................................................... 57
Holding Period for Project Data ....................................................................................... 58
Special Procedures for Sensitive Information................................................................... 58
Archival and Records Management .................................................................................. 58
Season Close-out ................................................................................................................... 58
Chapter 5: Personnel Requirements and Training ....................................................................... 59
Roles and Responsibilities ..................................................................................................... 59
Project Lead ...................................................................................................................... 59
Aquatic Biological Technician ......................................................................................... 60
Park-Based NPS Staff ....................................................................................................... 61
PACN Data Manager ........................................................................................................ 61
PACN GIS Specialist ........................................................................................................ 61
PACN Program Manager .................................................................................................. 61
Qualifications and Training .............................................................................................. 61
Chapter 6: Operational Requirements ........................................................................................... 63
Pre-Monitoring Task .............................................................................................................. 63
Pre-Monitoring Documents .............................................................................................. 63
Annual Workload and Field Schedule .............................................................................. 63
Facilities and Equipment................................................................................................... 63
Start-up Costs......................................................................................................................... 64
Annual Budget ....................................................................................................................... 65
Procedures for Making/Implementing Changes to the Protocol............................................ 67
Chapter 7: Literature Cited ........................................................................................................... 69
vii

Figures
Page
Figure 1.1. Conceptual model describing general ecosystem functioning. Green
boxes indicate vital sign components that are part of this protocol. ............................................... 2
Figure 1.2. Potential anthropogenic stressors during the lifecycle of native stream
organisms. ....................................................................................................................................... 3
Figure 1.3. Map showing the geographical region of the 11 Pacific Island Network
park units. Red areas on the maps represent the location of each National Park. .......................... 4
Figure 1.4. Amphidromous life cycle of fish, shrimp, and snails. ................................................. 6
Figure 1.5. Responses to natural and anthropogenic stressors. .................................................... 20
Figure 1.6. Location of sampling streams at each of the four parks. ........................................... 23
Figure 2.1. Precision analysis curves of 30m length stations on the islands of Maui
and Molokai by fish species.......................................................................................................... 35
Figure 2.2. Power curve estimation for Molokai fish population data. Estimates based
on two-sided tests with an α = 0.1 comparison between means. .................................................. 39
Figure 4.1. Idealized flow diagram of the cyclical stages of project information
management, from pre-season preparation to season close-out. Note that quality
assurance and documentation are thematic and not limited to any particular stage of
the information life cycle. ............................................................................................................. 49
Figure A.2.1. Guam fish identification guide. ............................................................................ 82
Figure A.2.2. Guam snail identification guide. ........................................................................... 83
Figure A.3.1. Hawaii stream species identification guide. ......................................................... 86
Figure A.4.1. Introduced stream species identification guide..................................................... 90
Figure A.5.1. General Prevention Procedures for Stopping Aquatic Hitchhikers:
methods for preventing the transporation of non-native (introduced) species. ............................ 98
Figure A.7.1. National Park of American Samoa stream monitoring sampling fixed
sites on Tau. ................................................................................................................................ 106
Figure A.7.2. National Park of American Samoa stream monitoring sampling fixed
sites for eastern Tutuila. .............................................................................................................. 107

ix

Figures continued
Page
Figure A.7.3. National Park of American Samoa stream monitoring sampling fixed
sites for western Tutuila. ............................................................................................................. 108
Figure A.7.4. War in the Pacific National Historical Park stream monitoring
sampling fixed sites..................................................................................................................... 110
Figure A.7.5. Haleakala National Park stream monitoring sampling fixed sites. ..................... 112
Figure A.7.6. Kalaupapa National Historical Park stream monitoring sampling fixed
sites. ............................................................................................................................................ 114
Figure A.13.1. Data model for the PACN Stream Monitoring database. .................................. 152
Figure A.15.1. Average abundance of Nakea, Nopili, and Alamo’o in Unknown
Stream at Station D (160 meters from the mouth) from 2000-2007. .......................................... 165
Figure A.15.2. Average abundance of Nopili in Unknown Stream at stations along a
longitudinal gradient from the mouth to the headwaters in 2005, 2006, and 2007 .................... 166

x

Tables
Page
Table 2.1. Number of fixed and rotating stations per stream with current sampling
strategy. ......................................................................................................................................... 28
Table 2.2. Coefficients of variation (CVs) for streams (CVSTR), stations (CVSTA),
and quadrats (CVQUAD) by fish species and island.................................................................... 32
Table 2.3. Precision estimates for three species of gobies. Estimates use fifteen 30 m
stations on a single 3,000 m stream with a 90% confidence interval and the CV data
from Table 2.1. .............................................................................................................................. 34
Table 2.4. Optimal fraction of fixed stations in streams to retain from one year to the
next in a panel design as a function of interannual correlation..................................................... 36
Table 2.5. Average sampling correlations in fish abundance for Waikolu, Molokai
(KALA). ........................................................................................................................................ 37
Table 2.6 Power to detect a difference between population means estimations for
three fish species on Molokai. ...................................................................................................... 40
Table 2.7. Modeled power to detect change over time with specific confidences based
on actual data from Maui, following the I&M protocol recommendations (15 sites 8
fixed and 7 random). ..................................................................................................................... 40
Table 4.1. Functional comparison of the master project database and the working
database ......................................................................................................................................... 51
Table 4.2. Preliminary approaches to analyzing stream community data. ................................... 56
Table 5.1 Personnel Roles and Responsibilities for the PACN Pacific Islands Stream
Monitoring: Fish, Shrimp, Snails and Habitat Characterization. .................................................. 60
Table 6.1 Annual (fiscal year) schedule of monitoring activity benchmarks, with
responsible individual(s) identified............................................................................................... 64
Table 6.2. Start-up costs. .............................................................................................................. 65
Table 6.3. Annual itemized expenses for the Pacific Islands Stream Monitoring
Protocol by park. ........................................................................................................................... 66
Table 6.4. Annual requirements for staffing of the Pacific Islands Stream Monitoring
Protocol: anticipated work days for identified personnel in each park. ..................................... 67

xi

Tables continued
Page
Table A.5.1. Recipe for 5% cleaning solution using either Quat128® or Sparquat
256® .............................................................................................................................................. 99
Table A.6.1. 25 year extrapolated results from two years of quarterly data collected in
Waikolu stream on the island of Molokai in Kalaupapa National Historical Park. .................... 101
Table A.6.2. Differences of the whole stream sampling power output vs. the station
by station power output............................................................................................................... 102
Table A.6.3. Differences of quarterly sampling vs. annual sampling power to detect
trends in population changes. ...................................................................................................... 102
Table A.6.4. Power output results of the Skalski Trend Analysis on the data set
collected by Anne Brasher in 1993 – 1994 in Waikolu Stream in Kalaupapa National
Historical Park on the Island of Molokai, Hawaii. ..................................................................... 103
Table A.7.1. Stream monitoring sampling fixed sites for National Park of American
Samoa.......................................................................................................................................... 109
Table A.7.2. Stream monitoring sampling fixed sites for War in the Pacific National
Historical Park. ........................................................................................................................... 111
Table A.7.3. Stream monitoring sampling fixed sites for Haleakala National Park. ................. 113
Table A.7.4. Stream monitoring sampling fixed sites for Kalaupapa National
Historical Park. ........................................................................................................................... 115
Table A.8.1. Aquatic Sampling Schedule at each park for each protocol.................................. 117
Table A.12.1 Identification of each task by project stage, indicates who is
responsible, and establishes the timing for each task.. ............................................................... 147

xii

Appendices
Page
Appendix 1: Species identification guide for American Samoa ................................................... 79
Appendix 2: Species identification guide for Guam ..................................................................... 81
Appendix 3: Species identification guide for Hawaii ................................................................... 85
Appendix 4: Introduced species identification guide................................................................... 89
Appendix 5: Logistics and Aquatic Hitchhikers ........................................................................... 91
Appendix 6: Additional statistical analyses and power estimates for preliminary
sample size determination ........................................................................................................... 101
Appendix 7: Fixed Sampling sites (maps and coordinates) ........................................................ 105
Appendix 8: Recommended field sampling schedule................................................................. 117
Appendix 9: Data sheets: American Samoa................................................................................ 119
Appendix 10: Data sheets: Guam .............................................................................................. 129
Appendix 11: Data sheets: Hawaii ............................................................................................. 139
Appendix 12: Yearly Project Task List ..................................................................................... 147
Appendix 13: Database Documentation .................................................................................... 151
Appendix 14: Analysis Log File Checklist ................................................................................ 163
Appendix 15: Pacific Islands Stream Monitoring Report: Example Summary of Vital
Signs Data ................................................................................................................................... 165
Appendix 16: Database User’s Guide ......................................................................................... 169
Appendix 17: Revision history log ............................................................................................ 213

xiii

Standard Operating Procedures
The following section consists of 35 Standard Operating Procedures (SOPs) that provide
comprehensive instructions for all aspects of conducting a monitoring program for stream
macrofauna (fish, shrimp, and snails) and habitat characteristics of Pacific Island Network
(PACN) National Parks. Included are SOPs on pre-season preparation; field surveys of fish,
shrimp, and snails; habitat characterization; data management, data analysis and report
preparation; and post-season activities. Appendices related to these SOPs include site maps,
species identification guides, and data sheets for each monitoring activity.
Page
Standard Operation Procedure (SOP) #1: Safety Protocol ........................................................ 219
Standard Operation Procedure (SOP) #2: Preparation for the Field Sampling ........................ 223
Standard Operation Procedure (SOP) #3: Locating Sampling Stations ..................................... 229
Standard Operation Procedure (SOP) #4: Using Garmin Global Positioning System
(GPS) Units ................................................................................................................................. 235
Standard Operation Procedure (SOP) #5: Downloading and uploading data between
Garmin GPS and ArcGIS ............................................................................................................ 243
Standard Operation Procedure (SOP) #6: Using the Ricoh GPS Camera ................................. 251
Standard Operation Procedure (SOP) #7: Training Field Personnel ........................................ 253
Standard Operation Procedure (SOP) #8: Conducting Surveys on Tau, American
Samoa.......................................................................................................................................... 255
Standard Operation Procedure (SOP) #9: Conducting Surveys on Tutuila, American
Samoa.......................................................................................................................................... 257
Standard Operation Procedure (SOP) #10: Conducting Surveys in Guam ................................ 259
Standard Operation Procedure (SOP) #11: Conducting Surveys in Hawaii .............................. 261
Standard Operation Procedure (SOP) #12: Fish Surveys on Tau, American Samoa ................. 263
Standard Operation Procedure (SOP) #13: Shrimp (ula vai) Surveys on Tau, American
Samoa.......................................................................................................................................... 267
Standard Operation Procedure (SOP) #14: Snail (sisi vai) Surveys on Tau, American
Samoa.......................................................................................................................................... 269

xv

Standard Operating Procedures (continued)
Page
Standard Operation Procedure (SOP) #15: Shrimp (ula vai) Surveys on Tutuila,
American Samoa ......................................................................................................................... 271
Standard Operation Procedure (SOP) #16: Snail (sisi vai) Surveys on Tutuila,
American Samoa ......................................................................................................................... 273
Standard Operation Procedure (SOP) #17: Fish (atot) Surveys in Guam .................................. 275
Standard Operation Procedure (SOP) #18: Shrimp (uhang) Surveys in Guam ......................... 279
Standard Operation Procedure (SOP) #19: Snail (akaleha) Surveys in Guam .......................... 281
Standard Operation Procedure (SOP) #20: Fish (oopu) and shrimp (opae) surveys in
Hawaii ......................................................................................................................................... 283
Standard Operation Procedure (SOP) #21: Snail (hihiwai) Surveys in Hawaii ......................... 287
Standard Operation Procedure (SOP) #22: Electrofishing for fish and crustaceans ................. 289
Standard Operation Procedure (SOP) #23: Habitat characterization at the reach and
transect scales ............................................................................................................................. 291
Standard Operation Procedure (SOP) #24: After Field Activities .............................................. 297
Standard Operation Procedure (SOP) #25: Workspace Setup and Project Records
Management ................................................................................................................................ 301
Standard Operation Procedure (SOP) #26: Data Entry and Verification .................................. 307
Standard Operation Procedure (SOP) #27: Post-season Data Quality Review and
Certification ................................................................................................................................ 311
Standard Operation Procedure (SOP) #28: Field Form Handling Procedures ......................... 313
Standard Operation Procedure (SOP) #29: Managing Photographic Images ........................... 315
Standard Operation Procedure (SOP) #30: Product Delivery Specifications ............................ 321
Standard Operating Procedure (SOP) #31: Metadata Development.......................................... 327
Standard Operating Procedure (SOP) #32: Data Analysis and Reporting ................................ 329

xvi

Standard Operating Procedures (continued)
Page
Standard Operating Procedure (SOP) #33: Sensitive Information Procedures ......................... 345
Standard Operating Procedure (SOP) #34: Product Posting and Distribution ......................... 351
Standard Operating Procedure (SOP) #35: Revising the protocol ............................................. 355

xvii

Abstract
Throughout the world, freshwater ecosystems are considered to be among the most vulnerable
systems. In the isolated Pacific islands there are a relatively small number of native freshwater
species, which are mainly endemic to these locations (found nowhere else in the world). These
species are characterized by an amphidromous lifecycle; reproducing in the stream, with larvae
drifting to the ocean and eventually returning to a stream as juveniles and spending the
remainder of their lifecycle there. Throughout the region, native flora and fauna face significant
threats from species introductions and habitat destruction. The National Parks in the Pacific
Island Network (PACN) protect some of the last relatively pristine stream systems. Monitoring
based on this protocol: Pacific Islands Stream Monitoring: Fish, Shrimp, Snails and Habitat
Characterization, will provide park managers with some of the information necessary to
understand status and trends in biotic integrity within park stream systems.
Vital Signs are physical, chemical, and biological elements and processes of ecosystems that are
selected to represent the overall health or condition of park resources, known or hypothesized
effects of stressors, or elements that have important human values. Two vital signs associated
with freshwater ecosystems were identified by the PACN network: Freshwater Animal
Communities—Streams and Freshwater Animal Communities—Anchialine Pools. This protocol
is specific to stream systems and a separate protocol is being developed for anchialine pools. The
Freshwater Animal Communities: Streams Vital Sign is closely linked with the Water Quality
Vital Sign, and monitoring efforts will be conducted in tandem to enhance the value of the data
collected.
The Pacific Islands Stream Monitoring Protocol will be implemented in four PACN parks: the
National Park of American Samoa in American Samoa, War in the Pacific National Historical
Park in Guam, Haleakala National Park in Hawaii, and Kalaupapa National Historical Park in
Hawaii. This protocol is designed to address two monitoring objectives: 1) Determine long-term
trends in population distribution and abundance, and community composition of freshwater fish
and invertebrates (including snails and crustaceans) and 2) Quantify associations among stream
animal communities (fish and invertebrates) and their habitat by correlating physical and
chemical habitat measures with observed species distribution and abundance.
This protocol employs a split-panel design with both fixed (sampled every year) and random
(new each year) stations that are sampled annually. This design provides both status and trend
information, and enhances the ability to use the data to conduct trend analyses. This design also
maximizes the statistical power to detect change over time by providing the ability to conduct
parameter corrections based on repeat analyses. Both native and introduced fish, shrimp, and
snail abundances will be monitored at selected sites along each stream. In addition, quantitative
and qualitative physical habitat information will be recorded. Water quality and discharge will
also be measured at each sampling station; methods are described in a separate protocol.

xix

Chapter 1: Background and Objectives
Overview
National Park managers across the country are confronted with increasingly complex and
challenging issues that require a broad-based understanding of the status and trends of each
park’s natural resources as a basis for making decisions, working with other agencies, and
communicating with the public to protect park natural systems and native species. The Natural
Resource Challenge, initiated in 1999 under the auspices of the Omnibus Act (1998), is an action
plan for preserving natural resources throughout the National Park Service (NPS) system. As part
of this plan, the NPS established 32 Inventory and Monitoring (I&M) networks across the nation,
encompassing 270 National Parks. A primary role of the I&M Program is to collect, organize,
and make available, natural resource data by facilitating the transformation of data into
information through analysis, synthesis, and modeling. Ultimately natural resource inventory and
monitoring information will be integrated into National Park Service planning, management, and
decision-making.
Standardized protocols are being developed by the I&M Program to facilitate long-term
monitoring of important resources (Vital Signs) which will serve as indicators of ecosystem
status within National Parks. The ability of a monitoring program to detect the ecological effects
of anthropogenic stressors is dependent upon interpreting trends in resource condition against the
backdrop of intrinsic variation. To enhance understanding of these processes, conceptual models
have been developed to summarize how natural drivers (e.g., climate variability, Figure 1.1) and
anthropogenic stressors (e.g., stream flow alteration or invasive introduced species, Figure 1.2)
affect aquatic ecosystem structure and functioning. Data collected following the Pacific Islands
Stream Monitoring Protocol will identify associations between biotic stream communities and
habitat conditions that can be linked to key drivers and stressors in the system. Over time, this
data will provide park managers with information on the long-term status and trends of aquatic
resources relative to natural processes and anthropogenic stressors, and will serve as a tool to
evaluate the effectiveness of management actions aimed at protecting or restoring aquatic
ecosystems.

1

2
Figure 1.1. Conceptual model describing general ecosystem functioning. Green boxes indicate vital sign components that are part of this protocol.

Figure 1.2. Potential anthropogenic stressors during the lifecycle of native stream organisms.

Eleven National Park units across the Pacific (Figure 1.3) form the Pacific Inventory and
Monitoring (I&M) Network (PACN). The PACN covers a large geographical area in the tropical
Pacific Ocean that is governed by four different entities: the Territory of American Samoa, the
Territory of Guam, the State of Hawaii, and the Commonwealth of the Northern Mariana Islands
(CNMI). National Park Service managers from the PACN identified freshwater animal
communities as a key indicator (vital sign) of ecosystem health. Freshwater ecosystems in these
parks include both anchialine pool systems (covered in a separate protocol) and stream systems.
This protocol for stream ecosystems focuses on fish, shrimp, and snails, the key macrofauna in
Pacific island streams. As part of the I&M monitoring program, both the status of these biota,
and information on their physical and chemical habitat conditions will be recorded. Stream
monitoring will be co-located in time and space with water-quality monitoring. To guide the
monitoring process, this protocol consists of (1) a narrative with background information on
Pacific stream systems, their unique fauna, a discussion of threats to these systems, the
importance of monitoring streams, and how monitoring results can be used in a management
context, (2) 35 Standard Operating Procedures (SOPs) that provide specific guidelines for
conducting the monitoring program (including field activities, data management, and report
preparation), and (3) a supplemental information section with 16 appendices (analysis of existing
data, details on operational requirements, species identification guides, data sheets, site specific
information including maps with station locations, Park and other contacts, and data
management).
3

4
Figure 1.3. Map showing the geographical region of the 11 Pacific Island Network park units. Red areas on the maps represent the location of
each National Park.

Stream Fauna of Tropical Pacific Islands
Life History Characteristics

Native stream fishes and the larger crustaceans and mollusks in tropical Pacific island streams
are derived from stream species elsewhere in the Indo-Pacific, which in turn originally derived
from marine species. These species have retained an oceanic larval life stage (McDowall 2003).
In this type of diadromy (called amphidromy), where part of the life cycle is spent in the stream
and part in the ocean (Figure 1.4), the adult life is spent in streams, and larval periods are spent
as marine or estuarine zooplankton (Ford and Kinzie 1982, Kinzie 1988, McDowall 1988, 2003,
Radtke et al. 1988). Some studies have indicated a seasonal (Ego 1956, Ha and Kinzie 1996,
McDowall 1995, Resh et al. 1990, 1992) or lunar (Erdman 1986) periodicity for freshwater
gobies and crustaceans. Many species appear to have multiple periods of reproduction
throughout the year (Manacop 1953, Couret 1976, Kinzie and Ford 1982, Kinzie 1990, 1993,
Bell and Brown 1995, Lindstrom 1998). In certain locations, some species appear to spawn
seasonally while others reproduce throughout the year (Resh et al. 1992, Brasher 1997c). Genetic
studies on some of the Hawaiian amphidromous gobies (Fitzsimons et al. 1990) and neritid snails
(Hodges 1992) indicate that adult populations are genetically undifferentiated throughout their
range, recruitment is from a well-mixed pool of larvae, and that larvae do not return to their natal
streams.
Adults of these amphidromous species reproduce in upstream habitats, and the larvae drift
downstream into estuaries or the ocean, eventually returning to the stream as bottom-dwelling
postlarvae and migrating upstream to grow and reproduce (Kinzie 1990, 1993). Newly hatched
fish and shrimp larvae drift downstream and maintain position in the water column by
alternatively swimming upward and passively sinking back down as they are carried toward the
sea (Bell and Brown 1995, Lindstrom 1998). Larvae that successfully drift to the ocean spend
from 1 to 5 months as plankton before recruiting back to fresh water (Radtke and Kinzie 1987,
Radtke et al. 1988, Benstead et al. 1999). This relatively long oceanic larval stage may be due to
the amount of time required to locate a freshwater settlement site as well as the developmental
complexities required to complete the marine-to-freshwater transition (Bell et al. 1995, Radtke et
al. 2001). A critical feature of the amphidromous life cycle is the need for unimpeded access to
and from the ocean for downstream dispersal of larvae and upstream migration of postlarvae
(Resh et al. 1992, McDowall 1995, Brasher 1996, Benstead et al. 1999, Fitzsimons et al. 2002,
McIntosh et al. 2002).

5

Figure 1.4. Amphidromous life cycle of fish, shrimp, and snails.

Fauna of Hawaii, American Samoa, and Guam

The stream fauna that are the focus of this protocol include native fishes of the families
Anguillidae, Eleotridae, Gobiidae, and Kuhliidae, crustaceans (shrimp and prawns) of the
families Atyidae and Palaemonidae, and snails of the family Neritidae. Introduced fish, shrimp,
and snails will also be monitored when they occur at a site. However, with the exception of
Macrobrachium lar (a widespread introduced prawn), introduced species are not described in
this protocol. The majority of studies on Pacific island stream fauna have been conducted in
Hawaii, and consequently substantially more information is available for the Hawaiian Islands
than for either American Samoa or Guam. When possible, ecologically relevant and phenotypic
information for a given species is included. However, when this information is not readily
available, a list of known species is provided. Morphometric characteristics are described below,
when available. Key characteristics of the crustaceans include the carapace (exoskeleton),
pereiopod (thoracic appendage), and carpus (a segment of the pereiopod). Picture guides to all of
the native fauna are available in Appendices #1-3. Pictures of the more common introduced
species are included in Appendix #4: “Introduced Species Identification Guide.” Excellent field
guides have been published for American Samoan (Vargo 2009) and Hawaiian (Yamamoto and
Tagawa 2000) stream fauna.

6

American Samoa
Published information is only available on some of these species, and is provided below. Photos
to assist in identification are provided in Appendix 1. The majority of information on fish,
shrimp and snails in American Samoa is taken directly from Vargo 2009.
Fish

Family: Anguillidae
There are three anguillids (eels) reported for American Samoa including: Anguilla marmorata,
Anguilla megastoma, and Anguilla obscura. These anguillids can reach lengths of 100 cm or
more.
A. marmorata, the giant mottled eel, can be readily distinguished from other eels by its mottled
color and dorsal fin position, which is more anterior than other Anguilla. Adults have black or
brown marbling on their backs with a grey-yellow background; marbling is harder to see on
young eels. They reach two meters and 20.5 kilograms and typically have 100-110 vertebrae.
A. megastoma can be either plain or mottled in color. A. megastoma has 110-114 vertebrae,
which is more than the other two anguillids.
A. obscura is always plain in color and has 102-108 vertebrae.
Family: Eleotridae
Eleotris fusca is the only eleotrid (sleeper fish) reported for American Samoa. They are dark
brown to black in color with horizontal lines on body and spots on fins of juveniles. This fish
lacks the fused pelvic fins of the gobies, and therefore is only found below the first waterfall.
Commonly 10–15 cm in length but can grow as large as 26 cm. This amphidromous fish lives in
brackish and freshwater habitats. Adults occur in streams (usually mud bottoms of lower
reaches), estuaries, and lagoons. Juveniles are usually found in the more saline areas of estuaries
and lagoons among mangrove roots. Their diet includes benthic animals (fish, crustaceans, and
insects). E. fusca lays its eggs on submerged plants with small leaves.
Family: Gobiidae
There are nine species of gobies found in American Samoa including: Awaous ocellaris,
Periophthalmus kalolo, Periophthalmus argentilineatus, Periophthalmus koelreuteri,
Sicyopterus caeruleus, Stiphodon elegans, Stiphodon hydoreibatus, Sicyopterus micrurus, and
Sicyopterus pugnans. Published information is only available on some of these species, and is
provided below.
A. ocellaris may grow to 8-13 cm and is found in estuarine environments and often burrows into
sandy substrates with only its eyes showing. Its diet includes green filamentous algae, worms,
small crabs, shrimps, and various insects.
P. kalolo grows to 10-12cm length. P. kalolo is an amphibious air-breathing gobiid that spends
the majority of its time out of water. In order to breathe P. kalolo needs to stay wet, and therefore
is typically found resting on mud, rocks, or mangrove roots with its tail dipped in water. This
species feeds on worms, small crustaceans, and insects.
7

S. caeruleus has a horseshoe-shaped band on its tail fin; however, this may be difficult to see.
Males can grow up to 6-7 cm, and larger males have scales embedded in a spongy tissue just
before the tail fin. S. caeruleus was previously identified as S. lagocephalus and is commonly
referred to as S. macrostetholepis or S. taeniurus in the literature.
S. elegans males often have neon green spots and reach a maximum size of 5 cm. Females are
golden-brown in color. This fish is found in a variety of stream habitats, especially in fast
flowing water. This species is generally found near the substrate and feeds on algal films
covering rocks.
S. hydoreibatus is easily mistaken for S. elegans but is about half the length of S. elegans.
Family: Kuhliidae
The two species of kuhliids reported for American Samoa include: Kuhlia rupestris and Kuhlia
salelea.
K. rupestris is identified by two separate dark spots on the caudal fin (one dorsal and the other
ventral). This fish can get as large as 45 cm, with an average weight of 50 g. This fish is widely
distributed throughout the streams in American Samoa and is a top predator in many ecosystems,
feeding on crustaceans and insects. K. rupestris can swim upstream through fast-flowing
cascades. .
K. salelea can be identified by a continuous dark border running along the trailing edge of its tail
fin. K. salelea is smaller (approximately 17 g) than K. rupestris, but may be more abundant in
some stream reaches. K. salelea has a more restricted range than K. rupestris and is known only
to occur in streams on Tutuila Island and Upolu Island.
Fish that are reported to inhabit Laufuti Stream on Tau include A. marmorata, A. megastoma, E.
fusca, S. pugnans, S. micrurus, and S. elegans (Cook 2004).
Crustaceans

Shrimp and prawns are referred to as Ula Vai in American Samoa.
Family: Atyidae
There are five species of atyids (shrimp) reported for American Samoa including: Atyoida
pilipes, Atya serrata, Atyopsis spinipes, Caridina serratirostris, Caridina typus, and Caridina
weberi.
A. pilipes do not have a carapace spine, and the width of the carpus of the second pereiopod is
greater than the length. Individuals can grow to be 4-5 cm in length and females are significantly
larger than males. Juveniles can often be found buried within the substratum in the lower reaches
to avoid predators. Adults are commonly seen in upper reaches above barrier waterfalls, prefer
hard substrates in riffle areas, and have long setae well suited for filter-feeding in fast moving
water.
A. spinipes has phenotypic characteristics similar to those of A. pilipes. The easiest way to
distinguish between the two is that A. spinipes has a lateral striping pattern along the carapace
8

and abdominal segments. Additionally, A. spinipes has a carapace spine on the anterior of the
carapace. Similar to A. pilipes, the width of the carpus of the second pereiopod is greater than the
length. A. spinipes can grow to 4-5 cm. This species has brushes on its chelae to aid in filter
feeding.
C. serratirostris is 10-15 mm and has brushes on its chelae. The length of the carpus of the
second pereiopod is greater than the width. The upper edge of the rostrum has teeth and extends
backward for at least half the carapace length, well behind the eyes.
C. typus is 10-15 mm and has brushes on its chelae. The length of the carpus of the second
pereiopod is greater than the width, and the upper edge of the rostrum does not have teeth. This
is the least common of the Caridina species found in American Samoa.
C. weberi is 10-15 mm in length with brushes on its chelae. Similar to the other Caridina spp.
the length of the carpus of the second pereiopod is greater than the width. The upper edge of the
rostrum has teeth that extend backwards no further than the eye. This is the most common
Caridina species found in American Samoa.
Family: Palaemonidae
There are five species of palaemonids (prawns) reported in American Samoa, all of the genus
Macrobrachium. They include M. australe, M. gracilirostre, M. hirtimanus, M. lar, and M.
latimanus. M. lar is an introduction from Tahiti.
M. australe have a “glassy” or transparent body and most larger specimens show three brown
vertical stripes on each side of the carapace and one stripe forward of these three, but at an angle.
The carpus of the second pereiopod is longer than the merus.
M. gracilirostre has conspicuous brown and blue stripes. However, when viewed from above the
tan saddle behind the carapace is the most obvious marking. The length of the carpus of the
second pereiopod is equal to the length of the merus.
M. hirtimanus - Vargo (2009) warns that M. hirtimanus very much resembles M. gracilirostre
and M. lepidactyloides. It was reported to be found in Laufuti Stream on Tau (Cook, 2004).
M. lar, an introduced prawn, may grow up 15 cm in length, and are brownish with long, thin
dark pincer legs and 8 or 9 spines on the dorsal surface of the rostrum.
M. Latimanus is approximately 10 cm in length. The length of the carpus of the second
pereiopod is shorter than the merus.
Snails

Neritid snails are referred to as Sisi Vai in American Samoa.
Family: Neritidae
There are seven species of snails in the family Neritidae in American Samoa, including: Clithon
corona, Clithon pritchardi, Neritina auriculata, Neritina canalis, and Neritina variegata,
9

Septaria sanguisuga, and Septaria suffreni. The shells of adult snails of all seven species are
approximately 1 cm in width.
C. corona has a rigid, brown to dark brown shell. Their shell lip and inner shell lining are white.
The color of the operculum is similar to the shell, with a narrow orange-brown horn border.
Smaller and younger specimens often have spines on their shells.
This common species found on rocks in pools and in flowing water anywhere along the stream
length.
C. pritchardi has a brown shell that is roughly wrinkled (distinguishes this species from C.
corona), and may or may not have spines. The shell lip is white to orange-yellow, and the inner
shell lining is white. The color of the operculum is similar to the shell with a narrow orangebrown border. This common species is found on rocks in pools and flowing water anywhere
along the stream length.
N. auriculata has a light brown shell with no obvious pattern which is often extended at the sides
to form wings. The shell lip is cream to grey in color. Their operculum is cream to dark brown
with gray radial lines and a red outer horn border. This species is restricted to estuarine
environments where it can be found on rocks or sandy substrates.
N. canalis has a brown to black shell with a shell lip and inner shell lining that are orange-yellow
to red. This relatively uncommon species is found on stones in flowing water.
N. variegata has a shell that ranges in color from olive to dark brown with a shell lip and inner
shell lining that are white with a reddish splash on the shell lip. The operculum is white to black
with no horn border. This species has been found in flowing water as well as in mud flats.
S. sanguisuga has a dark brown shell that is oblong-ovate, and sometimes has a fine network of
black lines. The shell lip is tinged orange and the inner shell lining is white. The operculum is
internal and orange in color with two horns of nearly equal length. The fleshy foot of this species
is pale yellow. This uncommon species can occasionally be found on rocks in flowing water, and
is usually found on walls of waterfalls.
S. suffreni has a yellow-brown shell that is oblong-ovate, and has variable markings ranging from
traverse wavy lines to triangles, or zig zags. The shell lip is often tinged yellow to orange. The
operculum is internal, orange, and has one horn. The fleshy foot of this species is gray. This
common species is found on rocks in pools and flowing water.
Guam
Fish

Family: Anguillidae
Anguilla marmorata is described above in section on fish in American Samoa.
Family: Eleotridae
Eleotris fusca is described above in the section on fish in American Samoa.
10

Family: Gobiidae
Freshwater gobies are referred to as Atot in Guam. There are a number of native gobies in Guam
including: Awaous guamensis, Mugilobius cavifrons, Sicyopterus lagocephalus, Sicyopterus
macrostetholepis, Sicyopus leprurus, Stiphodon elegans, and Stiphodon percnopterygionus.
Some of these species are described below.
A. guamensis are typically found in deeper slower moving waters (Ego 1956; Kinzie 1988). The
species is an omnivore; filamentous algae make up approximately 84% of the gut volume and
animal matter, especially chironomids, the other 16% (Ego 1956; Kido et al. 1993).
S. lagocephalus is on average 10-12.5 cm in length and is usually found in upper reaches, on
hard substrates, and in strong currents. S. lagocephalus is herbivorous.
S. macrostetholepis is generally about 10 cm in length.
S. elegans is described above in the section on fish in American Samoa.
S. percnopterygionus has an average length of 2.5 cm and is usually found in shallow upper
reaches on hard substrates. This species is herbivorous.
Family: Kuhliidae
Kuhlia rupestris is described above in the section on fish in American Samoa.
Crustaceans

Both freshwater and marine crustaceans are referred to as Uhang in Guam.
Family: Atyidae
The people of Guam, Chamorros, traditionally harvested stream atyids and prepared them in a
dish called kélaguen. There are six species of atyid shrimp found in Guam including:
Antecaridina lauensis, Atyoida pilipes, Caridina brachydactyla, Caridina mertonia, Caridina
typus, and Halocaridinides trigonophthalma.
Atyoida pilipes is described above in the section on shrimp in American Samoa. It is the most
common species of shrimp in the streams of Guam.
Caridina shrimp have both long and short setae enabling them to feed by scraping and filtering
in a wide range of habitats. Species in this genus are commonly seen in pools and runs of
streams.
Halocaridinides trigonophthalma and Antecaridina lauensis, two other species of atyids, have
red integumentary chromatophores and feed mostly by scraping the substrate. They are able to
adapt to a wide range of salinities and are commonly found in interstitial habitats such as
fissures, pools, and wells.

11

Family: Palaemonidae
Macrobrachium lar is present in many streams on Guam. M. lar is an introduction from Tahiti.
Additional information on M. lar characteristics can be found in the section above describing
stream fauna in American Samoa.
Snails
Neritid snails are referred to as Akaleha in Guam.
Family: Neritidae
There are at least three native neritid snails in Guam, including Neritina pulligera, Neritina
squamipicta, and Neritina variegata. Detailed information on the phenology and habitat
preferences of these species is currently unavailable.
Hawaii
Substantially more information on the ecology and life-history characteristics is available for the
Hawaiian taxa than for the stream organisms in American Samoa or Guam. In addition to
morphometric descriptions of the various species, ecological information is provided when
available.
Fish

Hawaiian stream gobies are known to separate out along the gradient from mouth to headwaters
(Brasher 1996). The eleotrid (Eleotris sandwicensis) and one goby (Stenogobius hawaiiensis) are
only found in estuaries or below the first waterfall. Awaous guamensis, the largest goby, tends to
be found in lower reaches, especially in streams with precipitous waterfalls. Sicyopterus
stimpsoni often overlaps with A. guamensis but may be found farther upstream as well. Lentipes
concolor is found at the highest elevation of all the gobies. The number and relative gradient of
waterfalls appear to play an important role in the overall distribution of species. In streams with a
terminal waterfall L. concolor can be found near the ocean (Nishimoto and Kuamoo 1991), while
in streams with relatively low gradient and no major waterfalls A. guamensis can be found
farther upstream.
Family: Gobiidae
Gobies are referred to in Hawaii as Oopu. There are four species of gobies in Hawaii. They
include Awaous guamensis, Lentipes concolor, Sicyopterus stimpsoni, and Stenogobius
hawaiiensis. Originally from Guam, A. guamensis is considered indigenous to Hawaii (native to
Hawaii, but not endemic, which would mean it is found nowhere else).
A. guamensis is the most common Hawaiian freshwater goby and is found in lower and middle
stream reaches (Ford and Yuen 1988). This species is found on all the major islands, although on
Oahu the population sizes are small and the number of streams inhabited are few (Kinzie 1990).
A fishery exists for A. guamensis on the island of Kauai, where they are caught in large numbers
during the annual spawning run to the stream mouth following heavy fall flooding. A. guamensis
probably competes with L. concolor for food, and to some extent space (Timbol et al. 1980).
Further details on A. guamensis can be found above in the section on fish in Guam.
L. concolor is the least common freshwater goby in Hawaii (Timbol et al. 1980). Mature L.
concolor typically reside in the middle to upper reaches of streams, although they can be found
12

near the stream mouth in streams that end in terminal waterfalls (Maciolek 1977; Nishimoto and
Kuamoo 1991). They appear to spend much more of their time in mid-water pools than other
species (Kinzie and Ford 1982), although they also have a strong affinity for fast riffles (Timbol
et al. 1980). L. concolor is known for its remarkable climbing ability and can be found at the
highest elevation of any Hawaiian goby. Lau (1973) found the diet of L. concolor to consist of
algae, insect larvae, and crustaceans, especially native mountain shrimp (opae). Larger gobies eat
more animal material while smaller ones eat more algae (Lau 1973). Mature males are
aggressive and show territorial behavior (Lau 1973; Maciolek 1977; Nishimoto and Fitzsimons
1986). Females tend to move freely up and down the stream and around pools, while males are
very site specific and defend a discrete territory (Nishimoto and Fitzsimons 1986).
S. stimpsoni is also found in the mid to upper stream reaches, and tends to utilize more rapid
stream velocities (Kinzie 1988). S. stimpsoni appear to be restricted to relatively undisturbed
streams with good water quality and a high rate of discharge (Kinzie 1990). Tomihama (1972)
reported that while S. stimpsoni can climb waterfalls, it is less adept than L. concolor. While the
two species’ distributions can greatly overlap, L. concolor may be found at higher reaches. A
tagging study by Kinzie and Ford (1982) showed S. stimpsoni to show high site fidelity. It is
herbivorous, feeding on diatoms and filamentous blue-green algae (Kinzie and Ford 1982;
Tomihama 1972).
S. hawaiiensis possesses fused pelvic fins; however, the species is apparently neither a strong
swimmer nor climber and occurs primarily along stream margins and other low flow areas near
the stream mouth (Fitzsimons and Nishimoto 1991). S. hawaiiensis typically occurs in lower
stream reaches and estuaries. S. hawaiiensis is the only Hawaiian goby that does not show strong
territorial behavior (Fitzsimons and Nishimoto 1990). It has a planktonic marine larval stage of
approximately 135 days (Radtke et al. 1988). S. hawaiiensis is omnivorous.
Family: Eleotridae
Eleotris sandwicensis lacks the fused pelvic fins characteristic of true gobies and thus is found
only in stream reaches below the first precipitous waterfall (Fitzsimons and Nishimoto 1991;
Kinzie and Ford 1982). The species is generally found in lower stream reaches and estuaries.
E.sandwicensis is a predatory carnivore; gut content analysis of E.sandwicensis has shown them
to prey on small benthic invertebrates, snails, shrimp, insects, and other fish (Kinzie and Ford
1982).
Crustaceans

Family: Atyidae
Atyid shrimp are referred to in Hawaii as opae. Atyoida bisulcata are small shrimp, up to three
inches (8 cm). The species appears to have a blunt head and can be identified by their small
bristled pincers. They can be found in habitats ranging from quiet pools to high velocity cascades
and can be typically found in the upper reaches of streams (Couret 1976; Kinzie 1990). A.
bisulcata inhabit all of the Hawaiian Islands and are harvested as a delicacy food and for bait.
Family: Palaemonidae
Macrobrachium lar were first introduced in 1956 into Pelekunu Stream on the island of Molokai;
in 1957-1958 into Nuuanu Stream on Oahu, and in 1961 into Punaluu Stream on Oahu. They
subsequently spread to every stream in Hawaii. Now they are found on all the major Pacific
13

islands. Several researchers have indicated potentially negative impacts of M. lar on native goby
and snail populations. Further details on M. lar characteristics are included above in the section
on shrimp in American Samoa.
Snails
Family: Neritidae
Neritina granosa is a limpet-like snail that typically hides under boulders and in crevices during
the day, coming out at night to forage and mate. They tend to be found in lower to mid-stream
reaches and are collected by humans for consumption, although a ban on commercial sale went
into effect in 1993. They require cool, clear, fast flowing and well-oxygenated water. They are
uncommon in, or absent from, streams that are modified, degraded, and easily accessible by
humans (Maciolek 1978). Relatively few streams in Hawaii contain substantial populations of N.
granosa (Hawaii Stream Assessment 1990). Because they are relatively uncommon and require
habitats typical of high quality streams (Ford 1979; Hathaway 1978; Hodges 1992; Maciolek
1978), N. granosa may serve well as an indicator species of habitat and water quality (Brasher
1997c).
Natural Drivers and Anthropogenic Stressors
As human population increases on islands across the Pacific, stream habitats and watersheds are
undergoing substantial alteration, resulting in conditions that differ greatly from those that once
sustained native stream communities (Brasher 2003). Because these ecosystems are located in
some of the more rapidly developing areas in the world, pressure on their natural resources is
intense. Land use changes result in habitat alteration and facilitate the establishment of invasive
introduced species (Figure 1.4). Streams are particularly vulnerable because of the spatially
concentrated human populations that characterize many of these island ecosystems (Smith et al.
2003). Human alteration of land and hydrologic systems on many tropical islands occurs
primarily along the coastal perimeter. This impacts not only native fauna living in or migrating
through these areas, but also humans that traditionally consume native species for subsistence
(Resh and deSzalay 1995; Haynes 1999).
Extreme examples come from the Hawaiian Islands where large-scale urbanization and
development has resulted in lower water quality and degraded physical habitats for many native
stream species (Brasher 2003; Anthony et al. 2004; Brasher et al. 2004). Stream quality can be
affected by stream channelization for flood control or roadways, increases in sedimentation from
construction and farming, contaminants from agricultural, urban, and industrial activities that get
transported in storm-water runoff, and diversions to redirect stream water to farms and other offstream uses (Oki and Brasher 2003). Even in relatively pristine areas, water diversions may
result in decreased flow and periodic dewatering of stream sections, reducing available habitat
and inhibiting downstream dispersal and upstream migration of native species (Resh et al. 1990;
McDowall 1995; Brasher 1997a; Benstead et al. 1999; Brasher 2003; March et al. 2003; Smith et
al. 2003).
Of the five native amphidromous fishes (E. sandwicensis, S. hawaiiensis, A. guamensis, S.
stimpsoni and L. concolor) in Hawaii, only the two species most tolerant of large variations in
environmental conditions, E. sandwicensis and S. hawaiiensis (Hathaway 1978), are numerous in
any Oahu streams (Hawaii Stream Assessment 1990; Kinzie 1990). The native fishes least
14

tolerant to habitat degradation (Hathaway 1978; Kinzie 1990), L. concolor and S. stimpsoni, are
rarely found on Oahu (Timbol et al. 1980; Fitzsimons et al. 1990; Higashi and Yamamoto 1993;
Luton et al. 2005; Brasher et al. 2006). The two native (M. grandimanus and A. bisulcata) and
one introduced (M. lar) amphidromous shrimp commonly occur in Oahu streams (Luton et al.
2005; Brasher et al. 2006).
A recent survey on the island of Tutuila in American Samoa, where development has been much
less intense than in the Hawaiian islands, showed that sites characterized by human activity
(including substantial amounts of trash, elimination of riparian vegetation, nutrients and
contaminants from household graywater, and raw sewage from piggeries) have species
composition, richness, and abundance that is similar to non-impacted sites (Wade et al. 2008).
While these more rural development impacts have not yet negatively impacted stream
communities in American Samoa, increasing human populations have resulted in road building
and the associated dredging, channelization and retaining walls, which are causing extensive
habitat destruction that may pose a serious threat to stream quality (Wade et al. 2008).
Channelization

Studies in Hawaii, and on the island of Oahu in particular where development has been
substantial, provide an indication of the habitat alteration that is beginning to occur across the
Pacific as other islands also begin to develop rapidly. Associated with population growth and
urbanization is an increase in the number of road crossings over streams, the flood control
projects being implemented, and channels realigned around housing projects (Brasher 2003;
Resh 2005). Channel modifications involve clearing riparian vegetation, realigning channels, and
reinforcing the altered banks, thereby creating straightened, concrete-lined channels (Hathaway
1978; Norton et al. 1978). Channel modification is severe in the state of Hawaii where almost
20% of the streams are channelized (Hawaii Stream Assessment 1990). Even more than 30 years
ago, 60% of the streams on the island of Oahu were channelized (Timbol and Maciolek 1978).
The result has been fragmentation of stream habitat through degradation of instream and riparian
areas (Brasher 2003, Brasher et al. 2004).
Artificially straightened reaches with concrete-lined flat-bottomed channels and reinforced banks
are common in the urban areas of Oahu. Such modifications are often accompanied by removal
of riparian vegetative cover, and a reduction in substrate complexity (removal of large boulders).
The end result is a wide, shallow, unshaded, and generally homogenous stream reach; a stark
contrast to the steep, heavily vegetated, boulder strewn reaches typical of the more pristine
streams in forested areas of Hawaii (Brasher et al. 2004). These conditions, along with a
proliferation of non-native fishes and crustaceans, have led to a decline in native freshwater
macrofauna on Oahu (Kinzie 1990). A recent study on Oahu showed that streams with the
highest degree of urbanization contain the fewest native fish larvae (Luton et al. 2005).
Sedimentation

In island settings, siltation levels are typically higher at stream mouths than farther upstream,
reflecting a natural elevation gradient (Brasher et al. 2006). Developed sites have also been
shown to have substantially higher levels of siltation and embeddedness and much smaller
substrate than undeveloped sites due to anthropogenic activities of channelization and removal of
larger rocks, thus magnifying the natural elevation gradient (Brasher et al. 2004). This creates
habitat more suitable for introduced species such as poeciliids (McRae 2001) than for native
15

species such as S. stimpsoni which, as a primarily benthic algal feeder requires substrate clear of
silt.
Deforestation in Fiji is another example from a Pacific island where development has resulted in
significant sediment loads being transported to a stream system. Insect diversity was shown to be
significantly lower in a stream with elevated loads of sediment due to logging, when compared to
a stream in a watershed where no logging had occurred (Haynes 1999). After logging, species
with patchy or sparse populations were slow to return, leading to the suggestion that a long-term
effect of sedimentation due to logging may be the extinction of some freshwater invertebrate
species (Haynes 1999).
Riparian Cover and Temperature

The increased width and decreased depth associated with channelization can also cause excessive
solar heating (Timbol and Maciolek 1978; Shier 1998). Channelized urban streams on Oahu
typically have higher daily mean and maximum water temperatures, and greater diel fluctuations
in water temperature than streams in more pristine forested areas of Hawaii (Brasher et al. 2004).
Additionally, in these urban streams increased solar radiation and elevated water temperature
promote excessive algal growth, which in turn results in strong diel fluctuations in pH and
dissolved oxygen (Norton et al. 1978). Water temperatures in sections of streams in lowelevation urbanized areas with sparse riparian canopy cover can reach above 30○ C (Brasher et
al. 2004), which can be lethal to native species (Hathaway 1978). However, introduced species
with high temperature tolerance such as the convict cichlid A. nigrofasciatus can thrive in these
areas (Brasher et al. 2006).
Contaminants

Urban and agricultural land uses are often associated with a variety of organochlorine,
organophosphate, trace element, and metal contaminants. These constituents are applied on land
as pesticides, herbicides, or fertilizers, or may have industrial uses. They are transported to the
water through industrial and municipal effluents, soil erosion, and other nonpoint-source runoff,
where they can have substantial negative impacts on stream biota (Nowell et al.1999; Oki and
Brasher 2003; Cain et al. 2004; Brasher and Wolff 2004; Brasher and Wolff 2007). While the
bulk of the research on contaminants in watersheds comes from the Hawaiian Islands, recent
work in American Samoa and Guam indicate that similar contaminants issues occur in those
islands. In addition, it can be expected that on all Pacific islands with urban and agriculture land
use, similar contamination of streams will exist.
Many metals (e.g. arsenic, copper, lead, mercury, and zinc) that occur naturally in the
environment are toxic to aquatic biota at high concentrations (Hare 1992; Cain et al. 2004). A
recent study of an urban stream on the island of Oahu showed elevated concentrations of lead,
zinc, copper, cobalt, and barium, that are associated with urban activities (such as fossil fuel
burning and vehicular exhaust) and arsenic that is associated with agricultural activities (DeCarlo
et al. 2004). Arsenic is a common impurity in fertilizer, and this may be the source of arsenic in
these areas (Anthony et al. 2004). Concentrations of arsenic measured in the sediment at this site
were approximately nine times higher than guidelines for the protection of organisms associated
with the sediment (Brasher and Wolff 2007). Leaded gasoline and lead-based paints were phased
out in the 1970s, but lead persists in soils and continues to enter Hawaiian streams with sediment
in runoff, and occurs at elevated concentrations in urban streams on Oahu (DeCarlo and Anthony
16

2002; Anthony et al. 2004). Concentrations of metals associated with anthropogenic activities
typically exceeded guidelines in developed watersheds while those that naturally occur in
Hawaiian rocks and soils (such as chromium, copper, and nickel) were elevated in forested areas
as well (DeCarlo et al. 2004; Brasher and Wolff 2007).
Organochlorine pesticides were heavily used from the mid-1940s to the mid-1980s in the United
States. The persistence of organochlorine pesticides, their tendency to accumulate in soil,
sediment, and biota, and their harmful effects on wildlife resulted in restriction or banning of
their use 20 to 30 years ago (Nowell et al.1999). Despite use restrictions, these compounds
continue to be detected in sediment and fish samples. Once in the system, these compounds
(which have low solubility) are mostly associated with bottom sediments that can be ingested by
benthic organisms. These organisms are then eaten by fish and birds, transferring the
contaminants to higher trophic levels in aquatic and terrestrial food chains. Studies conducted in
urban streams on Oahu from 1970 through 2000 have shown elevated concentrations of
organochlorine pesticides in stream sediment and fish (Bevenue et al. 1972; Tanita et al. 1976;
Schmitt et al. 1981, 1985, 1990; Hunter et al. 1995; Brasher and Wolff 2004).
In addition to direct impacts on stream fauna, contaminants can be transported from the stream to
near shore areas. Recent studies in Saipan (summarized in Denton et al. 2001, 2008) reported
numerous metal and organic compounds at elevated concentrations in the marine sediments and
marine organisms near the vicinity of the Puerto Rico dump (landfill).
Stream Flow Alteration

Recent studies in Hawaii clearly indicate that stream flow alteration is a significant threat to
native aquatic communities (Kido 1996; Brasher 1997a; Way et al. 1998; McIntosh et al. 2002;
Kinzie et al. 2006). Stream flow can be reduced by pumping groundwater from wells or by
directly diverting surface water (Oki and Brasher 2003). Results can range from a slight
reduction in discharge to complete drying of sections of the stream. In addition to the direct
impacts of reduced velocities and depths caused by water diversions, the reduced stream flow in
areas where streams have also been channelized can result in higher water temperatures and
decreased levels of dissolved oxygen (Timbol and Maciolek 1978; Brasher et al. 2004; Kinzie et
al. 2006). Furthermore, sublethal or indirect impacts, including competition, predation,
behavioral changes, changes in life history characteristics, and alterations of food chains, can all
potentially result from stream flow alterations (Brasher 1997a; McIntosh et al. 2002; Larned et
al. 2003).
Even in relatively pristine watersheds not yet affected directly by modern urban development,
stream diversions can result in reduced flow velocity and water depth, thereby changing habitat
conditions and potentially reducing habitat availability for native fish (Brasher 1997b, 2003;
McIntosh et al. 2002; Kinzie et al. 2006). Channel width, depth, and water velocity can be
reduced by water diversion; this reduction in habitat availability is then reflected in lower
densities of native fish and higher overlap in habitat use among species in the diverted stream
(Brasher 1997b). In addition, fewer fish and snails may be present in sampling areas above the
water diversions, presumably because of the difficulty in traversing the periodically dry reach
just downstream of the diversions (Brasher 1996, 1997b, 1997c).

17

Modifications of stream ecosystems are typically most intensive at the lower elevations, which
may have the greatest impact on the migrations of seaward-moving larvae and returning
juveniles (Kinzie and Ford 1982; Kinzie 1990; Resh et al. 1992; Pringle 1997; Pringle and
Ramirez 1998; Benstead et al. 1999; March et al. 2003). The larvae may be entrained (captured)
by diversion weirs and ditch systems as they wash downstream, and both downstream larval
dispersal and upstream juvenile migration is impeded by dry or low-flow stream reaches that
result from water diversion (Kinzie 1988; Resh et al. 1992; McDowall 1995; Brasher 1996,
1997a; Pringle 1997; Way et al. 1998; Benstead et al. 1999; Fievet 2000; Fievet et al. 2001;
Luton et al. 2005). This was demonstrated in a stream on Kauai where abundance and biomass of
drifting invertebrates was highest just above the dam and lowest just below the dam, suggesting
that most of the drifting invertebrates were entrained into the diversion ditch (Kinzie et al. 2006).
Invasive Species

Development can cause changes to stream habitat that result in lower habitat heterogeneity and
increased abiotic variability, creating an environment more suitable for some introduced species
than for the native fauna that evolved in these systems (Brasher et al. 2006). Introduced
generalist species are typically better adapted than native species to degraded habitats and once
established in these habitats, they can cause further reduction in native populations directly and
indirectly through competition, predation, and the introduction of parasites and diseases (Font
and Tate 1994, Brown et al. 1999, Brasher 2003; Font 2003; Larned et al. 2003; Brasher et al.
2006).
Hawaii’s extreme isolation has made it especially susceptible to invasive species because the
native flora and fauna evolved with minimal exposure to the biotic forces of competition and
predation, and are consequently unable to compete with invasive introduced species (Loope et al.
2001; Staples and Cowie 2001). In addition, predation on postlarvae of the native fish by
introduced species may be substantial as the postlarvae attempt to migrate through altered habitat
to the upstream reaches of streams or attempt to settle in the lower reaches (Brown et al. 1999;
March et al. 2003).
The native stream fauna of Samoa, Hawaii, and Guam is well adapted to the flashy nature of the
tropical streams and the steep topography of the watersheds. All of the native gobies have fused
pelvic fins, allowing them to cling to the substrate during torrential flows and to climb steep
waterfalls (Ford and Kinzie 1982; Kinzie 1990). While the native species are adapted to the
natural flashy hydrologic conditions in unaltered streams, the established introduced species are
typically adapted to more lentic habitats and may be unable to withstand higher velocities and
flows, thus limiting their distribution to the more disturbed systems (Brown et al. 1999, McRae
2001, Brasher et al. 2006). With increasing development, the habitat features required by native
species are disappearing, and streams are becoming more suitable for generalist introduced
species which are typically better adapted for altered habitats than native species (Maciolek
1977; Norton et al. 1978; Brown et al. 1999; Brasher et al. 2006). Introduced species are most
common in the more developed stream reaches, reflecting their higher tolerance for altered
habitat conditions including elevated water temperatures, slower water velocities, and increased
levels of siltation and embeddedness (Brasher et al. 2006). For example, a recent survey on
Tutuila in American Samoa found introduced poeciliids only in the terminal reaches of three
disturbed streams (Wade et al. 2008).
18

Surveys conducted on Oahu in the late 1970s showed that introduced fishes and crustaceans
formed 87 percent of the fauna in altered streams and that native species were absent from
cement-lined channels (Norton et al. 1978; Timbol and Maciolek 1978). Today more than 50
species of introduced fish, invertebrates, reptiles, amphibians, and aquatic plants are established
in streams and reservoirs in Hawaii (Maciolek 1984; Eldredge 1992; Brown et al. 1999;
Yamamoto and Tagawa 2000; Staples and Cowie 2001), with the number of introduced species
in Hawaiian streams much larger than the number of native species (Devick 1991). For mollusks
alone, 22 freshwater snails and slugs have been introduced to the Hawaiian Islands (Cowie
1997), and 12 are known to be established (Cowie 1998). In contrast to most of the native
species with distinct and limited reproductive seasons (Kinzie 1993, Ha and Kinzie 1996), many
of the introduced species can reproduce throughout the year in the tropics, even if they are
seasonally constrained where they originated (Kondratieff et al. 1997; Yamamoto and Tagawa
2000; Brasher et al. 2006) and are prolific breeders that reproduce large numbers very rapidly
(Yamamoto and Tagawa 2000), allowing them to reach very high densities.
In a recent study on three Hawaiian islands—Hawaii, Kauai, and Oahu—introduced species
dominated the samples (Brasher et al. 2006). Of the 28 fish and crustacean species that were
collected during the study, nearly two-thirds (19 species) were introduced. The Tahitian prawn
M. lar, which was introduced to Hawaii in 1956 and eventually spread to streams throughout the
state as a result of its amphidromous life cycle (Yamamoto and Tagawa 2000), was present in the
largest number of streams (71%) sampled. The introduced atyid shrimp (the grass shrimp N.
denticulata), which does not have an oceanic larval life stage and so cannot move between
stream systems without human intervention, had the highest abundance (46% of the individuals
collected during the study) on the islands it currently occurs.
The impact of introduced species on aquatic ecosystems ranges from relatively benign to highly
detrimental. Not only are the introduced species well suited for disturbed habitat conditions,
some actually create such conditions. For example, introduced catfish and crayfish dig holes in
stream banks, causing erosion and increasing water turbidity (Yamamoto and Tagawa 2000).
Other species, such as smallmouth bass, introduced as a sport fish, are voracious predators that
feed on native fish and shrimp (Yamamoto and Tagawa 2000). Many aquarium pets, such as the
cichlids, are also very aggressive and predatory. In addition to whatever competition and
predation they exert directly on native fishes in altered streams, introduced species can also serve
as a source of introduced parasites, which then infest the native fish species (Bunkley-Williams
and Williams 1994; Font and Tate 1994; Font 2003).
Measurable Objectives
Vital Signs are physical, chemical, and biological elements and processes of ecosystems that are
selected to represent the overall health or condition of park resources, known or hypothesized
effects of stressors, or elements that have important human values. Early detection of potential
problems allows park managers to take steps to restore ecological conditions of park resources
before serious damage occurs.
Responses to natural drivers and anthropogenic stressors can be evaluated at four spatial scales:
the individual (organism), population, community, and ecosystem (Figure 1.5). Individual
organisms will show physiological responses (e.g., oxygen consumption, feeding rates),
19

morphological responses (e.g., anatomical deformities, growth rates), and behavioral responses
(e.g., migration, prey vulnerability) to both natural drivers and anthropogenic stressors. At the
population level, abundance, distribution, and age structure may be affected. At the community
level, there may be shifts in species diversity and abundance and functional roles. At the
ecosystem level, alterations in food webs, nutrient dynamics, and spatial structure may occur.

Natural drivers

Anthropogenic stressors

ORGANISM

POPULATION

Responds to drivers
and stressors

Species composition and
abundance (fish, shrimp
and snails)

VITAL SIGN

COMMUNITY

ECOSYSTEM

Overall condition of
park resource

MONITORING
GOAL

Figure 1.5. Responses to natural and anthropogenic stressors.

The PACN has selected freshwater communities as a Vital Sign that can serve as an indicator of
watershed quality. With numerous potential threats to watersheds as well as the streams
themselves, monitoring the status of stream systems is a high priority.
The monitoring questions for this protocol are:
1. What are long-term trends in spatial distribution and abundance of freshwater fish and
invertebrates (including snails and crustaceans)?
2. How do changes in habitat characteristics affect the composition, distribution, and abundance
of freshwater fish and invertebrates?
The measurable sampling objectives (Objective I) are described as three components:
Objective Ia: Determine long-term trends in the spatial distribution and abundance of native fish
and invertebrates (shrimps and snails) in selected streams.
20

Objective Ib: Determine long-term trends in the spatial distribution and abundance of introduced
fish and invertebrates (shrimps and snails) in selected streams.
Objective Ic: Determine long-term trends in habitat characteristics in selected streams.
The management objective (Objective II) provides a link between habitat characteristics (that can
potentially be affected by management activities) and biotic characteristics:
Objective II: Improve understanding of associations between stream animal communities (fish
and invertebrates) and their habitat by examining the associations among physical/chemical
habitat characteristics and spatial distribution and abundance of animal communities in different
streams or with changes in habitat (natural and anthropogenic) over time.
The primary monitoring goals are to provide information on the spatial distribution and
abundance of key fauna (fish, shrimp, and snails), and to measure habitat characteristics
associated with these fauna. This will provide the necessary information to assess natural
variation in distribution and abundance over time, as well as population responses to human
activities that alter habitat characteristics.
Management Implications
The data collected following this monitoring protocol will provide park managers with
information on the long-term status and trends of aquatic resources relative to natural processes
and anthropogenic stressors, and will serve as a tool to evaluate the effectiveness of management
actions aimed at protecting or restoring aquatic ecosystems. The monitoring questions are
designed to address management concerns. Specifically, what is the status of the stream fauna?
At what point does a manager need to take action? For example, the presence of any new
introduced fauna would serve as a trigger. Likewise, under the current statistical design, a
decline for two consecutive years of 50% of the population (which is outside of the estimated
natural variation of approximately 30% from year to year based on preliminary analyses) would
serve as a trigger. After five years of monitoring there should be sufficient information to begin
determining thresholds and trigger points for each stream system. The collection of physical
habitat data and co-location with water quality sampling will provide a link between
management activities (that can influence habitat characteristics) and the spatial distribution and
abundance of the stream fauna.
Parks and Streams Where Protocol Will Be Implemented
Stream sampling will be implemented in selected perennial streams in four parks: the National
Park of American Samoa (NPSA) on the islands of Tau and Tutuila, War in the Pacific National
Historical Park (WAPA) on the island of Guam, Haleakala National Park (HALE) on the
Hawaiian island of Maui, and Kalaupapa National Historical Park (KALA) on the Hawaiian
island of Molokai (Figure 1.6). Four streams will be sampled at NPSA: three on Tutuila
(Fagatuitui in the village of Fagasa, Leafu in the village of Vatia, and Amalau in the village of
Amalau) and one on Tau (Laufuti). The streams on Tutuila were selected to represent a forested
site (Fagatuitui), an urbanized site (Leafu), and a rural site where an invasive plant removal and
native forest restoration project is occurring (Amalau). Laufuti is the only perennial stream in the
park on Tau. One stream will be sampled at WAPA: Asan. This is the only perennial stream at
21

WAPA. Two streams will be sampled at HALE: Palikea (which consists of Palikea and the
tributary Pipiwai, which together flow in to Oheo Gulch) and Alalele. One stream will be
sampled at KALA: Waikolu. These are the only perennial streams in HALE and KALA.

22

23
Figure 1.6. Location of sampling streams at each of the four parks.

Chapter 2: Sampling Design
Background
The purpose of this chapter is to describe the factors considered in selecting the sampling design,
sampling frame, methods for site selection and co-location, biotic and habitat components to be
monitored, and frequency of monitoring. Based on discussions with NPS and USGS scientists,
PACN staff, and bio-statisticians, the sampling design for the stream monitoring protocol will
consist of a combination of permanent (fixed) sampling station locations and random station
locations that are newly selected each year. The sampling stations in each stream will be sampled
annually.
The primary monitoring goals are to collect information on the spatial distribution and
abundance of key fauna (fish, shrimp, and snails), and to measure habitat characteristics
associated with these fauna. This will provide the necessary information to assess natural
variation in abundance and habitat characteristics over time, as well as population responses to
human activities (such as water diversion). In addition, these surveys will address management
objectives of understanding how species distribution and abundance vary with habitat
characteristics and how changes in species composition, distribution, and abundance correspond
with changes in habitat (natural and anthropogenic) over time.
A number of methods have been used to survey stream fauna in American Samoa, Guam, and
Hawaii. The three most common strategies are snorkeling (quadrat, line, and reach methods),
electrofishing, and trapping/netting. Each of these methods may be used in one or more streams
in the PACN, depending on logistical considerations and ongoing or past survey activities in a
given stream.
Target taxa for this protocol are fish, shrimp, and snails. Other potential taxa that could be
monitored include benthic macroinvertebrates (such as insects) and algae. The target taxa were
selected based on time and fiscal constraints, but others could be added in the future. Baseline
data on fish, shrimp, and snails are already available for the streams in the Hawaiian parks;
HALE (Palikea and Alelele) and KALA (Waikolu). This focus is also compatible with work
being done in Guam and American Samoa. The major federal stream assessments, NAWQA and
EMAP, include algae and macroinvertebrates as part of their surveys.
Important Considerations
One of the Inventory and Monitoring program’s goals is the ability to statistically detect trends
over time. Consequently study design and site selection are based upon statistical considerations
that influence replication, namely number and spatial distribution of sampling locations. These
are discussed in detail in this chapter. In addition to statistical concerns, a number of practical,
logistical, and fiscal constraints also have influenced the final design of the Pacific Islands
Stream Monitoring: Fish, Shrimp, Snails and Habitat Characterization protocol.
Maximizing Personnel Safety
Conducting monitoring work in the aquatic environment presents special challenges and hazards.
The safety of field personnel during each site visit is a critical consideration. For example,
sampling in narrow steep canyons during and immediately following rain events can be

25

particularly hazardous. During and after rain, which may be located far up the watershed, there is
always the risk of flooding. Flooding creates multiple hazards including strong currents, rapidly
moving objects, and the elimination of safe escape routes, all of which can lead to serious
physical harm or even death. Additionally, because the rocks are often covered with algae,
hiking in streams presents the possibility of slipping, which can lead to serious physical injury.
In the event of a mishap, it is important to have at least three field crew members, so that one can
stay with the injured person, and the other can go for help. At a minimum, all field crew should
be certified in CPR and first aid. In addition, training in wilderness first aid and swift water
rescue is recommended because much of the fieldwork will occur in remote areas. Additional
details regarding safety are included in SOP #1: “Safety Protocol.”
Logistical and Fiscal Constraints
Field activities such as site selection and sampling events are constrained by personnel and
equipment availability, site location, topography, and weather. Thus, each park has a limited
window of time when field activities can be conducted, restricting the number of sites that can be
completed within the sampling design. The two largest logistical constraints for the stream
protocol are the extensive travel required to reach a given stream, and the limited window of
time when field activities can be safely conducted (during the dry season).
Ultimately, the implementation of this protocol will strongly be influenced by fiscal
considerations. Fiscal constraints within this program will affect staffing levels, frequency of
sampling, and the number of monitoring locations that can be visited.
The recommended sampling frame (sample each stream one time per year, each year) is
presented as the template. This design is feasible given current budget allocations. As the highest
cost is simply getting to a site, reducing costs would be most effective by reducing the number of
streams (parks) visited each year rather than reducing sampling activity within a given stream
(park) on a single trip.
Integration with Other Vital Signs
To enhance the value of the datasets collected, the stream protocol was designed to be integrated
with the PACN water quality vital sign protocol. Co-locating and co-visiting during identical
sampling periods lends greater correlative power among the environmental variables (physical
and chemical habitat conditions) and the stream biota. In addition, integrating the water quality
and stream protocols provides an economic benefit, by reducing travel costs (which can be a
substantial percentage of the total sampling costs).

26

Sampling
Stream Selection

This protocol is designed for monitoring the larger perennial streams in each park. Smaller and
intermittent streams are not included, but the SOPs could be modified to include such streams if
requested by park management. Four streams will be sampled at NPSA: three on Tutuila
(Fagatuitui in the village of Fagasa, Leafu in the village of Vatia, and Amalau in the village of
Amalau) and one on Tau (Laufuti). The streams on Tutuila were selected to represent a forested
site (Fagatuitui), an urbanized site (Leafu), and a rural site where an invasive plant removal and
native forest restoration project is occurring (Amalau). Laufuti is the only perennial stream in the
park on Tau. One stream will be sampled at WAPA: Asan. This is the only perennial stream at
WAPA. Two streams will be sampled at HALE: Palikea (which consists of Palikea and the
tributary Pipiwai, which together flow in to Oheo Gulch) and Alelele. One stream will be
sampled at KALA: Waikolu. These are the only perennial streams in HALE and KALA.
Station Selection

The location of both permanent fixed sites and variable (rotating) stations will be selected
randomly. If a generated random location has been selected previously for a fixed station then an
alternative random location will be selected. In instances where stations have already been either
surveyed or monitored (Alelele, Palikea, and Waikolu), a subset of the established sites will be
randomly selected as permanent fixed stations for this protocol. The original stations were all
selected randomly.
Sampling Units

The fundamental sampling unit for PACN stream biota monitoring is a sampling station. A
sampling station is defined as a randomly chosen 30-meter reach in the stream. Some stations
will be fixed (permanent) and some will be variable (new each year). Multiple sampling stations
will be located along each stream. The number of stations within a stream will vary (Table 2.1)
by stream. Currently there are no variable (rotating) stations in American Samoa, this may
change over time. Inference from the data collected following this protocol is to the stream in
which the stations are located. Each station will be divided in to quadrats or segments for biota
sampling, depending on the stream location and the target biota (described in the SOPs for each
sampling component).

27

Table 2.1. Number of fixed and rotating stations per stream with current sampling strategy.
Park

Stream

Fixed

Rotating

NPSA

Laufuti

4

na

Leafu

3

na

Fagatuitui

3

na

Amalau

2

na

WAPA

Asan

8

8

HALE

Palikea

6

7

Alelele

2

1

Waikolu

8

8

KALA

Target Population

The target populations for this protocol are the fish, shrimp, and snails in selected perennial
freshwater stream reaches. The longitudinal distributions of fish, shrimp, and snails are limited
by the presence of cliffs or waterfalls and the variable climbing ability among different species.
Sampling will occur from the mouth to the known upper limits of the taxa within PACN park
boundaries. Inference from this sampling will be to fish, shrimp, and snail populations within a
given stream.
Rationale for Sampling Design

Several different spatial and temporal sampling designs were considered for this protocol. Spatial
designs included simple random sample, systematic sample (grid), stratified random sample,
cluster sample, and Generalized Random Tessellation Stratified (GRTS) (DeBacker et al. 2005).
Each of these spatial designs has advantages and disadvantages. The stream monitoring protocol
is based on the simple random sample for the following reasons:
1.

This is the simplest strategy to set up and implement within a Geographic Information
System (GIS).

2.

This strategy ensures that every portion of the sampling frame has an equal probability of
being selected. Some of the PACN parks have abundance population parameters that are
relatively unknown; therefore it would be difficult to stratify or cluster sampling units
based on known habitats, geomorphological structures, or organism distribution patterns.

3.

The GRTS system, while appealing, is complicated to implement without trained
statisticians (DeBacker et al. 2005).

Temporal designs considered in this protocol included sites always revisited, sites never
revisited, rotating panels with sites sampled on 3 consecutive occasions, and split panels which
partition sites into two or more revisit designs (McDonald 2003). The split panel sampling
strategy will give the PACN both status and trends, spatially and temporally.
The PACN stream protocol uses a split-panel design for the following reasons:
1.

A split panel sampling design allows for increased spatial sampling while simultaneously
examining multiple temporal scales and permitting broader ecological and statistical

28

inference beyond that provided by fixed or permanent sampling locations alone (Skalski
2005).
2.

The split-panel design maximizes spatial replication while reducing the within-site effort,
using a combination of fixed and rotating panels to maximize power.

3.

Sampling a new set of sites annually minimizes the bias in estimates of status and
continually updates prior estimates through time series calculations (Skalski 1990).

4.

Leaving fixed sites within the design is useful for several reasons. First, the majority of
the historical data uses fixed sampling locations so spatial comparisons will be simpler.
Second, after the initial random setup, the fixed transects should be easier to resample,
thus reducing preparation time and ultimately costs to generate the random grid for
subsequent transect measurements (Green and Smith 1997). Third, utilizing exclusively
randomized sampling without fixed sites makes it difficult to detect change if it occurs
dramatically over time: random design measures inherent spatial variation at each
sampling period, which adds variance associated with spatial heterogeneity rather than
changes or patterns that are time-related (Green and Smith 1997). Fourth, fixed sites can
provide additional information in variance structure that is difficult to obtain with random
transects (Connell et al. 1997).

Establishing Sampling Stations (Spatial Design)

Sufficient spatial coverage throughout each stream is needed to provide broad inference beyond
the exact sampling locations. Sampling stations will be located from the mouth to the upper
distribution limits of the biota. The spatial coverage outlined in this design should be sufficient to
make inferences to the entire target population within the sampling frame, in other words,
inference to the entire stream.
To determine the location of the sampling units for monitoring, spatial coordinates for potential
sampling stations will be randomly generated. Fixed sampling stations in HALE and KALE will
be located at sites from which is there is already monitoring data, to lend to the interpretation of
trend data. Although fixed for this protocol, these sites were randomly chosen in the original
studies. The initial random selection regime for these sites fits the sampling methods of this
protocol, allowing data to be compared among previously established fixed sites and newly
established fixed sites. Both fixed and rotating sites in other parks will be selected randomly.
Randomly selected alternative locations will also be generated in case the initial locations are
unsuitable with respect to safety, accessibility, or resource availability (for example, presence of
water).
Full details regarding locating and documenting site locations can be found in SOP # 3:
“Locating Sampling Stations,” Appendix #5: “Logistics,” Appendix #7: “Sampling Sites (Maps
and Coordinates),” and in a brief narrative provided below. When all sites are selected, they
should be sampled in an order that minimizes travel time and prevents disturbance of other
sampling locations. Before starting field work, the site coordinates and station ID numbers
should be entered into a Global Positioning System (GPS) (SOP #4: “Using GARMIN Global
Positioning System (GPS) Units”; Also see SOP #5: “Downloading and Uploading Data
Between Garmin GPS and ArcGIS” and SOP #6: Using the Ricoh GPS Camera”).
29

Temporal Design and Sampling Frequency

The sample timing for each park is based primarily on environmental conditions. Sampling needs
to occur during base flow for safety, ecological (behavioral changes during higher flows), and
logistical (snorkeling needs to be done in clear water) reasons. To minimize delays due to stream
flooding, sampling should occur during the dry season. Stream sampling will also be scheduled
to coincide with the water quality protocol sampling.
Sampling all possible sites would greatly increase the breadth of ecological and statistical
inference that could be achieved, but would be prohibitively expensive and limit the temporal
scale at which repeat sampling could be done, increasing the length of time to detect any trend.
Because of the inherent variability of the data, increased time (i.e. sampling every other year)
between samples greatly increases the time required to detect potential issues. Given these
considerations, targeted (random) stations within each stream will be sampled once per year,
during the designated sampling window. Sampling windows are based on two criteria: (1)
sampling should occur during the same season each year, and (2) weather conditions. The
currently recommended level of replication will be evaluated as data are collected in the 3-5
years following implementation of the monitoring program, and modified as needed.
The current sampling design is based on consideration of safety issues, logistical limitations,
financial constraints, analyses of previously collected data sets, and consultation with
statisticians and experienced aquatic ecologists. The design for this monitoring plan has been
developed with the best available data, but modifications within an adaptive sampling design
framework will be necessary as implementation proceeds. It is critical to this monitoring
program that the data be collected and analyzed annually, and that the results be used to
adaptively “fine tune” the design to optimize effort, statistical power, and inference.
Sampling Methodology
Faunal survey methods (described in detail in the SOPs) are based on established methods
currently used by state, territory, and federal agencies for their stream monitoring programs, or
methods already being used in a given park (the selected methods are described in Chapter 3).
Habitat characterization (described in detail in the SOPs) is based on established EPA EMAP
(Peck et al. 2006) and USGS NAWQA (Fitzpatrick et al. 1998) protocols, and methods currently
being used in other I&M networks (Brasher et al. in press). A complete habitat characterization
(using data from 6 transects) will be conducted in Guam, to be consistent with ongoing sampling
activities by the Guam DEQ, and because the stream is located in an urbanizing watershed.
Rapid habitat assessments will be conducted in all other parks, and are a modified version of the
complete characterization method. In the event of changes in land use (from forested to
developed, or changes in water withdrawal activities, for example) in any of the other parks, a
switch to the complete habitat characterization would be appropriate prior to any land use
changes. Habitat sampling is further described in Chapter 3, and complete details are provided in
the SOPs.
Statistical Evaluation of Existing Data Sets
Preliminary analyses for sample design and sample size estimation using data collected in
Waikolu stream (Brasher, 1996), and in several streams on Maui (Brasher, unpublished data) are
presented below. John Skalski (Skalski, 2005) utilized this data for estimation of variance
30

components between streams, between stations, and between quadrats, by year and by stream.
Power analyses and precision estimates are also discussed in this chapter, to provide preliminary
information on the number of stations and number of quadrats to be sampled per stream. As the
monitoring program continues, data will become available to refine these calculations for
Waikolu and to conduct these analyses for the other streams in other parks. Additional
preliminary analyses can be found in Appendix #6: “Additional Statistical Analyses and Power
Estimates for Preliminary Samples Size Determination.”
Annual Precision Calculations

Precision in estimating variables (e.g. species abundance) is affected by spatial, temporal, and
human sources of variation, including identification and counting. Increasing precision is
possible by increasing replication within the largest component of variation. Precision is affected
by three levels of source variability:
1) at the level of the stream - Coefficient of Variation1 (CVSTR)
2) at the level of the sampling station - Coefficient of Variation2 (CVSTA)
3) at the level of the quadrat - Coefficient of Variation3 (CVQUAD).
To determine the precision of the estimate, it is first necessary to quantify the existing estimates
of expected variation.
Existing estimates of expected variation
Begin by estimating variance components associated with
2
1) stream variance (σ STR
);
2
2) station variance within a stream (σ STA
);
2
3) quadrat variance within a station (σ QUAD
).

This relatively simple calculation by year and season showed variance estimates changed
considerably over time (Appendix #6: “Additional Statistical Analyses and Power Estimates for
Preliminary Samples Size Determination”). However, when coefficients of variation (CV) were
calculated, the estimates were more numerically stable. The CV for streams was calculated using
CVSTR =

2
σˆ STR

x

(2.1)

where x is the grand average calculated across streams. The same equation can be used to
calculate the CV for stations or quadrats, using the variance and grand average data for stations
and quadrants respectively (Table 2.2).

31

Table 2.2. Coefficients of variation (CVs) for streams (CVSTR), stations (CVSTA), and quadrats
(CVQUAD) by fish species and island.
Island
Maui

Species
A. guamensis
L. concolor
S. stimpsoni
A. guamensis
L. concolor
S. stimpsoni

Molokai

CVSTR
0.24
0.79
1.29
0.67
0.15
0.21

CVSTA
0.44
0.92
0.82
0.92
0.47
0.74

CVQUAD
1.57
1.24
1.27
2.28
0.81
0.83

Once the CVs are known, it is possible to then calculate the precision of the estimates.

Precision Calculations
Precision can be defined in terms of relative error ( ε ),
 x −µ

< ε  =−
P
1 α.
 µ


(2.2)

This implies that the design of this monitoring strategy will have an inherent quantifiable relative
error in estimation, and the parameters driving that estimation can be set to programmatically
acceptable limits. For example, to estimate the population status within ±10% of the true value
90% of the time set ε = 0.10, 1 − α = 0.90, to get
 x −µ

< 0.10  =
P
0.90 ,
 µ


The ultimate choice of ε and 1 − α is at the discretion of the program or project manager;
however, this monitoring strategy design is based on estimating the population status within
±10% of the true value 90% of the time.
Solving equation (2.2) for ε , then rewriting in the form of variance, we get

ε ≈Z

1−

where Z

1−

α
2

α
2

Var ( x )
.
x

(2.3)

(

= standard normal deviation value corresponding to P Z < Z

1−

α
2

1−α .
)=

Expanding to our anticipated error levels in sampling data collection, we get equation (2.3)
expressed as

ε ≈Z

1−

α
2

2
2
2
(1 − f3 ) CVQUAD
(1 − f1 ) CVSTR
(1 − f 2 ) CVSTA
+
+

n

nm

32

nmk

,

(2.4)

where

n = number of streams sampled

f1 = fraction of streams within the sampling frame sampled (i.e., n N )
m = number of stations sampled per stream

f 2 = fraction of possible stations within a stream sampled (i.e., m M )
k = number of quadrats within a station sampled

f3 = fraction of possible quadrats within a station sampled (i.e., k K )
Substituting the results of Table 2.2 with equation (2.4) we calculate the anticipated precision for
the relative error estimate of each species’ population estimate based on the sampling parameters
For example, looking at S. stimpsoni in Waikolu stream on Molokai, we see
.
This data was collected from one stream with 23 thirty-meter stations using 10 one-meter
quadrats per station along the 3,000 meter stream. Again, substituting these values for our n, m,
and k values as well as using our 90% confidence interval, we get

Substituting these values into the equation gives us

.
Next, we consider the sampling fractions of the data and get

f1 ≈ 1, meaning there was only one stream and it was sampled;
f 2 ≈ 0.23 meaning 23% of the possible stations on the stream were sampled;

f3 ≈ 0.033, meaning that only 3.3 percent of the possible quadrat locations within a
station were sampled.
Substituting these values, we get
33

In other words, this study (which estimated the average S. stimpsoni abundance in Waikolu
stream) was determined to have a precision of ± 24%, with 90% confidence. The study design
for this monitoring protocol will follow similar methods but not be as intensive as the 1993-1994
Molokai study or the 1991-2000 Maui study. Because this monitoring protocol’s study design is
less intensive than the earlier studies, precision estimates are expected to be slightly less precise.
Table 2.3 shows the precision estimates for fish populations by species and island for these two
studies.
Equation (2.4) can be used to look at any combination of n, m, and k to determine the desired
level of precision. Creating precision analysis graphs provides a visual way to assess the best
estimates of target number and length of stations on a stream as well as the number of quadrats
for fish population sampling (Figure 2.1).

Table 2.3. Precision estimates for three species of gobies. Estimates use fifteen 30 m stations on a single
3,000 m stream with a 90% confidence interval and the CV data from Table 2.1.
Species
A. guamensis
L. concolor
S. stimpsoni

Island
Maui
Molokai
Maui
Molokai
Maui
Molokai

Estimate Value
0.211
0.401
0.373
0.194
0.336
0.297

34

Precision Estimate
21%
40%
37%
17%
34%
30%

L. concolor at Maui (30 m Stations)

Molokai L. concolor (30 m Stations)
100

100

90

90

80

80
5 Stations
70
10 Stations
60
15 Stations

Precision

Precision

70
60

5 Stations
10 Stations
15 Stations

50
20 Stations

20 Stations
25 Stations

20

25 Stations
40
30 Stations
30
35 Stations
20

10

10

50
40
30

0

30 Stations
35 Stations

0
5

10

15

20

25

30

35

5

10

15

Number of Quadrats

A. guamensis at Molokai (30 m Stations)

30

35

A. guamensis at Maui (30 m Stations)
100

90

90

80

80
5 Stations
70 Stations
10

5 Stations

60 Stations
15

15 Stations

20
50 Stations
25 Stations
40
30 Stations
30 Stations
35

20 Stations

60

Precision

Precision

25

100

70

50
40
30
20

20

10

10

0

10 Stations

25 Stations
30 Stations
35 Stations

0
5

10

15

20

25

30

35

5

10

Number of Quadrats

15

20

25

30

35

Number of Quadrats

S. stimpsoni at Molokai (30 m Stations)

S. stimpsoni at Maui (30 m Stations)

100

100

90

90

80

80
5 Stations
70
10 Stations
60
15 Stations

Precision

70

Precision

20

Number of Quadrats

60
50

20
10

10

30

0

10 Stations
15 Stations

50
20 Stations
25 Stations
40
30 Stations
30
35 Stations
20

40

5 Stations

20 Stations
25 Stations
30 Stations
35 Stations

0
5

10

15

20

25

30

35

5

Number of Quadrats

10

15

20

25

30

35

Number of Quadrats

Figure 2.1. Precision analysis curves of 30m length stations on the islands of Maui and Molokai by fish
species.

It is apparent from the precision curves that doubling the number of quadrats from k = 5 to k =
10 gives the greatest jump in precision within stations, while increases in precision estimates
beyond k = 10 yields very little in the way of increase in precision within a station. It is much
more effective to increase the station numbers than to increase the number of quadrats within a

35

station, indicating that the greatest variability is between stations and not quadrats. It can also be
seen that the benefits gained in precision with increasing station numbers begins to be
significantly reduced at 15 stations.
The most efficient use of resources would dictate using the asymptote of the curves, which,
based on these precision graphs, give us an annual sample size of 15 stations with 10 quadrats at
each station, for Waikolu Stream in KALA. Surveying this sample size in each park should be
feasible given current logistical and financial constraints.
Proportion of Fixed Versus Random Panels (Stations)
The purpose of this monitoring effort is to detect change over time with sufficient statistical
power to make meaningful statements about the resource status and trends. The split-panel
design selected for this protocol maximizes the spatial replication while reducing the within-site
effort, using a combination of fixed and rotating panels to maximize power. The optimal
proportion of fixed to rotating panels can be estimated from the correlation (r) between years
within stations.
The optimal fraction of stations to rotate or replace each year in a panel design depends on the
correlation of the annual observations. When the annual correlations (r) are low, the fraction of
fixed stations is higher than when the correlations are high. The optimal fraction of stations to
retain each year is
Proportion of fixed to random stations= fratio =

1− r2
1+ 1− r2

.

(2.5)

Table 2.4 illustrates the relationship between r2 and fratio based on the above equation.
Table 2.4. Optimal fraction of fixed stations in streams to retain from one year to the next in a panel
design as a function of interannual correlation.
2

r

0
0.1
0.2
0.3
0.4
0.5

fratio
0.50
0.499
0.495
0.488
0.478
0.464

2

r

0.6
0.7
0.8
0.9
0.95
0.99

fratio
0.444
0.417
0.375
0.304
0.238
0.124

For Waikolu stream on Molokai, the temporal correlation between 1993−1994 was calculated for
each of the three species. For L. concolor, A. guamensis and S. stimpsoni, there was virtually no
correlation from one year to the next (Table 2.5).
For the observed r2 values in Table 2.4 (0.0866−0.2544), the optimal fixed: random ratio should
be approximately 50% for the lowest value. The fixed: random ratio in this protocol is based on

36

the most conservative estimate (the lowest r value). Practical considerations, in particular the
cost of working stream stations, suggest this fixed ratio is realistic.
Table 2.5. Average sampling correlations in fish abundance for Waikolu, Molokai (KALA).
2

Species

r

r

A. guamensis

0.0075

0.0866

L. concolor

0.0262

0.1619

S. stimpsoni

0.0647

0.2544

Statistical Power Estimation
When determining the power to detect change over time it is important to consider that there can
be inherent and potentially serious statistical analysis issues associated with distributions, (which
can be skewed or normal), outliers, cycles (e.g., diurnal, seasonal), missing values, censored data
(zero values), and serial correlations (Helsel and Hirsch 2002). Often the most effective methods
for parameters that are variable (i.e., uncommon species abundances) and non-normally
distributed are non-parametric methods. This protocol measures multiple populations with
skewed and truncated distributions and outliers at multiple sites. Therefore, non-parametric
methods may be especially useful for trend analyses of this stream monitoring dataset.
In addition, non-parametric methods can be used sooner than parametric methods to determine if
there is an increasing or decreasing trend in any monitored parameter. This is because the
relative robustness and structural design of non-parametric methods enables them to be relatively
insensitive to skewed data and missing values. Therefore, non-parametric methods allow
management to be informed of resource trend and alert them to the need of possible action much
sooner than parametric methods.
Overall, analysis of data previously collected at Waikolu indicate that 15 stations, 8 of which are
fixed and 7 random, with 10 quadrats per station, is the most appropriate sampling design for
Waikolu Stream. After 5 years of data have been collected at Waikolu Stream, it will be
important to revisit the parametric power to detect change calculations to determine more
precisely the actual power to detect change given this sampling design. After 3-5 years of data
collection in the other parks, similar calculations can be run to determine the best long-term
sampling design for those streams.
Two of the potential methods that can be used for detecting trends are the Sen slope estimator
and the seasonal Kendall trend test. These methods can handle missing and non-normal data.
While these two methods are similar in approach, the trend slope estimator will give an estimate
of the slope of temporal data by comparing every sampling event against every other sampling
event, ranking the results, and taking the median as the trend slope estimate. This can be
compared with the Kendall trend test which is slightly more sophisticated, taking the differences
in all sampling events, replacing values with normalized change indicators (+ slope gets a 1, no
slope gets a 0, and – slope gets a -1), computing the year weighted variance for each sampling
event, then computing the test statistic for that variance. The result will give a trend with a
significance p-value (Helsel and Hirsch 2002). Using these two tests is a powerful method of
determining if there is a trend (increasing or decreasing) present in biotic data, and whether that

37

trend is significant. However, these tests do not detect specific changes (i.e. 25% decrease in
population with 95% confidence over 10 years).
To approach these types of questions, we need to use parametric power estimations. With
parametric methods, a specific change can be detected with a specific confidence over a
specified timeframe, but parametric methods are much more rigid in their requirements and often
take longer and require more samples to get statistically significant results. Despite these
additional requirements, parametric statistical methods can be useful when trying to understand
variability. When other methods are inconclusive, parametric statistical methods can detect
trends in environmental samples and can even help determine necessary sample sizes (National
Park Service, Roy Irwin, Biologist, pers. comm., 2008).
Sample size for this protocol is based both on precision of the estimates and on logistical
constraints. Even with large replicate data sets, variability is high, yet low variance is essential to
achieve high powers to detect change. Working within the current PACN budget to gather the
data necessary at precision levels that will be most helpful dictate an estimate of 10 working days
with 5 reserve days for inclement weather as the maximum estimated time available for
fieldwork at each park. Based on preliminary pilot work, it is realistically possible for a single
team of three to sample two sites per day, including hiking up streams with gear to an individual
station location.
For this protocol, sample size estimations and power results were determined using two methods:
a paired t-test analysis using an online calculator (SS Two samples at statsalive.com)
recommended by the National Park Service Water Resources Division NPS-WRD (National
Park Service, Roy Irwin, Biologist, pers. comm., 2008) and by a sample size independent power
calculator created by a statistician hired by the PACN network to consult on statistical sampling
designs for monitoring protocols (Skalski 2005). The t-test was good at estimating the sample
sizes and power, but lacked the ability to test for a specific change (i.e. β). With the Skalski
calculator, variance is the primary driver: if increased sample sizes decrease variance, the power
increases but a priori knowledge of the change in variance with sample size is not required.
Based on the variability associated with annual analyses from previous work, the Skalski
methods appeared more appropriate and conservative.
Power curves were created to visually indicate the power to detect change given 15 stations with
10 quadrats per station, and 8 fixed and 7 random sites (Figure 2.2). The results indicate that
power to detect change is relatively low for all three species on Molokai: A. guamensis 17% 20%, L. concolor 28% - 33%, and S. stimpsoni 50% - 59% (Table 2.6). By changing the replicates
to 10 fixed and 10 random for each of the species, the power was increased by 3%, 5%, and 9%
respectively for A. guamensis, L. concolor, and S. stimpsoni. This protocol cannot recommend
more than 20 sites, because this would exceed the number of sites feasible to sample given the
current budget and speed with which samples can be collected. Furthermore, the benefit gained
by increasing the number of sample sites does not appear to offset the time and fiscal constraints
of the program. Nevertheless, Figure 2.2 illustrates the value of increasing sample sizes by
showing the corresponding increase in power.

38

100.0%

Percent Power

80.0%

Red Curve = 20 stations
Blue Curve = 15 Stations

60.0%

A. guamensis Power Curve
Mean = 0.176
SD = 0.284
r = 0.087

40.0%
20.0%
0.0%
0.176
100.0%

Percent Power

80.0%

0.278

0.380

0.482

0.584

0.685

0.787

Red Curve = 20 stations
Blue Curve = 15 Stations

60.0%

L. concolor Power Curve
Mean = 4.400
SD = 4.617
r = 0.254

40.0%
20.0%
0.0%
4.400
100.0%

Percent Power

80.0%

5.869

7.339

8.808

10.278

11.747

13.216

Red Curve = 20 stations
Blue Curve = 15 Stations

60.0%
40.0%

S. stimpsoni Power Curve
Mean = 4.400
SD = 4.617
r = 0.254

20.0%
0.0%
2.144

2.552

2.960

3.368

3.776

4.184

4.592

5.000

Alternate Mean

Figure 2.2. Power curve estimation for Molokai fish population data. Estimates based on two-sided tests
with an α = 0.1 comparison between means.

39

Table 2.6 Power to detect a difference between population means estimations for three fish species on
Molokai. Estimates based on two-sided tests with an α = .1 comparison between means. Estimates use
either 15 sampling stations with 8 fixed and 7 random or 20 sampling stations with 10 fixed and 10
random.
Species

15 stations

20 stations

A. guamensis
L. concolor
S. stimpsoni

17%
28%
50%

20%
33%
59%

Further parametric statistical power estimations using the Skalski equations (Skalski 2005) on
the data from Maui yield additional information about the ability to detect trend over time. This
is distinguished from the ability to detect a difference in the means, in that a trend estimates
continuing small changes in mean over time, as opposed to specific differences between two
means. Data from Maui were modeled over a 25 year period (Table 2.7).
Table 2.7. Modeled power to detect change over time with specific confidences based on actual data
from Maui, following the I&M protocol recommendations (15 sites 8 fixed and 7 random). Relative change
value is read as x% chance of detecting a population change of y% with a confidence of 1-α% in z years
(i.e. 0.797 on the table corresponds to a 79.7% [or read 80%] chance of detecting a 50% change in the
population with 95% confidence in 20 years).
Power Output
Relative Change
=0.05
10%
25%
50%
=0.10
10%
25%
50%

5 yrs
0.110
0.159
0.321

10 yrs
0.121
0.228
0.548

15 yrs
0.131
0.286
0.689

20 yrs
0.142
0.344
0.797

25 yrs
0.152
0.398
0.868

0.215
0.290
0.507

0.230
0.369
0.704

0.243
0.435
0.818

0.256
0.496
0.891

0.268
0.551
0.935

Based on these results it would initially appear that the ability to detect trends over time has a
relatively low statistical power. However, this sample design increases in the ability to detect
change over time, especially larger changes (such as 50%) that are probably more ecologically
relevant. Following this protocol results in a minimum of an 11% chance of detecting a 10%
change in the fish population means in 5 years with 95% confidence based on the current
variability, as well as an 82% chance of detecting a 50% population shift in 15 years with 90%
confidence. Changes in population may very likely bring about changes in variability. If there is
a decrease in population, power would correspondingly increase. The Skalski power equations
allow for varying variability over time, calculating power by using a mean of the variances for
each monitoring event, and a corresponding mean of the means.
Targeted Detection Level
Based on the analysis of the existing data sets and incorporating logistical and fiscal constraints,
the targeted detection level is ±50% of the baseline population mean for all biological
populations, expressed as a relative measurement of change. For example, in regions where a
baseline parameter is 2.4 fishes/m2, our target detection level is ± 1.2 fishes/m2 change in
absolute value (50% relative).

40

Quality Assurance of Data
This protocol takes a multi-phased approach to quality assurance. The first phase of this
approach is training (SOP #7: “Training Field Personnel” provides details of the training
process). Prior to any fieldwork, all individuals participating in the fieldwork must have
thorough understanding of the field sampling activities. This will be accomplished by having all
crew members read the protocol and attend training each year. In addition, crew members should
always carry a copy of the SOPs pertinent to the sampling location
Once in the field, phase two of the quality assurance plan will begin. The crew should carry at
least one waterproof copy of the species identification key (preferably one for each surveyor) to
verify species identification. An in-field examination will verify ability to identify different
species. When field instrumentation is being used to collect data measurements, both a data
recorder and an instrument operator will be needed. The recorder will always repeat back the
data on each measurement to verify that the data was communicated and recorded correctly.
After data collectors return from the field, the data sheets will be washed, dried, and then
scanned into a .pdf file, with the original sent to, and stored by, the PACN Aquatic Ecologist for
a minimum of three years. The data will be entered into the computer by the Aquatic Biological
Technician, or another available biological technician. A technician will then verify 100% of the
data entries by comparing them to the data sheets for each station to ensure that no errors were
made in the entry of the data. All errors will be corrected following standard procedures
described in Chapter 4 (Data handling, analysis and reporting). The data will then be certified for
analysis.

41

Chapter 3: Field Methods
Field Season Preparations

The Field Lead (Aquatic Biological Technician) and Project Lead (PACN Aquatic Ecologist)
should be thoroughly familiar with the objectives of the stream monitoring protocol. They should
also have a solid working knowledge of all field sampling methods and techniques listed in this
protocol. The Field Lead is responsible for the majority of field season preparations, but may be
assisted in some tasks by the Project Lead.
Training

An important component of pre-season preparation is adequate training of the field crew.
Because year-to-year consistency in implementing the protocol directly affects the quality of the
monitoring data and their ability to demonstrate trends in the system, the need for high-quality
training cannot be overemphasized. SOP #7: “Training Field Personnel” provides details on
hiring and training personnel. The most essential component for the collection of credible, highquality data is a competent observer. As a result, field crew training is a critical component of the
monitoring program. Each observer should receive extensive training before the field season, and
should periodically be tested for quality assurance.
Field Schedule

A sampling timeframe has been established for each park (Appendix #8: “Recommended Field
Sampling Schedule”). This is coordinated with water quality monitoring, and has been selected
to avoid the times of likely stream flooding. A tentative schedule should be constructed for the
entire field season, taking into account all logistical considerations. Ultimately, the sampling
scheduling should provide a plan for the entire season, but flexibility for unforeseen
circumstances should be built into the schedule.
Supplies and Equipment

All of the necessary supplies for the season should be located and inspected to ensure that they
are in adequate condition. This includes, for example; field guides, data forms, GPS units, maps,
and all sampling equipment. Supplies should be grouped together in containers according to
sampling activity, and each container should have an attached check-list of all of the necessary
supplies.
All field equipment should be available and organized at least one month before field work is
scheduled to begin. All equipment should also be examined for functionality and completeness
before fieldwork begins. For example, sampling traps should be clean and free of holes, and a
sufficient supply of replacement batteries and pencils should be available. Wetsuits and waders
should be inspected to ensure that they are clean and free of tears.
Each field season a new set of data forms will need to be photocopied onto waterproof paper. In
addition, station and quadrat, transect, or pool locations should be determined and copied onto
waterproof paper. This will include permanent sampling stations as well as randomly generated
ones for a particular site visit.

43

It is very important that all gear (including personal items such as boots or tabis) be thoroughly
cleaned to avoid inadvertently transporting introduced species to a new location.
Permits

Obtaining all necessary permits is the responsibility of the Aquatic Biological Technician, who
may be assisted by park staff or the Project Lead. Permits can be especially time consuming to
obtain and therefore, applications for these permits should be submitted well before the season
begins. Scientific collecting permits need to be obtained from the appropriate state or territory
agency, and from each individual park where sampling will occur.
Logistics

Adequate preparation and advance planning is essential for a successful trip to the field (see SOP
#2: “Preparation for Field Sampling”). Each park and each stream will require a number of pretrip arrangements, well in advance of the planned sampling event, such as acquiring proper
permits (both from the park and from the state or territory), notifying park personnel of the
planned monitoring trip, arranging transportation to the park (airplane flights, vehicle rentals,
boat transportation), making housing or camping arrangements, and arranging transportation
within the park. In some instances local agency staff or park staff may be available (or
necessary) for assistance. At least two months prior to starting fieldwork, appropriate persons in
the park should be contacted (Chief of Resource Management, Chief Ranger, other applicable
staff that may be required to assist). Details, recommendations, and contacts for managing these
logistics are provided in Appendix 5: “Logistics.”
Overview of Sampling Methods for Pacific Island Streams
A number of sampling methods have been used for sampling Pacific island streams. The most
common methods include: (1) snorkeling, using either quadrats (Hodges 1994; Brasher 1996,
1997c; Baker and Foster 1992; Higashi and Nishimoto 2007), transects (Kido et al. 1999), or
swimming through a reach (Government of Guam Department of Aquatic and Wildlife
Resources, Brent Tibbats, Aquatic Biologist, personal communication, 2008); (2) electrofishing
(Cook 2004; Brasher et al. 2006), and (3) trapping (Hodges 1994; Cook 2004). Sampling in
PACN streams will include a combination of these methods based upon logistics and previous
sampling efforts in a given park stream.
Conducting Field Surveys—Fish, Shrimp, and Snails
The steps for conducting field surveys are outlined in SOP #8: “Conducting Surveys on Tau,
American Samoa”, SOP #9: “Conducting Surveys on Tutuila, American Samoa”, SOP #10:
“Conducting Surveys in Guam”, and SOP #11: “Conducting Surveys in Hawaii”. Associated
Data Sheets for each island are in Appendices #9-11. Detailed directions to the sampling sites
can be found in Appendix 5: “Logistics”. The first step in conducting field surveys is setting up
the sampling reach. After the sampling reach has been located in the stream (SOP #3: “Locating
Sampling Stations”), the reach is marked with flagging tape and the location documented with a
GPS (SOP #4: “Using Garmin Global Positioning System (GPS) Units”). It is helpful at this
point to mark with flagging tape the five sections along the reach where shrimp will be sampled
(in American Samoa and Guam). Water quality sampling (see the Water Quality Protocol for
details) is conducted at the top of the reach so that other sampling activities do not influence the
water sample. A discharge measurement is made at this location as well. If there are a sufficient

44

number of crew members the biota surveys can begin at the same time, and follow the order of
fish sampling then shrimp sampling, followed by snail surveys. If specimens are collected for
later identification, they are preserved in alcohol for follow-up packaging and transportation
(SOP #24: After Field Procedures). Sampling always occurs from downstream to upstream.
Lastly the habitat survey is conducted.
Conducting Surveys on Tau, American Samoa

Fish surveys are always conducted first (SOP #12: “Fish Surveys on Tau, American Samoa”).
Ten randomly placed 1m2 quadrats are surveyed, each for three minutes. Using a mask and
snorkel, the observer starts at the lowest quadrat and moves up stream as each is completed. All
fish within each quadrat are recorded, noting species and size (total length) of each individual.
Both native and introduced fish are recorded. If an introduced species is not able to be identified,
observers should catch the specimen for expert identification. For shrimp surveys (SOP #13:
“Shrimp (ula vai) Surveys on Tau, American Samoa”), the 30 m reach is divided into five
sections each 6 m long. Observers use a variety of strategies including dip nets, opae nets, and
turning over rocks, to collect all shrimp within the section. Shrimp are identified, measured, and
returned unharmed to the stream. Snail surveys are conducted last, again utilizing 10 randomly
placed 1m2 quadrats (SOP #14: “Snail (sisi vai) Surveys on Tau, American Samoa”). The
observer first counts all of the egg capsules within the upper right 1/4m2 of the quadrat. The
observers then proceed to collect and measure all snails, and return them unharmed to the stream,
and then count all post-larval snails (less than 5mm) in the 1m2 quadrat.
Conducting Surveys on Tutuila, American Samoa

Fish surveys are not conducted in streams on Tutuila. For shrimp surveys (SOP #15: “Shrimp
(ula vai) surveys on Tutuila, American Samoa”), the 30 m reach is divided into five sections each
6 m long. Observers use a variety of strategies including dip nets, opae nets, and turning over
rocks, to collect all shrimp within the section. Shrimp are identified, measured, and returned
unharmed to the stream. Snail surveys are conducted next, utilizing 10 randomly placed 1m2
quadrats (SOP #16: “Snail (sisi vai) Surveys on Tutuila, American Samoa). The observer first
counts all of the egg capsules within the upper right 1/4m2 of the quadrat. The observers then
proceed to collect and measure all snails, and return them unharmed to the stream, and then
count all post-larval snails (less than 5mm) in the 1m2 quadrat.
Conducting Surveys on Guam

Fish surveys are always conducted first (SOP #17: “Fish (atot) Surveys in Guam”). Ten
randomly placed 1m2 quadrats are surveyed, each for three minutes. Using a mask and snorkel,
the observer starts at the lowest quadrat and moves up stream as each is completed. All fish
within each quadrat are recorded, noting species and size (total length) of each individual. Both
native (including eels) and introduced fish are recorded. If an introduced species is not able to be
identified, observers should catch the specimen for expert identification. For shrimp surveys
(SOP #18: “Shrimp (uhang) Surveys in Guam”), the 30 m reach is divided into five sections each
6 m long. Observers use a variety of strategies including dip nets, opae nets, and turning over
rocks, to collect all shrimp within the section. Larger shrimp (Macrobrachium lar) are identified,
measured, and returned unharmed to the stream. The smaller atyid shrimp are placed in marked
sample jars filled with ethanol for later identification. Snail surveys are conducted last, within the
five sections of the reach (SOP #19: “Snail (akaleha) Surveys in Guam”). This method is a full
section search. One or two observers use mask and snorkel to observe and collect snails. Another
45

person on shore identifies and measures each snail, and returns it to the stream unharmed. The
in-water observers count snail egg capsules and post larval snails (< 5 mm) as they are observed
moving along the segment and report them to the data recorder.
Conducting Surveys in Hawaii

Fish and shrimp surveys are conducted simultaneously in Hawaii (SOP #20: “Fish (oopu) and
Shrimp (opae) Surveys in Hawaii”), and this is the first activity during the survey. Ten randomly
placed 1m2 quadrats are surveyed, each for three minutes. Using a mask and snorkel, the
observer starts at the lowest quadrat and moves up stream as each is completed. All fish within
each quadrat are recorded, noting species and size (total length) of each individual. Atyoida
bisulcata are counted but size is not estimated as they are all very small. Both native and
introduced fish and shrimp are recorded. If an introduced species is not able to be identified,
observers should catch the specimen for expert identification. In the case of large pools, quadrats
are established around the perimeter of the pool. Snail surveys are then conducted, utilizing 10
randomly placed 1/16m2 quadrats (SOP #21: “Snail (hihiwai) surveys in Hawaii”). The observer
first counts all of the egg capsules within the upper right 1/64m2 of the quadrat. The observers
then proceed to collect and measure all snails, and return them unharmed to the stream, and then
count all post-larval snails (less than 5mm) in the 1/16 m2 quadrat.
Electrofishing for Fish and Crustaceans
In some instances, the PACN aquatic ecologist may choose to conduct an electrofishing survey
on either Tutuila or Guam. This is an optional activity (SOP #22: “Electrofishing for Fish and
Crustaceans”). Due to logistical and other considerations including the protection of native
gobies, electrofishing will not be conducted on Tau or in Hawaii. Electrofishing works by
temporarily stunning stream animals that are then quickly scooped out of the water with a
sampling net and placed in buckets of aerated water. As soon as a reach has been sampled,
organisms in the buckets are identified, measured, and returned to the stream unharmed.
Electrofishing may be conducted along selected reaches, typically in the same reach that the
habitat survey is conducted. This activity requires additional training, additional gear (including
safety gear), the presence of at least one person with appropriate certification and experience in
electrofishing, and that all persons have first aid and CPR training. This activity also requires
that extreme care be taken to avoid harming any animals.
Additional information about electrofishing is available in the Western EMAP protocol (Peck et
al. 2006) and in the Fisheries Techniques book (Nielsen and Johnson 1983). It is recommended
that all crew members who will electroshock read Chapter 8 on electrofishing by James
Reynolds in the Fisheries Techniques book (Nielsen and Johnson 1983). Information on training
programs is available from the U.S. Fish and Wildlife Service National Conservation Training
Center website (http://training.fws.gov/BART/courses.html).
Conducting Field Surveys—Habitat
Physical habitat characteristics will be measured at the reach and the transect scale (as described
in SOP #23: “Habitat Characterization at the Reach and Transect Scales”). This monitoring
protocol is compatible with USGS guidelines for habitat assessments as part of the NAWQA
program (Fitzpatrick et al. 1998) found electronically at http://water.usgs.gov/nawqa/ protocols/
bioprotocols.html) and the U.S. Environmental Protection Agency (EPA) Environmental
46

Monitoring and Assessment Program (EMAP) (see Peck et al. 2006, found electronically at
http://www.epa.gov/wed/pages/publications/authored/EPA620R-06003EMAPSWFieldOperation
sManualPeck.pdf), as well as habitat assessments being conducted in National Parks in the
Colorado Plateau (Brasher et. al, in press).
Reach length for habitat characterization corresponds to the sampling reach for the fauna (30
meters). If possible, all physical habitat measurements should be made at each site on the same
day that faunal surveys are conducted. Within each reach, six equally spaced transects will be
established perpendicular to the direction of flow. Habitat will measured at 3 transects in Samoa
and Hawaii and 6 transects in Guam.
Reach scale measurements include curvilinear reach length, geomorphic channel units (e.g.
riffle, run, pool, etc.) and riparian land use (anthropogenic alterations and disturbances). Transect
measurements include dominant habitat type, wetted channel width, riparian canopy closure, and
substrate size estimation (pebble count). In addition, five point measurements are made across
each transect of water depth and velocity.
Conducting Field Surveys—Water Quality and Discharge
Sampling for the stream protocol will be co-located with sampling for the water quality protocol,
which includes measurements of both water quality and discharge.
After Field Activities
Post-field procedures fall into five categories: (1) equipment, (2) data management, (3)
summaries of field notes or trip reports, and (4) reporting scientific collecting activities. These
activities are detailed in SOP #24: “After the Field Season”.

47

Chapter 4: Data Handling, Analysis, and Reporting
Data handling, analysis, and reporting are treated as three interrelated steps in managing stream
macrofauna monitoring information. Additional details and context for this chapter may be found
in the PACN Data Management Plan (Dicus 2006), which describes the overall information
management strategy for the network. The PACN website 1 also contains guidance documents on
various information management topics (e.g., report development, GIS applications, GPS use).
Project Information Management Overview
Project information management may be best understood as an ongoing or cyclic process, as
shown in Figure 4.1. Specific yearly information management tasks for this project and their
timing are described in Appendix #12: “Yearly Project Task List.” Readers may also refer to
each respective chapter section below for additional guidance and instructions.

Figure 4.1. Idealized flow diagram of the cyclical stages of project information management, from preseason preparation to season close-out. Note that quality assurance and documentation are thematic and
not limited to any particular stage of the information life cycle.

The stages of this cycle are described in greater depth in later sections of this chapter, but can be
briefly summarized as follows:
• Preparation – Training, logistics planning, printing forms and maps
• Data acquisition – Field trips to acquire data
• Data entry & processing – Data entry and uploads into the working copy of the database,
GPS data processing, etc.
1

http://www1.nature.nps.gov/im/units/pacn/data.cfm

49












Quality review – Data are reviewed for quality and logical consistency
Metadata – Documentation of the year’s data collection and results of the quality review
Data certification – Data are certified as complete for the period of record
Data delivery – Certified data and metadata are delivered for archival and uploaded to the
master project database
Data analysis – Data are summarized and analyzed
Product development – Reports, maps, and other products are developed
Product delivery – Deliver reports and other products for posting and archival
Posting & distribution – Distribute products as planned and/or post to the Integrated
Resource Management Applications Portal (IRMA Portal).
Archival & records management – Review analog and digital files for retention (or
destruction) according to NPS Director’s Order 19 2. Retained files are renamed and
stored as needed.
Season close-out – Review and document needed improvements to project procedures or
infrastructure, complete administrative reports, develop work plans for the coming season

Pre-season Preparations for Information Management
Set up Project Workspace

A section of the networked PACN server at is reserved for this project, and access permissions
are established so that project staff members have access to needed files within this workspace.
Prior to each season, the Project Lead should make sure that network accounts are established for
each new staff member, and that the Data Manager is notified to ensure access to the project
workspace and databases. If network connections are too slow for efficient data entry and
processing, individual staff members may set up a workspace on their own workstation, with
periodic data transfer to the PACN server. Daily backups of the workstation to an external hard
drive will ensure that no data is lost. Additional details may be found in SOP #25: “Workspace
Setup and Project Records Management”.
GPS Loading and Preparation

The GIS Specialist and Project Lead should work together to ensure that target coordinates and
data dictionaries are loaded into the GPS units prior to the onset of fieldwork, and that GPS
download software is available and ready for use. Additional details on GPS use and GPS data
handling may be found in SOP #4: “Using Garmin Global Positioning System (GPS) Units”,
SOP #5: “Downloading and Uploading Data between Garmin GPS and ArcGIS”, SOP #6:
“Using the Ricoh GPS Camera”, and on the PACN website 3.
Implement Working Database Copy

Prior to the field season, the Data Manager will implement a blank copy of the working database
and ensure proper access on the part of the project staff. Refer to Overview for Database Design
(below) for additional information about the database design and implementation strategy.

2
3

http://data2.itc.nps.gov/npspolicy/DOrders.cfm
http://www1.nature.nps.gov/im/units/pacn/gis/SOP.cfm

50

Overview of Database Design
PACN data management staff designed customized relational database applications to store and
manipulate the data associated with this project. The design of the stream macrofauna monitoring
database follows the hierarchical data table organization of the Natural Resource Database
Template 4, the standard for the NPS I&M Program (see the data dictionary and other
documentation in Appendix #13: “Database Documentation”). The PACN data management
staff is responsible for development and maintenance of the database, including customization of
data summarization and export routines.
The database is divided into two components: (a) one for entering, editing and error-checking
data for the current season (i.e., the “working database copy”), and (b) one that contains the
complete set of certified data for the monitoring project (i.e., the “master project database”). A
functional comparison of these two components is provided in Table 4.1.
Table 4.1. Functional comparison of the master project database and the working database
Project database functions and capabilities

Working database

Software platform for back-end data

MS Access

Contains full list of sampling locations and taxa

X

Portable for remote data entry

X

Forms for entering and editing current year data

X

Quality assurance and data validation tools

X

Preliminary data summarization capabilities

X

Master database
MS SQL Server or MS
Access
X

X

Full analysis, summarization and export tools

X

Pre-formatted report output

X

Contains certified data for all observation years
Limited editing capabilities, edits are logged
Full automated backups and transaction logging

X
X
X

Each of these components is based on an identical underlying data structure (tables, fields, and
relationships, as documented in Appendix #13: “Database Documentation”). The working
database is implemented in Microsoft Access to permit greater flexibility for computers with
limited or unreliable network access. Eventually, the master database will be implemented in
Microsoft SQL Server in order to take advantage of the backup and transaction logging
capabilities of this enterprise database software.
Both components have an associated front-end database application (“user interface” with forms
and queries) implemented in Microsoft Access. The working database application has separate
screens for data entry, data review, and quality validation tools. The master database application
contains the analysis and summarization tools, including pre-formatted report output and exports
to other software (e.g., for analysis and graphics production). This front-end application
arrangement allows for modification and update of the user interface with no disruption to data
entry continuity. The improved front-end file can be distributed to data entry staff, who link it to
the back-end file, discard the out-dated front-end file, and proceed with their data entry work.
4

http://science.nature.nps.gov/im/apps/template/index.cfm

51

Under this arrangement, data entry staff has no need to open the back-end file, thereby reducing
the risk of improper deletions or other inadvertent data loss occurring within the protocolspecific data tables. In addition, a multi-user environment can be accommodated by storing the
back-end file on a server available to all users via a computer network.
During the field season, each project crew will be provided with their own copy of a working
database into which they enter, process, and quality check data for the current season (refer to the
next section and SOP #26: “Data Entry and Verification”). Once data for the field season have
been certified they will be uploaded into the master database, which is then used to inform all
reporting and analysis. This upload process is performed by the Data Manager, using a series of
pre-built append queries.
Data Entry and Processing
The functional components for data entry into the working database are described in SOP #26:
“Data Entry and Verification”. Each data entry form is patterned after the structure of the field
form, and has built-in quality assurance components such as pick lists and validation rules to test
for missing data or illogical combinations. Although the database permits users to view the raw
data tables and other database objects, users are strongly encouraged only to use these pre-built
forms as a way of ensuring the maximum level of quality assurance.
Regular Data Backups

Upon opening the working database, the user will be prompted to make a backup of the
underlying data (see SOP #26: “Data Entry and Verification”). It is recommended that this be
done on a regular basis – perhaps every day that new data are entered – to save time in case of
mistakes or database file corruption. These periodic backup files should be compressed to save
drive space, and may be deleted once enough subsequent backups are made. All such backups
may be deleted after the data have passed the quality review and been certified.
Data Verification

Analyses performed to detect ecological trends or patterns require data that are recorded properly
and have acceptable precision and minimal bias. Poor quality data can limit detection of subtle
changes in ecosystem patterns and processes, and may lead to incorrect conclusions. Quality
assurance/quality control (QA/QC) procedures applied to ecological data include four procedural
areas (or activities), ranging from simple to sophisticated, and inexpensive to costly:






defining and enforcing standards for electronic formats, locally defined codes,
measurement units, and metadata
checking for unusual or unreasonable patterns in data
checking for comparability of values between data sets
assessing overall data quality
To the greatest extent possible, the stream macrofauna database application incorporates
QA/QC strategies involving the first activity (defining and enforcing standards). The
database design and the allowable value ranges assigned to individual fields within the
data tables help to minimize the potential for data entry errors and/or the transcription of
erroneously recorded data. The other activities are integrated in the validation phase (see

52

Data Quality Review and SOP #27: “Post-Season Data Quality Review and Certification”
for more details.)
Field Form Handling Procedures

As the field data forms are part of the permanent record for project data, they should be handled
in a way that preserves their future interpretability and information content. To minimize the
possibility of data loss, hardcopy data forms and field notebooks should be stored in a well
organized fashion in a secure location, with photocopies and scanned data forms stored in a
separate location (e.g., on the PACN data server). Refer to SOP #28: “Field Form Handling
Procedures” for more details.
Image Handling Procedures

Photographic images should also be handled and processed with care. Refer to SOP #29:
“Managing Photographic Images” for details on how to handle and manage these files.
GPS Data Procedures

The following general procedures should be followed for GPS data (see SOP #4: “Using Garmin
Global Positioning System (GPS) Units” and Appendix #12: “Yearly Project Task List”):
1.

2.
3.
4.

GPS data should be downloaded by the field crew from the units at the end of each field
trip and stored in the project workspace (see SOP #25: “Workspace Setup and Project
Records Management”).
Raw files should be sent in a timely manner to the GIS Specialist for processing and
correction.
The GIS Specialist will process the raw GPS data and store the processed data in the
project workspace.
The GIS Specialist will upload corrected coordinate information into the database and
create any GIS data sets.

The Field Lead should periodically review the processed GPS data to make sure that any
problems are identified early in the data collection process.
Data Quality Review
After the data have been entered and processed, they need to be reviewed by the Project Lead for
quality, completeness, and logical consistency. The working database application facilitates this
process by showing the results of pre-built queries that check for data integrity, data outliers and
missing values, and illogical values. The user may then fix these problems and document the
fixes. Not all errors and inconsistencies can be fixed, in which case a description of the resulting
errors and why edits were not made is then documented and included in the metadata and
certification report (see Metadata Procedures and Data Certification and Delivery and SOP #27:
“Post-Season Data Quality Review and Certification”).
Data edits after certification

Due to the high volume of data changes and/or corrections during data entry, it is not efficient to
log all changes until after data are certified and uploaded into the master database. Prior to
certification, daily backups of the working database provide a crude means of restoring data to
the previous day’s state. After certification, all data edits in the master database are tracked in an

53

edit log (refer to Appendix #13: “Database Documentation”) so that future data users will be
aware of changes made after certification. In case future users need to restore data to the certified
version, we also retain a separate, read-only copy of the original, certified data for each year in
the PACN Digital Library (refer to SOP #30: “Product Delivery Specifications”).
Geospatial Data

The Project Lead and GIS Specialist may work together to review the surveyed coordinates and
other geospatial data for accuracy. The purpose of this joint review is to make sure that
geospatial data are complete and reasonably accurate, and also to determine which coordinates
will be used for subsequent mapping and fieldwork.
Metadata Procedures
Data documentation is a critical step toward ensuring that data sets are usable for their intended
purposes well into the future. This involves the development of metadata, which can be defined
as structured information about the content, quality, condition, and other characteristics of a
given data set, both tabular and spatial. Additionally, metadata provide the means to catalog and
search among data sets, thus making them available to a broad range of potential data users.
Metadata for all PACN monitoring data will conform to Federal Geographic Data Committee
(FGDC) guidelines and will contain all components of supporting information such that the data
may be confidently manipulated, analyzed, and synthesized.
At the conclusion of the field season (according to the schedule in Appendix #12: Yearly Project
Task List), the Project Lead will be responsible for providing a completed, up-to-date metadata
interview form to the Data Manager. The Data Manager and GIS Specialist will facilitate
metadata development by consulting on the use of the metadata interview form, by creating and
parsing metadata records from the information in the interview form, and by posting such
records to national clearinghouses. Refer to SOP #31: “Metadata Development” for specific
instructions.
Data Certification and Delivery
Data certification is a benchmark in the project information management process that indicates
that: 1) the data are complete for the period of record; 2) they have undergone and passed the
quality assurance checks (Quality Review); and 3) that they are appropriately documented and in
a condition for archiving, posting and distribution as appropriate. Certification is not intended to
imply that the data are completely free of errors or inconsistencies which may or may not have
been detected during quality assurance reviews.
To ensure that only quality data are included in reports and other project deliverables, the data
certification step is an annual requirement for all tabular and spatial data. The Project Lead is
primarily responsible for completing a PACN Project Data Certification Form, available from
the Data Manager or on the PACN website. This brief form should be submitted with the
certified data according to the timeline in Appendix #12: “Yearly Project Task List”. Refer to
SOP #27: “Post-Season Data Quality Review and Certification” and SOP #30: “Product Delivery
Specifications” for specific instructions.

54

Data Analysis
Data analysis addresses data validation issues and helps translate raw data into meaningful
management information. The two initial steps for all Pacific Island stream monitoring data that
have been identified are summarization and establishing range of variation. These initial steps
are encompassed in the larger construct of data management and data stewardship which are
discussed in SOPs #25-31, and in SOP #32: “Data Analysis and Reporting”. Ultimately, analyses
of the monitoring data are intended to 1) detect long-term trends in size and abundance of
freshwater fish and invertebrates, and 2) quantify associations among stream macrofauna size
and abundance and their habitat by correlating habitat measures with observed biological data.
Analytical Approach

Two basic initial steps are identified in data analysis for this protocol: summarization, and
establishing the range of variation. These steps are part of the larger data management and data
stewardship which is discussed in SOPs #:25-31. There are two levels for evaluating the
monitoring data: station level and stream level, both of which utilize descriptive statistics (Table
4.2). Additional data analysis includes trend assessment and synthesis. Quadrat (Hawaii and Tau)
or segment (Guam and Tutuila) abundance and size data is used to calculate summary statistics
and range of variation (mean and standard deviation) for biological data at each station.
Similarly, transect data is used to calculate summarization and range of variation data for habitat
characteristics (e.g. velocity, substrate characteristics, etc.). The station level data includes mean
and standard deviation abundance, size, and habitat characteristic data at a given station over
time. Stream level data includes mean and standard deviation abundance, size, and habitat
characteristic data for each station along the longitudinal gradient in a stream at a given time.
Trend assessment integrates station or stream level abundance, size, and habitat characteristic
summarization and range of variation data over time to detect change. Typically some form of
regression approach is used to identify the slope or trend. In addition trend assessment can
include multivariate statistics to integrate station and stream level abundance and size data with
habitat characteristics. Synthesis examines relationships between temporal and spatial trends in
stream macrofauna size and abundance, community structure, habitat characteristics, and water
quality data. Station level, stream level, and trend assessments are described here. Synthesis will
be addressed within and across multiple Vital Signs and is therefore left for network level or
broader scientific consideration in the future.
Status and Trend Analyses

The primary analytical strategies of interest to managers are anticipated to be status and longterm trends assessment (change detection). SOP #32: “Data Analysis and Reporting” identifies
the some specific processes and methods that could be used when preparing these analyses. The
station and stream level analyses identified above are anticipated to be an initial step in the
analytical process. Sites with historical data sets will need to be evaluated by the PACN Aquatic
Ecologist to ensure that the correct conversion factors and metrics are utilized for comparisons
with current data sets.
Additional analytical techniques (e.g., multivariate analysis) may also be employed beyond those
specified here or in SOP #32: “Data Analysis and Reporting,” primarily in collaboration with
other agencies and researchers.

55

Table 4.2. Preliminary approaches to analyzing stream community data.
Analysis

Description

Responsible Party

Station Level

Quality assurance and control routines and calculation of statistics from
monitoring data (abundance, size, habitat):
Step 1 (Summarization): Measures of mean, median, variation, and
other basic statistics. Include graphical presentation of data.
Step 2 (Range of Variation): Establish historical or expected range of
values, relation to relevant regulatory levels, confidence estimates.

Stream Level

Quality assurance and control routines and calculation of statistics from
monitoring data (abundance, size, habitat):
Step 1 (Summarization): Measures of mean, median, variation, and
other basic statistics. Include graphical presentation of data.
Step 2 (Range of Variation): Establish historical or expected range of
values, relation to relevant regulatory levels, confidence estimates.

Trend
Assessments

Biological Technician
with oversight by
PACN Aquatic
Ecologist and with
assistance from park
staff

Biological Technician
with oversight by
PACN Aquatic
Ecologist and with
assistance from park
staff

Step 1: Integration of station and stream level summary statistics over
time, potentially using regression analysis.
Step 2: Integration of station and stream level variation over time,
potentially using regression analysis. Includes establishing a direction
and rate of change of variation that may provide early warnings of
trends in resources condition.

PACN Aquatic
Ecologist and
researchers from
other institutions
(e.g. USGS)

Step 3: Integration of station and stream biological data with habitat
characteristics and water quality parameters using a multivariate
approach.

Reporting and Product Development
Refer to Appendix #12: “Yearly Project Task List” and SOP #30: “Product Delivery
Specifications” for the complete schedule for project reports and other deliverables and the
people responsible for them. Additionally, a checklist for data analysis and reporting tasks is
included in Appendix 14: “Analysis Log File Checklist.”
Report Content

A summary report will be produced annually for each stream/island, with a more detailed report
produced every five years. Analysis is conducted at two levels: the station level and stream level,
a trend assessment is conducted once adequate data is available. The annual report should:





Calculate summary statistics and variance estimates for biological data (fish, shrimp, and
snail size and abundance) by species using quadrat or segment data from each station.
Calculate summary statistics and variance estimates for physical habitat characteristics
across transects at each station.
Present station level data at the stream level, for each station along the longitudinal
gradient of a given stream.
Provide detailed trend results for abundance for each species (after the initial five years of
data have been collected) at the station and stream levels.

56




When possible include synthesis level analyses such as multivariate techniques to
summarize associations of biota with physical habitat or water quality data.
Evaluate operational aspects of the monitoring program, such as whether any sampling
locations need to be eliminated or moved due to access problems, whether the sampling
period remains appropriate.

Detailed reporting guidelines and table structures are provided in SOP #32: “Data Analysis and
Reporting”.
A more in-depth analysis and report should be produced every five years. In addition to the
above, the five-year report should also:




Provide detailed trend results for biological and physical habitat data the station and
stream levels.
Synthesize data by examining patterns within and across Vital Signs (such as water
quality data).
Evaluate sampling data using accumulated data to determine optimal sample size and
sample design for trend detection.

Standard Report Format
Annual reports and trend analysis reports will use the NPS Natural Resource Publications
template, a pre-formatted Microsoft Word template document based on current NPS formatting
standards. Annual reports will use either the Natural Resource Report or the Natural Resource
Data Series template, and trend analysis and other peer-reviewed technical reports will use the
Natural Resource Technical Report template. These templates and documentation of the NPS
publication standards are available at the NPS Natural Resource Publications website 5. An
example of report content is provided in Appendix #15: “Pacific Islands Stream Monitoring
Report: Example Summary of Vital Signs Data.”
Review Products for Sensitive Information

Certain project information related to the specific locations of rare or threatened taxa may meet
criteria for protection. In this case, the data should not be shared outside NPS except where a
written confidentiality agreement is in place prior to data sharing. Before preparing data in any
format for sharing outside NPS—including presentations, reports, and publications—the Project
Lead should refer to the guidance in SOP #33: “Sensitive Information Procedures”. Certain
information that may convey specific locations of sensitive resources may need to be screened or
redacted from public versions of products prior to release.
Product Delivery, Posting, and Distribution
Refer to SOP #30: “Product Delivery Specifications” for a schedule for project deliverables and
detailed instructions on how to deliver final products. Upon delivery products will be posted to
the IRMA Portal 6 as appropriate (refer to SOP #34: “Product Posting and Distribution” for more
information).
5
6

http://www.nature.nps.gov/publications/NRPM/index.cfm
http://irma.nps.gov/App/Portal/Home

57

Holding Period for Project Data

To permit sufficient time for priority in publication, certified project data will be held upon
delivery for a period not to exceed two years after it was originally collected. After the two year
period has elapsed, all certified, non-sensitive data will be posted to the IRMA Portal. Note that
this hold only applies to raw data, and not to metadata, reports or other products which are
posted to IRMA Portal immediately after being received and processed.
Special Procedures for Sensitive Information

Products that have been identified upon submission by the Project Lead as containing sensitive
information will either be revised into a form that does not disclose the locations of sensitive
resources, or withheld from posting and distribution. When requests for distribution of the
unedited version of products are initiated by the NPS, by a federal agency, or by a partner
organization (e.g., a research scientist at a university), the unedited product (e.g., the full data set
that includes protected information) may only be shared after a confidentiality agreement is
established between NPS and the other organization. Refer to SOP #33: “Sensitive Information
Procedures” for more information.
All official Freedom of Information Act (FOIA) requests will be handled according to NPS
policy. The Project Lead will work with the Data Manager and the park FOIA representative(s)
of the park(s) for which the request applies.
Archival and Records Management

All project files should be reviewed, cleaned up, and organized by the Project Lead annually.
Decisions on what to retain and what to destroy should be made following guidelines stipulated
in NPS Director’s Order 19, which provides a schedule indicating the amount of time that the
various kinds of records should be retained. Refer to SOP #25: “Workspace Setup and Project
Records Management”.
Season Close-out
After the conclusion of the field season, the Project Lead, Aquatic Biological Technician, Data
Manager, and GIS Specialist should meet to discuss the recent field season, and to document any
needed changes to the field sampling protocols, the working database application, or to any of
the SOPs associated with the protocol. Refer to the section on Data Entry and Processing for
additional close-out procedures not specifically related to project information management.

58

Chapter 5: Personnel Requirements and Training
Roles and Responsibilities
The Pacific Islands Stream Monitoring Protocol will be implemented using a combination of the
existing PACN I&M Aquatic Ecologist (serving as the Project Lead), an Aquatic Biological
Technician (serving as the Field Lead), additional technicians when available, and in-park NPS
staff. Table 5.1 lists the current roles and responsibilities for individuals carrying out these tasks
and Appendix 12: “Yearly Project Task List” lists specific yearly tasks for this project and their
timing. Implementation of the Pacific Islands Stream Monitoring Protocol requires a team
approach, with a minimum of three personnel for field activities (in most instances five people
would be preferable for stream monitoring). The PACN Aquatic Ecologist is the primary liaison
with the parks, ensuring this monitoring effort continues to address park management needs. One
or more Biological Technicians will be part of the PACN team. The Aquatic Biological
Technician assists the Aquatic Ecologist in coordination efforts, data management, quality
assurance, and analysis and is responsible for pre- and post-field visit preparations, and assisting
in fieldwork. The PACN Aquatic Ecologist and other PACN staff help facilitate Vital Sign
monitoring operations, ensure database management, conduct detailed status and trend analyses
and reporting, and provide other reporting and operational assistance at a network and national
level. Researchers from universities and other agencies (such as the U.S. Geological Survey)
may also assist in data analysis and reporting activities. Individual park staff may provide some
in-park coordination for field efforts as well as participate in sampling activities.
Project Lead

The PACN Aquatic Ecologist will serve as the Project Lead and will be responsible for
implementing this monitoring protocol with the assistance of PACN Aquatic Biological
Technicians and in some instances, park staff. The Project Lead will be the PACN I&M
Program’s lead point of contact. The Project Lead will be responsible for overseeing field
implementation, data entry, data verification, data analysis, final report preparation and
dissemination, and ensuring that data has been managed and archived appropriately. The Project
Lead works with the PACN Data Manager to ensure that the data management needs of this
protocol are met, that data products are made available according to schedule, and that any
required edits to archived data are documented according to network standards.
The Project Lead will be responsible for all I&M programmatic reporting including annual trend
analysis and park-based status reports. The Project Lead will also communicate budget and other
program needs to the PACN Program Manager. The Project Lead will coordinate periodic
programmatic reviews of this protocol to ensure the continuing relevance and applicability of the
protocols and data, and suggest and implement changes to the protocol design when necessary.
Overall field program coordination, analysis, and reporting to the each park’s resource manager
and/or designated ecologist is the responsibility of the Project Lead. Each year, the Project Lead
will review the sampling activities as well as data management and analysis, to help ensure that
operations and results meet the guidelines outlined in this protocol. The Project Lead and the
Field Lead (Aquatic Biological Technician) will review the protocol and previous year’s field
notes prior to sampling at a given park each year.

59

Table 5.1 Personnel Roles and Responsibilities for the PACN Pacific Islands Stream Monitoring: Fish,
Shrimp, Snails and Habitat Characterization.
Role
Project
Lead/Aquatic
Ecologist

Data Analyst
Field
Lead/Aquatic
Biological
Technician

Technicians
Data Manager

GIS Specialist

Program
Manager
Park staff

Responsibilities
Project oversight and administration
Track project objectives, budget, requirements, and progress toward project objectives
Facilitate communications between NPS and collaborators
Coordinate and ratify changes to protocol
Assist in training field crews
Assist Field Lead in performing data summaries and analysis
Conduct interpretation and report preparation (with assistance from Field Lead)
Review annual reports and other project deliverables for completeness and compliance with
Inventory and Monitoring Program specifications
Maintain and archive project records
Project operations and implementation
Certify each season’s data for quality and completeness
Complete reports, metadata, and other products according to schedule
Perform data summaries and analysis, assist interpretation and report preparation
Train and ensure safety of field crew
Plan and execute field visits (including contact with park staff)
Acquire and maintain field equipment
Acquire necessary permits and compliance
Oversee data collection and entry, verify accurate data transcription into database
Conduct data summaries and analysis (with assistance from the Project Lead)
Assist Project Lead with interpretation and report preparation
Complete a field season report
Review protocol and previous year’s field notes prior to the start of sampling
Collect, record, enter and verify data
Consult on data management activities
Facilitate check-in, review, and posting of data, metadata, reports, and other products to national
databases and clearinghouses according to schedule
Maintain and update database application
Provide database training as needed
Consult on spatial data collection, GPS use, and spatial analysis techniques
Facilitate spatial data development and map output generation
Work with Project Lead and Data Analyst to analyze spatial data and develop metadata for
spatial data products
Primary steward of GIS data and products
Review annual reports for completeness and compliance with I&M standards and expectations
Facilitate logistics planning and coordination
Ensure project compliance with park requirements
Review reports, data and other project deliverables

Aquatic Biological Technician

The Aquatic Biological Technician will serve as the Field Lead, and will be responsible for
assisting in both pre- and post-field activities. The primary responsibilities will be logistical
coordination, field data collection, data entry, data management, and equipment management.
The Aquatic Biological Technician will travel to parks as needed to assist with and conduct onsite field monitoring. Data will be entered by the technician into an established database. This
individual will conduct some data analyses for annual reporting and participate in the preparation
of annual data reports. The Aquatic Biological Technician may be assisted in data collection and
data entry activities by other staff technicians, when available.
60

Park-Based NPS Staff

In some cases, existing park-based resource staff will assist the Project Lead and Field Lead with
field-related activities, including data collection. Additionally, park staff may be trained to
conduct and carry out monitoring when logistical constraints preclude the PACN Aquatic
Ecologist (Project Lead) or the Aquatic Biological Technician (Field Lead) from conducting
monitoring directly.
PACN Data Manager

The Data Manager will provide guidance and, if appropriate, assistance with data management,
archiving, adaptive database design, maintenance, database integration, and data distribution.
The PACN Data Manager will not be responsible for day-to-day activities required implementing
this protocol, but will review the data and database-related practices of the Project Lead and the
Aquatic Biological Technician to ensure they meet programmatic and Vital Sign standards and
needs.
PACN GIS Specialist

The GIS Specialist will generate individual park-based sampling maps with geo-referenced
sampling points provided by the Project Lead. The PACN GIS Specialist will also be responsible
for generating mapping locations and geo-referenced graphical representations of spatial
analyses for reports.
PACN Program Manager

The PACN Program Manager will be responsible for general oversight of the stream monitoring
program. This includes periodic review of reports, decisions regarding allocation of funds and
staffing plans, and the overall quality and performance of the Project Lead. The Program
Manager is responsible for bringing any general monitoring issues beyond the scope of the
Project Lead responsibilities to the governing body of the PACN (PACN Board of Directors).
Qualifications and Training

All technical field staff will be trained in, and responsible for, familiarity with the SOPs, the
protocol narrative, and the protocol database. Periodic training and recertification are required.
These items are outlined in SOP #7: “Training Field Personnel”, and involve a minimum of
reading the full protocol (including narrative, SOPs, and appendices), receiving instruction in the
proper completion of all data forms, and receiving on-site training by the Project Lead in field
implementation. Prior to the start of field sampling, all participating field personnel must refresh
their methodological skills by reviewing SOP #7: “Training Field Personnel” and ensure their
certifications are complete and up to date.
Each position requires minimum background knowledge, skills, and abilities. The PACN
Aquatic Ecologist will serve as the Project Lead. This position requires a graduate degree or
equivalent experience in related discipline(s) (e.g., aquatic ecology, or other applicable
biological/natural science field), experience in the field data collection, experience in statistics,
data manipulation, and data management.
Park staff will typically be a park-based ecologist or resource manager, with experience and
expertise that enables them to assist with all aspects of the program.

61

The Aquatic Biological Technician will serve as the Field Lead. This position requires at
minimum a bachelor’s degree or equivalent experience in related discipline(s) (e.g., biological
sciences or natural history). Anyone filling this position must be capable of underwater field
operations, data collection, data management, post-processing, basic data analysis, and
equipment maintenance.
The Data Manager requires experience in database management, records certification, SQL
programming, and archiving. This position is hired through the PACN Program Manager and is
responsible for the entire PACN data management program. The minimum qualification is a
bachelors degree in computer science or related concentration, or other equivalent experience,
plus experience with the aforementioned skills.
The GIS specialist requires a Bachelors degree in computer science or related concentration, plus
specific experience with geo-referencing databases and programs. This position also requires
experience in geographic information systems.

62

Chapter 6: Operational Requirements
This chapter outlines preparatory work necessary before monitoring occurs (pre-monitoring
documents), annual workloads and field schedule, facility and equipment needs, start-up costs,
and annual budgets.
Pre-Monitoring Task
Pre-Monitoring Documents

Preparations for annual monitoring activities are summarized in SOP #2: “Preparation for the
Field Sampling.” At minimum, the Project Lead, and Aquatic Biological Technician should
review all SOPs, associated databases, and the previous year’s field notes prior to initiating
annual monitoring activities. As needed, the protocol narrative, appendices, SOPs, and databases
shall be updated prior to initiating field-based monitoring efforts.
Annual Workload and Field Schedule

Field sampling will be conducted annually. Scheduling sampling events can be difficult because
of inclement weather, particularly weather bringing rain that raises the stream level above lowflow conditions, personnel workloads, or other factors. In order to better accommodate these
factors, a three-week window will be used to plan when monitoring may occur at each park.
Table 6.1 outlines a schedule of programmatic and monitoring related activities for this Vital
Sign.
Facilities and Equipment

Facility support, office space, and supply requirements will be coordinated through the PACN
Program Manager, in consultation with the Aquatic Ecologist. Field equipment and supply needs
are outlined in SOP #2: “Preparation for the Field Sampling”. In some instances, parks will
provide space for long-term storage of field gear.

63

Table 6.1 Annual (fiscal year) schedule of monitoring activity benchmarks, with responsible individual(s)
identified.
Month

Preparation & Maintenance

Responsible Party

Oct

Finalize budget for fiscal year

Project lead (PACN aquatic
ecologist)

Nov

Initial annual data analysis and report writing

Project lead, assisted by aquatic
biotech (field lead), and park
staff

Nov

Permit Requests

Project lead, assisted by aquatic
biotech

Dec

Submit necessary IAP/IAGP’s

Project lead

Jan

Complete annual reporting (protocol summary and annual
)
analysis – may be completed earlier, this is the annual
report for the previous year.

Project lead, assisted by aquatic
biotech

Jan

Establish monitoring dates and personnel commitments.

Project lead, aquatic biotech,
and park staff

Feb

Re-evaluate budget status for fiscal year

Project lead

Feb

Review protocol and previous year’s field notes

Aquatic biotech, assisted by
project lead

Feb

Training/safety needs evaluation for Project Lead, Aquatic
Biological Technician, NPS Lead and park-based staff

Project lead, aquatic biotech,
and park staff

Mar

Mid-year equipment evaluation. Begin equipment
purchases

Aquatic biotech, assisted by
project lead

Apr

Field Monitoring WAPA

Aquatic biotech, other
technicians, may also be
assisted by park staff or project
lead

May

Write contracts/agreements for next FY work

Project lead

Jun

Field Monitoring HALE

Aquatic biotech, other
technicians, may also be
assisted by park staff or project
lead

Jul

Field Monitoring KALA

Aquatic biotech, other
technicians, may also be
assisted by park staff or project
lead

Aug

Plan budget for next FY

Project lead

Sep

Field Monitoring NPSA

Aquatic biotech, other
technicians, may also be
assisted by park staff or project
lead

Sep

Close out year-end budget

Project lead

Sep

End of the year equipment evaluation

Aquatic biotech

Start-up Costs
Start-up costs are identified separately from annual, implemented monitoring, and maintenance
expenses. Start up costs related to the Aquatic Biological Technician are provided in Table 6.2.
64

In general, start-up costs are anticipated to be somewhat substantial for some field equipment
related to the water quality monitoring (covered in a separate protocol), as well as specific to this
protocol (flow meter, GPS equipment, and so forth). It is not feasible to incorporate all start-up
costs into a single fiscal year because a substantial amount of the cost is in the monitoring
equipment (approximately $35,000 per park for all parks to have their own equipment), so a
phase-in plan will be used with this protocol. Some equipment will be centrally located with
I&M and moved between parks by the Field Lead. Annually recurring fixed costs include
equipment maintenance, salaries, training, certification, and travel-related expenses.
Table 6.2. Start-up costs.
Start-up Costs for Aquatic
Biological Technician
Equipment

$2,500

Training and certification

$2,000

Computer and software

$3,500

Desk and office supplies

$2,000

Position rating and recruitment

$3,000

TOTAL

$13,000

Annual Budget
Annual expense estimates for the stream monitoring protocol are outlined in Table 6.3 and are
expected to be approximately $66,939 for 2010, of which, approximately 30% is anticipated to
be utilized for data management, data analysis, and reporting. These expenses are based on
annual sampling in each park, and a base staff of an Aquatic Biological Technician and the
PACN Aquatic Ecologist, with assistance from existing park-based staff. Time for data entry,
analysis and reporting is also included. As this protocol, sample design, field visit schedule, and
safety and other considerations evolve, this budget will need refining. Estimates presented below
are based on 2010 expenses.

65

Table 6.3. Annual itemized expenses for the Pacific Islands Stream Monitoring Protocol by park.
Parks

HALE

KALA

NPSA

WAPA

Project Lead

$ 5,485

$ 5,485

$ 5,485

$ 5,485

Field Lead

$ 3,002

$ 3,002

$ 3,002

$ 3,002

Data Manager

$ 458

$ 458

$ 458

$ 458

GIS Specialist

$ 114

$ 114

$ 114

$ 114

Program Manager

$ 326

$ 326

$ 326

$ 326

Sub-Total

$ 8,288

$ 8,288

$ 8,288

$ 8,288

Camping Cost

$ 600

$ 600

$ -

$

Hotel Cost

$ -

$

-

$ 3,700

$ 4,200

Per Diem Cost

$ -

$

-

$ 1,700

$ 2,000

Airfare Cost

$ 800

$ 800

$ 4,000

$ 4,000

Vehicle cost

$ 1,000

$ 600

$ 700

$ 700

Sub-Total

$ 2,400

$ 2,000

$ 10,100

$ 10,900

Field Equip.

$ 100

$ 100

$ 100

$ 100

Crew Equipment

$ 700

$ 700

$ 700

$ 700

Sub-Total

$ 800

$ 800

$ 800

$ 800

Training

$ 100

$ 100

$ 100

$ 100

Office necessities

$ 100

$ 100

$ 100

$ 100

Sub-Total

$ 200

$ 200

$ 200

$ 200

Totals

$ 11,688

$ 11,288

$ 19,388

$ 20,188

Salaries

Travel
-

Equipment & Supplies

Other

Grand Total

$66,939

These expenses are for direct implementation of the monitoring protocol, and are outlined below
in detail. These include salary (with COLA and benefits), travel, computer and office supplies,
office space, personal equipment, and mandatory training. When actively monitoring, the
Aquatic Biological Technician’s time as Field Lead is anticipated to be devoted to this Vital
Sign, and the salary amounts in Table 6.3 reflect this. Personnel salaries were assumed to be GS7, step 5, using the 2010 pay schedule for all of park technicians and GS-7 step 4 for the Field
Lead. Personnel salaries were assumed to be GS-11, step 5, using the 2010 pay schedule for the
Data Manager and GIS Specialist. Again, using the 2010 pay schedule, the Project Lead was
assumed to be GS-12, step 5 and the Program Manager was estimated to be a GS-13, step 5.
These costs were based on the following estimate of days required to complete protocol work
(table 6.4):

66

Table 6.4. Annual requirements for staffing of the Pacific Islands Stream Monitoring Protocol:
anticipated work days for identified personnel in each park.
Personnel
Project Lead
Field Lead
Data Manager
GIS Specialist
Program Manager

HALE
20
20
2
0.5
1

KALA
20
20
2
0.5
1

NPSA
20
20
2
0.5
1

WAPA
20
20
2
0.5
1

For the Project Lead and park-based staff, existing funds will be used to support these
individuals’ personnel costs and associated supplies, travel, and training expenses. The expenses
directly related to this protocol are identified in Table 6.3. Costs associated with existing parkbased staff are not incorporated, as these positions already exist with assigned duties not related
to this Vital Sign. Should this collaboration with existing staff not be available, additional
expenses should be expected. Not included in Table 6.3 are other park-based support personnel
costs which are estimated to be GS-7, Step 5, for 6 pay periods/year [25% FTE] with 25%
COLA, 25% hazard and 25% benefits per park ($39,000/year).
Procedures for Making/Implementing Changes to the Protocol
Revisions to the protocol narrative and SOPs are expected over time. Explicit documentation of
these changes is critical for proper acquisition, processing, interpretation, and analysis of the
data. Procedures for changing the protocol narrative and related SOPs are documented in SOP
#35: “Revising the Protocol”. The Protocol Narrative and all SOPs are labeled with version
numbers and included in a Revision History Log (see Appendix #16: “Revision History Log”).
Changes to either document type are to be accompanied by changes in version numbers. Version
numbers and dates, the changes, reasons for the changes, and the author of the changes are to be
recorded in the Revision History Log. The updated version numbers must be recorded in the
PACN Stream Monitoring Master Version Table and provided to the Data Manager for proper
updating
of
the
Master
Version
Table
database.

67

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Appendix 1: Species identification guide for American Samoa
The species identification guide to be used for monitoring in American Samoa will be the guide
created by Don Vargo (2009). It is important to note that this was not developed by the National
Park Service, but is a technical report from the American Samoa Community College
(http://www.ctahr.hawaii.edu/adap/ASCC_LandGrant/Dr_Brooks/TechRepNo55.pdf).
This
guide is intended to be used as a half page size booklet. The page numbering assumes a saddle
stitch down the center fold.
References cited:
Vargo, D. 2009. Stream fauna of American Samoa; an illustrated guide to snails, shrimps, and
fishes of American Samoa streams. Technical Report 55. P. 38. Community and Natural
Resources, American Samoa Community College. Pago Pago, American Samoa.

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Appendix 2: Species identification guide for Guam
The shrimp identification guide is continuing to be developed. All crustaceans in Guam are
currently collected, preserved and processed by a lab with professional identification capabilities.
It is not at this time feasible for the staff of War in the Pacific National Historical Park to do all
identifications in the field. The field identification guide will updated one the identification has
come back from the lab. Future plans include training park staff in crustacean identifications in
Guam when feasible.

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Stiphodon sp.

Sicyopus sp.

Sicyopterus lagocephalus
(Photo: Brent Tibbats Used by permission)

82
Eleotris fusca
Figure A.2.1. Guam fish identification guide.

Awaous guamensis

Kuhlia rupestris

Neritina pulligera

Neritina variegata

Neritina squamipicta

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Septaria porcellana (top)
Figure A.2.2. Guam snail identification guide.

Septaria porcellana (underside)

Nertina petiti

Appendix 3: Species identification guide for Hawaii

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Lentipes concolor oopu alamoo

86

Sicyopterus stimpsoni oopu nopili

Awaous guamensis oopu nakea
Figure A.3.1. Hawaii stream species identification guide.

Eleotris sandwicensis oopu akupa

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Stenogobius hawaiiensis oopu naniha

Kuhlia sandvicensis aholehole (flagtail)
Figure A.3.1. Hawaii stream species identification guide (continued).

Macrobrachium grandimanus opae oeaha

Neritina granosa Hihiwai

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1 cm
Atyoida bisulcata opae

Figure A.3.1. Hawaii stream species identification guide (continued).

Appendix 4: Introduced species identification guide

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Figure A.4.1. Introduced stream species identification guide.

Appendix 5: Logistics and Aquatic Hitchhikers
This appendix includes logistical considerations and will be added to as logistical constraints
arise or change. Fieldwork on Pacific Islands in remote locations can be logistically challenging
and ample buffer time should be built in to field schedule to allow for unforeseen problems such
as weather or transportation issues. This appendix also includes information on the prevention of
transportation of introduced species (aquatic hitchhikers).
American Samoa
Travel to American Samoa
The initial point of entry to American Samoa is Pago Pago on the main island of Tutuila. Flights
are only on Thursday and Sunday direct from Honolulu (HNL) to Pago Pago (PPG) exclusively
on Hawaiian Airlines. A current passport is required for travel to American Samoa. American
Samoa is -11:00 Greenwich Mean Time (GMT) or 1 hour earlier than Hawaiian Standard Time
(HST). A water filter is highly recommended to filter drinking water especially on outer islands
or during periods of heavy rainfall. Hotels and smaller lodges are easily available on Tutuila.
Transportation on Tutuila
Rental cars are available on Tutuila through Friendly rental car, Avis, and certain hotels. The
I&M program currently shares ½ of a lease on a vehicle with the National Park of American
Samoa, which can be made available to staff with advanced notice.
Directions to Tutuila Field Sites
Leafu stream is accessed by traveling the main road to Pago Pago and the road over the mountain
to the village of Vatia. Note there are no official road names in American Samoa. Roads are
distinguished by the villages they connect. Village chiefs and the mayor must be notified prior to
arrival in the village. This should take place several days to preferably at least a week in
advance. FTUT01 is accessed through a villager’s backyard. Consult homeowners before
sampling. It is helpful to have employees that speak Samoan assist in communication efforts.
FTUT02 and FTUT03 are accessed by a trail that follows on the banks of the stream. Permission
is needed from the mayor of the Vatia to access these sites. Again notification of the mayor in
advance is required. Trail is marked with blue flagging tape.
Fagatutui Stream (FTUT04-FTUT06) is accessed by traveling the road from Pago Pago towards
the village of Fagasa. Park at the Mount Alava trailhead, proceed up trail 2 miles until specified
GPS point. Local staff know how to access these sites. It is helpful to have local knowledge.
Trail is a very steep slope down and marked with pink flagging tape though there may be other
trails in the area that can cause confusion. There are many streams in the area that look quite
similar. It is extremely important to have accurate GPS coordinates when accessing the stream
via trail. This stream can also be accessed via boat on days with calm sea conditions. The boat
can is launched from the Fagasa boat ramp and driven 3 bays over to Fagatuitui Bay. Fagatuitui
Bay is a distinctive looking bay with two streams that pour into the Bay. The sampled stream is
the one on the right coming in from the ocean. Depending on sea conditions, crew capabilities,
and boat specifications it may be possible to get relatively close to shore. However, it will be

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necessary to swim some distance to shore with all sampling gear. A float for the equipment will
be required.
Amalau stream is accessed via the road from Pago Pago towards Vatia to the village of Amalau.
Visitors must ask local villagers for permission to sample in Amalau stream. Permission should
be obtained the day of, as well as several days in advance so they know to expect you. Site
FTUT07 is at the mouth of the stream near the village fales. The site is accessed through private
land. Remember to obtain permission. FTUT08 is easily accessed by walking upstream crossing
highway and following stream until specified GPS point is reached.
In all travels to sites on Tutuila where village access is required, it is vitally important to
recognize that you are traversing private land. When specific dates and times are established for
sampling, these need to be honored. Local villagers get extremely upset when expected
intrusions do not happen as planned. Also, following local customs is required. While sampling
in village areas, dress must necessarily be modest and no work is to be conducted in village areas
on Sundays. Contact park staff for any questions regarding local customs.
Travel to Tau
Flights to Tau are available on Inter Island Air based in Pago Pago Airport. It is advisable to
contact local staff for assistance with booking flights to Tau. Flights can then be paid for, in
person, at the local airport office at least one day prior to departure. Flights generally fly daily,
however, they are extremely weather dependant and changeable at any moment. Call the Inter
Island Air office the day before to determine exact flight time (varies depending on the day) and
arrive at airport 2-3 hours ahead of scheduled flight time. It is not uncommon for the flight to
leave early to try and beat the weather, or to leave several hours late. Be prepared to spend the
entire day at the airport waiting for flights to happen. When flying with extra baggage, it is
advisable (almost required) to arrive very early and secure a spot in the check in line. Luggage is
taken on a first come first serve basis and no guarantees are made that excess luggage will make
it on the flight. Additionally, if there is a village chief, talking chief, mayor, or local dignitary,
their luggage will take priority over your luggage, regardless of order in line. Another option is
to package gear ahead of time and ship it over beforehand via plane or boat (M/V Sili). Mauga
Nofoaiga (park VIP) can receive packages in Tau. Contact local staff for assistance.
Housing on Tau
Homestays can be arranged through local NPSA staff. Generally, there are two options, Mele’s
Place and Mauga’s Place. Mele’s place is set up more like a traditional hotel. Rooms are separate
from the family’s living quarters. They offer basic, shared cooking facilities. Food should be
brought over from Tutuila, though there is a small store on Tau, it has a very limited supply of
options and is not regularly restocked. Mauga’s Place has 4 rooms and a kitchen/dining area that
is shared by the family and guests. The family will prepare local style meals for an additional
fee.
Camping is possible only in the lower portion of the Laufuti Stream or at the end of the access
road at the beginning of the trail to Laufuti. Solid tents are essential as the mosquitoes in the area
are vicious. Extra rope/parachute cord is necessary to tie down tents as stakes do not work well
in sand. The best camping is on the sandy beach 15 minutes before you reach the stream.
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Camping hammocks are unsuitable due to the mosquitoes. Camping in the upper portion of the
stream is not possible due to the steep and heavily forested terrain. All camping gear (tents, water
filter, sleeping bags, cooking gear) must be brought over from Tutuila; there are no supplies
available on Tau. There is no camp fuel available on Tutuila. Fuel is not allowed on airplanes,
therefore, fuel must be shipped over via boat well in advance. The M/V Sili is a cargo ship that
makes sporadic trips to the outer islands. Contact local staff for boat schedule and to arrange
cargo transport.
Directions to Tau field sites
All fixed field sites (FTAU01-FTAU04) are accessed via the beach trail at the end of the 4WD
road. The trail leads over a short sandy beach, a boulder beach, and a relatively smooth forested
trail. The trail then splits to access lower Laufuti and middle/upper Laufuti. Allow 30 minutes to
trail junction. The trail down to lower Laufuti (FTAU01-FTAU02) is a steep, slippery slope that
ends at a rocky beach. The trail was improved and a ladder installed in 2010 to assist hikers.
Follow the coast along sandy and boulder beaches until the mouth of Laufuti stream. This takes
approximately 2 hours from the split due to the rough terrain and heavy gear. To access the
middle and upper sections of Laufuti (FTAU03-FTAU04), the trail follows the ridgeline up a
steep climb. This trail can be extremely overgrown and may take extra time to cut through the
vegetation with machetes. It is helpful to ask NPSA staff to cut the trail in advance. This saves
hours of hacking through the jungle. Notify staff of intended arrival at least 2 months prior to
facilitate trail clearing. The trail is flagged with blue and pink flagging tape though they may not
be entirely visible if overgrown. The trail climbs through mostly fern forest. Many large
boulders, exposed roots, moss covered lava rocks, and thick vegetation present hazards. Pants,
long sleeve shirts, and mosquito repellant are essential. VIP Tuiluiga Simolea and NPSA Marine
Technician Bert Fuiava know all field sites and access routes.
NPSA Park contacts 684-633-7082
Tim Clark, Marine Ecologist
Bert Fuiavia, Marine Technican
Jim Nimz, Marine Technician
Visa Vaivai, I&M Biological Science Technician

Guam
Travel to Guam
Daily flights are available on Continental and American Airlines to A.B. Wonpat International
Airport (GUM). A passport is necessary. Guam is +10 hours GMT. It is over the International
Dateline, therefore Guam is 1 day ahead and 4 hours behind Hawaii Standard Time. Rental cars
are easily available on Guam from most major American companies. Park staff may be able to
make a vehicle available if enough advanced notice is given (preferably 1-2 months). Most
hotels are located in the Tumon and Taumuning areas of Guam, roughly a 20-30 minute drive
from WAPA’s main office in Hagatna. It is also possible to rent an apartment in Guam for
extended stays. Arrangements can be made through the park and require at least 2 months
advanced notice.

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Directions to field sites
All field sites are located on Asan stream in the Asan Unit of War in the Pacific National Park.
From the Airport or Tumon take highway 10A to Marine Corps Drive (Guam Route 1). Turn left
and go approximately 6 miles. Turn left onto Jose Leon Guerrero Street. Park on street near
bridge over Asan stream. Access the lower sites by heading upstream in the river. The first fixed
site is approximately 70 meters upstream from the parking location, just immediately past the
overhanging vegetation on the stream. Heading upstream, there is a trail on the left stream bank
(right side when facing upstream) just past the second banana plantation where there are several
limestone rocks in the bend of the stream. This trail can be used to facilitate quicker access to
central river sites up to the dam. All sites can be accessed by hiking upstream in the stream;
however, this is recommended only for sites downstream of FWAPA02 (lower sites).
Middle stream sites can be accessed by turning left onto Guam Route 6 from Marine Corps Drive
toward the Asan Unit Overlook. Turn left onto Mama Sandy Road toward a residential area.
Turn onto the small dirt road labeled J Street. Follow this road over the hill and then take the first
dirt road to the right (it is unmarked as of January 2011). Follow this dirt road downhill until you
reach the lowest cleared lot (the road will turn left and then start heading uphill again). Park in
this cleared lot. At the entrance to the cleared lot, you will find an overgrown access road.
Follow this road along the ridge until it turns to the left. Don’t turn left (This is an extremely
important direction note). Continue hiking over the ridge in front of you (the main ridge). All
middle stream sites can be accessed from points along the main ridge. If luck is on your side, you
will find a hash/pig trail that runs along the top of the main ridge. Follow this trail along the main
ridge and use your GPS to access all sites in the middle portion of the stream. The uppermost
middle site, FWAPA06, can be accessed by crossing this main ridge from the access road and
continuing to head down the side ridge to the stream. You will enter the stream about 100 meters
downstream of the site (this is not the current preferred route as it is presently overgrown with
sword-grass, but it is an access route, and the frequent fires may change the vegetation making it
an excellent access point in the future). As you access the middle trail sites, remember to keep
the main valley to your right. There are several side ridges, which, if taken, will lead you into
sword-grass fields and wasp lairs, which are better avoided. All sites in the middle stream can be
access by heading upstream from the previous location.
Upper sites can be accessed by turning left onto Guam Route 6 from Marine Corps Drive toward
the Asan Unit Overlook. Then turn left onto Mama Sandy Road toward a residential area. Turn
onto the small dirt road labeled J Street and park. Walk through the lower cleared lots to the
furthermost corner of the second cleared lot. There is a short, 15 minute trail down to the stream.
This trail goes directly to the uppermost fixed site on Asan stream, FWAPA16.

Park contacts 671-477-7278
Barbara Alberti, Park Superintendant
Mike Gawel, Chief of Resources

94

Maui
Travel to Maui
Flights are available on multiple airlines to Kahului International Airport (OGG). Rental cars are
available from most major American companies at the airport.
Directions to Field Sites
All field sites are located in the Kipahulu area of Haleakala National Park. From OGG follow the
Hana Hwy/HI-360 (Hana way or north route) to Kipahulu or follow Haleakala Hwy/HI-37 to
Piilani Hwy/HI-31 (south route) to Kipahulu. It takes approximately 3 hours each way from the
airport to Kipahulu.
FHALE01 is located near the mouth of the stream and is accessed via the Seven Sacred Pools
trail from the Kipahulu visitor’s center. FHALE07 is accessed by taking the 2 mile long Pipiwai
trail then following the rarely used Makahiku Falls trail (marked only by an old sign). Cross the
bridge, and follow trail to the stream. Cross the stream to the right bank and follow the stream to
appointed GPS point. FHALE02, FHALE08, and FHALE03 are located just off the Pipiwai trail.
FHALE02 is at the lower USGS gauging station. FHALE08 is accessed by hiking upstream in
Pipiwai Stream just after the confluence of Palikea and Pipiwai. FHALE03 is at the base of
Waimoku falls just upstream of where the trail crosses the stream. FHALE09 is accessed by
hiking in the stream up Palikea just after the confluence of Palikea and Pipiwai. Temporary sites
on Palikea or Pipiwai streams can be accessed via the Pipiwai trail.
FHALE05, FHALE06, and all temporary sites on Alelele are accessed by following highway 31
south from Kipahulu to the Alelele bridge. Park in the pullout near the mouth of the stream.
Follow the trail on the left bank of the stream to access all sites.
Housing
Camping is available in the Kipahulu maintenance yard by prior arrangement. Contact Stephen
Anderson or April Gragas for more information about camping reservations. There is a small
communal cabin that is used for cooking. There is a propane stove, refrigerator, tables, and
chairs. Bring all food, cookware, and dishes from Kahului. There is a small store in Hana if
additional supplies are necessary (40 minutes north of Kipahulu). Bring adequate drinking water
or a filter as no potable water is available in Kipahulu. There is catchment water that can be
boiled for cooking, filtered, and used to wash dishes. This cabin is shared by all employees
camping in Kipahulu. Ample tent space is available just outside the cabin. Bring all camping
gear. It rains regularly in Kipahulu.
Park contacts
Stephen Anderson, Natural Resource Program Manager, 808-572-4480
Sarah Creachbaum, Superindentant, 808-572-4401
April Gragas, Adminstrative Assistant, 808-572-4432
Molokai

95

Travel to Kalaupapa
There are two options for travel to Kalaupapa. There are regular flights to Hoolehua Airport
(MKK) located topside Molokai. It is then possible to take a cab to the trailhead down to
Kalaupapa and hike 3 miles down the Pali Trail to the settlement. The trail is very steep with
numerous switchbacks. The hike down is about 45 minutes while the hike up is 1-1 ½ hours.
This requires preplanning by shipping gear 2 weeks in advance (Fedex 2 day takes 5-7 working
days to reach Kalaupapa). The other option is to fly directly to Kalaupapa airport (LUP) on
Pacific Wings. This is significantly more expensive, but less hassle as you can carry equipment
as baggage. In either case, at least 2 weeks advance notice is required to enter Kalaupapa.
Contact local staff for more information. All guests must be sponsored by local staff and escorted
from the airport or the trailhead. Lodging in the settlement must also be prearranged with local
staff.
Travel to Field Sites
All field sites are located on Waikolu Stream. There are 3 access options. The first is to hike
from Kalawao (20 minute drive from main Kalaupapa settlement) down to the boulder beach and
across to Waikolu. The trail follows the coast alongside steep sea cliffs. Hardhats are required.
The hike is not advised during periods of heavy rain as this can cause loose rocks to fall from
cliffs. The hike is approximately 1.5 miles over a boulder beach with loose and slippery rocks.
The hike takes 1-1 ½ hours depending on pack weight and weather conditions. The 2nd option is
boat from the settlement around the point to Waikolu. This requires extensive planning with
local staff and calm sea conditions. The drive is approximately 45 minutes. Launching and
loading the boat takes approximately 1 hour. The boat can be anchored in the bay for near shore
gear unloading. Gear unloading takes approximately 1 hour. Camping is possible at the mouth of
the stream with proper permission. The 3rd option is to drive through the water diversion tunnel
from topside. This allows easier access to sites above the pumphouse. Prior permission must be
obtained through the Molokai Irrigation System part of the Department of Agriculture. A 4WD
vehicle that meets the tunnels specifications must be obtained. Jeep Wranglers that meet these
specifications are available for rent through Island Kine Rental Car (808-553-5242) located in
Kaunakakai. Arrangements with workers must be made for directions to the tunnel and to borrow
keys to access the tunnel. Contact Oscar Ignacio at 808-336-0587 for tunnel access. The drive
takes approximately 2 ½ hours from Kaunakakai.
Once in Waikolu Valley, all sites below the tunnel can be accessed by hiking up the stream or
from the trail. The trail goes from the mouth of the river to the pumphouse, and continues as a
road to the tunnel. All sights above the tunnel must be accessed by taking the catwalk that goes
from the tunnel to the diversion dam, and then hiking up stream. Sites near the tunnel and
waterfalls can be accessed by taking the catwalk that crosses the valley to the collection pool at
the base of the waterfalls, and then scrambling down to the stream below. The main trail along
Waikolu stream starts on the left Bank of the lefter most branch of the stream (the extreme right
of the valley facing upstream). Hike to the rocks that form the valley wall and begin walking
upstream. This trail is unmarked in this location so some faith must be taken the trail is there.
You will be touching the cliff as you hike the initial several meters of the trail. The trail then
becomes somewhat more distinct and travels along both sides of the stream crossing in several
places. GPS is useful in locating sites, but not always accurate or dependable as the signal gets

96

degraded the further upstream you travel. Navigation by topographic maps is advisable, and at
times required to locate the sites.
Housing Kalaupapa
Housing in settlement is available by prearrangement with local staff. Camping is possible in
Waikolu Valley with prior permission from the patient’s council. Camping is also possible near
the pumphouse about halfway up the stream. All camping gear including water filter, stoves,
tents, sleeping bags must be brought in. All travel to this stream must be arranged in advance
(preferable 1-2 months) to allow time for all proper permissions to be obtained.
Park contacts 808-567-6802
Eric Brown, Marine Ecologist ex 1502
Kim Tice, Inventory & Monitoring Biological Science Technician ex 1510

97

General Prevention Procedures for Stopping Aquatic Hitchhikers: methods for preventing the
transporation of non-native (introduced) species.
Follow a general set of procedures every
time you come in contact with any body
of water. By doing so, you can protect
your waters from harmful aquatic
hitchhikers. Because you never know
where a nuisance species has been
introduced, but has yet to be discovered.
Remove all visible mud, plants,
fish/animals.
Before leaving any body of water, it is
important to examine all your equipment,
boats, trailers, clothing, boots, buckets
etc and:

Eliminate water from all equipment
before transporting anywhere.
Much of the recreational equipment used
in water contains many spots where
water can collect and potentially harbor
these aquatic hitchhikers. Thus, make
sure that you:

Clean and dry
anything that came
in contact with the
water.
(boats, trailers,
equipment, dogs,
boots, clothing, etc.).
Basic procedures
include:










Remove any visible plants, fish or animals.
Remove mud and dirt since it too may contain a hitchhiker.*
Remove even plant fragments as they may contain a hitchhiker.*
Do not transport any potential hitchhiker, even back to your
home. Remove and leave them at the site you visited.

*The larvae (immature form) of an animal can be so tiny that you cannot
see it. However, it can live in mud, dirt, sand, and on plant fragments.





Eliminate all water from every conceivable item before you leave
the area you are visiting.
Remove water from motors, jet drives, live wells, boat hulls,
scuba tanks and regulators, boots, waders, bait buckets,
seaplane floats, swimming floats.
Once water is eliminated, follow the cleaning instructions listed
below.

Use hot (< 40° C or 104° F) or salt water to clean your equipment.
In some instances you may use a dilute clorox bath, if that is what is available. 2
cups of chlorox in five gallons of water can be put in a cooler or rubbermaid
container, and equipment dipped in that.
The following recipes are recommended for cleaning hard-to-treat equipment that
cannot be exposed to hot water:
o Dipping equipment into 100% vinegar for 20 minutes will kill harmful
aquatic hitchhiker species.
o A 1 % table salt solution for 24 hours can replace the vinegar dip. This
table provides correct mixtures for the 1 % salt solution in water:
Gallons of Water
5
10
25
50
100




Cups of Salt
2/3

3
6 1/4
12 2/3

If hot water is not available, spray equipment such as boats, motors, trailers,
anchors, decoys, floats, nets, with high-pressure water.
DRY Equipment. If possible, allow for 5 days of drying time before entering new
waters.

Figure A.5.1. General Prevention Procedures for Stopping Aquatic Hitchhikers: methods for preventing
the transporation of non-native (introduced) species.

98

There are hundreds of different harmful species ranging from plants, fish, amphibians,
crustaceans, mollusks, diseases or pathogens. Some organisms are so small, you may not even
realize they are hitching a ride with you. So, it is important to follow this general procedure
every time you leave any body of water.
It is recommended that the field crews use a separate set of equipment (including personal gear
such as boots) for each island group (Hawaii, Guam, and American Samoa). Regardless, all gear
should be cleaned at the end of a sampling event and before moving to a new site.
Prevention, where possible
• Avoid dumping water directly from one stream or lake into another.


Avoid obtaining water from multiple sources during a single operational period unless
drafting/dipping equipment is sanitized between sources.



Minimize driving equipment through water bodies.

Sanitation


Set up a portable disinfection tank using a 5% cleaning solution of quaternary ammonium
compound – common cleaning agents used in homes, swimming pools, and hospitals that
are safe for gear and equipment when used at the recommended concentration. Two
brands are readily available from GSA or local suppliers: Quat128® (by Waxie) or
Sparquat 256® (by Spartan). Costs and effectiveness are comparable; use either.
®

Table A.5.1. Recipe for 5% cleaning solution using either Quat128 or Sparquat 256





®

Volume of tap water

Volume of Quat128

Volume of Sparquat 256

100 mL water
1 gallon water
1 gallon water
1 gallon water
100 gallons water
1000 gallons water

4.63 mL
6.35 liquid oz.
12.7 tbsp
0.79 cups
4.96 gallons
49.6 gallons

3.00 mL
4.12 liquid oz.
8.2 tbsp
0.51 cups
3.22 gallons
32.2 gallons

®

®

Where feasible dip gear or equipment (e.g. helicopter buckets) into the cleaning solution.
Alternatively, put the 5% cleaning solution in backpack spray pumps to clean portable
equipment. The solution must be in contact with the surface being sanitized for at least 10
minutes and then rinsed with water.
Under the direction of the Resource Advisor, test cleaning solution at least daily
according to the directions below. The cleaning solution can be used repeatedly for up to
a week unless heavily muddied or diluted. If the concentration is too weak, dispose of the
used solution properly and make a new solution.

Safety
• Use protective, unlined rubber gloves and splash goggles or face shield when handling
the cleaning solution and take extra precautions when handling undiluted chemicals.
Have eye wash and clean water available on-site to treat accidental exposure.
99



Consult the product label and Material Safety Data Sheet for additional information.

Testing Solution
• To determine if the solution is below the 5% strength use “Quat Chek 1000” Test Papers
(purchase these from the supplier of the cleaning compound). The used cleaning solution
needs to be diluted to about 600 ppm of ammonium compounds before it can be tested
with these papers.
o Take one cup of used Sparquat 256® cleaning solution, pour into a bucket. Add 5
cups of water. Mix. OR
o Take one cup of used Quat128® cleaning solution, pour into a bucket. Add 4 cups of
water. Mix.
• Test the diluted solution with “Quat Chek” Test Paper. Match up the color of the paper
with the ppm’s on the color chart. For optimal disinfection, the diluted solution should
have a concentration between 600 and 800 ppm. If it is too dilute, dispose of properly and
make a new cleaning solution.
Disposal
• Do not dump cleaning solution into any stream or lake, or on areas where it can migrate
into any stormdrain, waterbody, or sensitive habitat. It may be possible to dispose of used
cleaning solution over open land. Consult Resource Advisor before using this method.


Depending on volume, used cleaning solution may be disposed of by trucking off-site for
disposal in a wastewater treatment facility..



Used cleaning solution may or may not be suitable for disposal in on-site septic systems.
Consult the local agency’s Utilities Supervisor or Facilities Manager prior to disposal.

Storage
Sparquat 256® and Quat128® can be stored up to two years in an unopened container without
losing its effectiveness. Both should be stored in a cool, dry place, out of direct sunlight.
Temperatures can range from 32º to 110º F.
Purchase
Both products are available from GSA (https://www.gsaadvantage.gov) and are commonly
available through local janitorial and swimming pool chemical suppliers.
• Quat 128® by Waxie’s Enterprises Inc.; GSA (NSN No. 170304) =$36/case (4 gal);
Additional info can be found at http://www.waxie.com
• Sparquat 256® by Spartan Chemical Company; GSA (NSN No. 1025-04) = $54/case (4
gal); Additional info can be found at http://www.spartanchemical.com
• Remember to buy “Quat Chek 1000” test papers when you purchase the chemicals.

100

Appendix 6: Additional statistical analyses and power
estimates for preliminary sample size determination
Parametric statistical power estimations using equations developed for the Pacific Island
Inventory and Monitoring Network (Skalski 2005), yield further information about the ability to
detect trends over time. These preliminary analyses are presented here as examples to guide
analyses of sample size determination and sampling strategies once several more years of data
have been collected on Molokai, and for sites where no preliminary data was available. The
Skalski power equations allow for changing variability over time, calculating power by using a
mean of the variances for each monitoring event, and a corresponding mean of the means. This is
distinguished from the ability to detect a difference in means such as a t-test would detect, in that
a trend estimates continuing small changes in mean over time, as opposed to specific differences
between two means.
Based on the results (Table A.6.1), it would initially appear that the ability to detect trend over
time has a relatively low power. It is important to note that this is a parametric method of
detecting trend with significant limitation resulting from the relatively small data set (2 years),
subsequently resulting in a relatively large population variability among sample dates, decreasing
calculated power. Based on these calculations, this protocol has a 34% chance of detecting a
50% change in Alamo’o population means for Waikolu stream with 95% confidence based on the
current variability. However, changes in population may very likely bring about changes in
variability and increased samples from which to perform analyses should reduce variability. Both
changes should cause power to correspondingly increase. Due to the small data set, these
analyses were deemed currently inappropriate to base the power to detect change portion of the
monitoring protocol on and the other analyses were used as a more accurate measure of power
(described in the narrative). Nevertheless, the Skalski equations should be re-evaluated for
relevancy in future years.
Table A.6.1. 25 year extrapolated results from two years of quarterly data collected in Waikolu stream on
the island of Molokai in Kalaupapa National Historical Park.
Power Output Comparison of Stream Analysis vs. Station Analysis (25 yr)

Quarterly
Sampling
Annual
Sampling

Whole Stream Analysis

Stream Analysis by Station

50%
Change
Value

Nakea

Nopili

Alamo'o

Nakea

Nopili

Alamo'o

=0.05
=0.10

0.105
0.207

0.127
0.236

0.143
0.257

0.091
0.181

0.153
0.270

0.159
0.277

=0.05

0.103

0.179

0.174

0.101

0.220

0.214

=0.10

0.200

0.300

0.295

0.198

0.347

0.343

This analysis was done to determine how frequently to conduct sampling surveys, and to
determine whether statistical analyses should be based on individual stations, or a composite of
data from all the sampling stations. From a biological standpoint annual sampling with a station
by station analysis makes the most sense intuitively as different species of fish occupy different
sections and reaches of the stream, i.e. Nakea tends to be in lower reaches in pools while

101

Alamo’o tends to be further upstream. Analyzing on a whole stream basis would aggregate
reaches not occupied by the fish and therefore increase variability.
The analysis indicates that for two of the fish species (Nopili and Alamo’o), the station by station
analysis is more effective and for one of the species (Nakea) the stream analysis was more
effective. When comparing the difference between the increase in power to detect change based
on a whole stream analysis vs. a station by station analysis (Table A.6.2) the station by station
analysis generally gives a higher increase in power over the whole stream analysis with the
notable exception of Alamo’o vs. Nakea in quarterly sampling at α=0.10 (-2.0% vs. 2.6%). These
results would then indicate that when doing a population analysis to detect trends in abundance, a
station by station analysis of the individual species would be the appropriate analysis to begin
with, followed by a whole stream analysis of selected species.
Table A.6.2. Differences of the whole stream sampling power output vs. the station by station power
output. Negative percentages indicate percentages favoring station by station comparisons and positive
percentages indicate percentages favoring whole stream analysis.
Power Output Comparison of Stream Analysis vs. Station
Analysis (25 yr)
50%
Nakea
Nopili
Alamo'o
Change
Value
Quarterly
Sampling

=0.05
=0.10

1.363%
2.587%

-2.575%
-3.356%

-1.519%
-1.964%

Annual
Sampling

=0.05

0.127%

-4.032%

-3.950%

=0.10

0.250%

-4.695%

-4.799%

A trend analysis was run using quarterly and annual sampling regimes to evaluate the frequency
of sampling events. The annual sampling was compared August of 1993 to August of 1994
which correlates to the dry season and low flow stream conditions. The quarterly sampling
compared all 4 sampling dates within each year (8 total sampling time periods). The results
(Table A.6.1) were then compared to each other (Table A.6.3) to determine which method would
yield the greatest power to detect trends in population changes. With the notable exception of
Nakea using whole stream analysis methods, all comparisons indicate that annual sampling
yields higher power to detect change than quarterly sampling would produce. These results
support an annual sampling frequency. The complete results of the analysis are presented in
Table A.6.4.
Table A.6.3. Differences of quarterly sampling vs. annual sampling power to detect trends in population
changes. Negative percentages favor quarterly sampling and positive percentages favor annual sampling.
Power Output Difference Comparison of Annual vs. Quarterly Sampling (25 yr)
Whole Stream Analysis

Stream Analysis by Station

50%
Change
Value

Nakea

Nopili

Alamo'o

Nakea

Nopili

Alamo'o

Annual

=0.05

-0.25%

5.21%

3.09%

0.99%

6.66%

5.52%

Quarterly

=0.10

-0.67%

6.36%

3.73%

1.67%

7.70%

6.56%

102

Table A.6.4. Power output results of the Skalski Trend Analysis on the data set collected by Anne Brasher in 1993 – 1994 in Waikolu Stream in
Kalaupapa National Historical Park on the Island of Molokai, Hawaii. Headings in yellow indicate power outputs based on whole stream analysis
and headings in blue indicate station by station analysis.
Stream Power Output Nakea all dates

Power Output Nakea Aug

Mean Station Power Output Nakea all dates

Relative Change

Relative Change

Relative Change

Mean Station Power Output Nakea Aug
Relative Change

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

10%

0.013

0.016

0.020

0.022

0.025

10%

0.010

0.012

0.015

0.016

0.018

10%

0.015

0.019

0.023

0.026

0.029

10%

0.015

0.019

0.022

0.025

0.028

25%

0.032

0.041

0.049

0.055

0.061

25%

0.024

0.031

0.036

0.041

0.046

25%

0.037

0.048

0.056

0.062

0.068

25%

0.037

0.047

0.055

0.061

0.066

50%
 =0.10

0.064

0.082

0.098

0.104

0.105

50%
 =0.10

0.048

0.061

0.073

0.082

0.091

50%
 =0.10

0.070

0.082

0.091

0.098

0.103

50%
 =0.10

0.068

0.080

0.089

0.096

0.101

25 yrs

10%

0.025

0.033

0.039

0.044

0.049

10%

0.019

0.024

0.029

0.033

0.036

10%

0.030

0.038

0.045

0.051

0.056

10%

0.029

0.037

0.044

0.050

0.056

25%

0.064

0.082

0.097

0.110

0.122

25%

0.047

0.061

0.072

0.082

0.090

25%

0.074

0.095

0.111

0.123

0.134

25%

0.073

0.093

0.110

0.122

0.131

0.127 0.163 0.193 0.205
Power Output Nopili all dates

0.207

50%

0.095 0.121 0.144 0.163
Power Output Nopili Aug

0.181

50% 0.139 0.162 0.178 0.191 0.200
Mean Station Power Output Nopili all dates

50%

Relative Change

Relative Change

50% 0.135 0.159 0.176 0.188 0.198
Mean Station Power Output Nopili Aug

Relative Change

Relative Change

103

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

10%

0.031

0.040

0.048

0.054

0.060

10%

0.044

0.056

0.067

0.076

0.084

10%

0.049

0.062

0.071

0.077

0.080

10%

0.059

0.073

0.081

0.086

0.090

25%

0.078

0.101

0.104

0.106

0.108

25%

0.103

0.106

0.109

0.111

0.113

25%

0.085

0.095

0.103

0.109

0.114

25%

0.097

0.107

0.115

0.122

0.128

50%
 =0.10

0.106

0.111

0.117

0.122

0.127

50%
 =0.10

0.110

0.122

0.132

0.143

0.153

50%
 =0.10

0.109

0.129

0.146

0.163

0.179

50%
 =0.10

0.120

0.149

0.173

0.197

0.220

25 yrs

10%

0.062

0.080

0.095

0.107

0.119

10%

0.087

0.112

0.133

0.151

0.167

10%

0.097

0.123

0.140

0.151

0.157

10%

0.118

0.144

0.160

0.169

0.176

25%

0.156

0.199

0.206

0.208

0.210

25%

0.204

0.208

0.212

0.215

0.218

25%

0.168

0.185

0.198

0.207

0.215

25%

0.191

0.206

0.217

0.226

0.235

0.209 0.216 0.223 0.230
Power Output Alamo'o all dates

0.236

50%

0.216 0.231 0.244 0.258
Power Output Alamo'o Aug

0.270

50%

Relative Change

50% 0.212 0.238 0.260 0.281 0.300
Mean Station Power Output Alamo'o all dates

Relative Change

50% 0.229 0.265 0.294 0.322 0.347
Mean Station Power Output Alamo'o Aug

Relative Change

Relative Change

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

25 yrs

 =0.05

5 yrs

10 yrs

15 yrs

20 yrs

10%

0.039

0.051

0.060

0.068

0.076

10%

0.046

0.059

0.070

0.080

0.088

10%

0.049

0.063

0.073

0.081

0.087

10%

0.061

0.076

0.085

0.092

0.096

25%

0.099

0.105

0.107

0.109

0.111

25%

0.103

0.107

0.109

0.112

0.115

25%

0.093

0.100

0.104

0.109

0.114

25%

0.102

0.111

0.117

0.123

0.129

50%
 =0.10

0.108

0.118

0.126

0.135

0.143

50%
 =0.10

0.111

0.124

0.136

0.147

0.159

50%
 =0.10

0.109

0.127

0.143

0.159

0.174

50%
 =0.10

0.122

0.147

0.170

0.192

0.214

25 yrs

10%

0.079

0.101

0.119

0.135

0.150

10%

0.092

0.117

0.139

0.158

0.175

10%

0.098

0.124

0.144

0.160

0.171

10%

0.122

0.151

0.169

0.181

0.188

25%

0.196

0.207

0.210

0.213

0.215

25%

0.205

0.209

0.213

0.216

0.220

25%

0.185

0.195

0.201

0.208

0.214

25%

0.202

0.214

0.222

0.231

0.238

50%

0.213

0.225

0.235

0.247

0.257

50%

0.217

0.233

0.248

0.263

0.277

50%

0.211

0.235

0.256

0.276

0.295

50%

0.233

0.265

0.292

0.318

0.343

References:
Skalski, J.R. 2005. Long-term monitoring: Basic study designs, estimators, and precision and
power calculations., National Park Service Pacific Island Network Inventory and Monitoring
Program Unpublished Report, Hawaii National Park, Hawaii, USA.

104

Appendix 7: Fixed Sampling sites (maps and coordinates)

105

106
Figure A.7.1. National Park of American Samoa stream monitoring sampling fixed sites on Tau.

107
Figure A.7.2. National Park of American Samoa stream monitoring sampling fixed sites for eastern Tutuila.

108
Figure A.7.3. National Park of American Samoa stream monitoring sampling fixed sites for western Tutuila.

Table A.7.1. Stream monitoring sampling fixed sites for National Park of American Samoa.
Stream
Name

Sampling Site Easting

Northing

Datum

Laufuti

FTAU01

-14.249783

-169.446147

WGS84

Laufuti

FTAU02

-14.248405

-169.445216

WGS84

Laufuti

FTAU03

-14.243942

-169.446533

WGS84

Laufuti

FTAU04

-14.241296

-169.450716

WGS84

Leafu

FTUT01

-14.25173

-170.676063

WGS84

Leafu

FTUT02

-14.251391

-170.679734

WGS84

Leafu

FTUT03

-14.252227

-170.682755

WGS84

Fangatuitui

FTUT04

-14.27248

-170.71915

WGS84

Fangatuitui

FTUT05

-14.273727

-170.717871

WGS84

Fangatuitui

FTUT06

-14.274838

-170.717156

WGS84

Amalau

FTUT07

-14.25301

-170.6583

WGS84

Amalau

FTUT08

-14.256213

-170.660067

WGS84

109

110
Figure A.7.4. War in the Pacific National Historical Park stream monitoring sampling fixed sites.

Table A.7.2. Stream monitoring sampling fixed sites for War in the Pacific National Historical Park.
Stream
Name

Sampling
Site

Easting

Northing

Datum

Asan

FWAPA01

13.46154

144.712392

WGS84

Asan

FWAPA02

13.465656

144.711946

WGS84

Asan

FWAPA03

13.462656

144.712898

WGS84

Asan

FWAPA04

13.467695

144.711613

WGS84

Asan

FWAPA05

13.469684

144.712748

WGS84

Asan

FWAPA06

13.460675

144.711708

WGS84

Asan

FWAPA15

13.465867

144.711317

WGS84

Asan

FWAPA16

13.458263

144.710807

WGS84

111

112
Figure A.7.5. Haleakala National Park stream monitoring sampling fixed sites.

Table A.7.3. Stream monitoring sampling fixed sites for Haleakala National Park.
Stream Name Sampling Site

Easting

Northing

Datum

Pipiwai

FHALE01

20.662974

-156.041852

WGS84

Palikea

FHALE02

20.66807714

-156.0519163

WGS84

Pipiwai

FHALE03

20.677879

-156.056814

WGS84

Alelele

FHALE05

20.648204

-156.084768

WGS84

Alelele

FHALE06

20.65035042

-156.0860841

WGS84

Pipiwai

FHALE07

20.66514633

-156.0464213

WGS84

Pipiwai

FHALE08

20.67218713

-156.0558619

WGS84

Palikea

FHALE09

20.66954272

-156.056356

WGS84

113

114
Figure A.7.6. Kalaupapa National Historical Park stream monitoring sampling fixed sites.

Table A.7.4. Stream monitoring sampling fixed sites for Kalaupapa National Historical Park.
Stream
Name

Sampling
Site

Easting

Northing

Datum

Waikolu

FKALA01

21.16919

-156.93028

WGS84

Waikolu

FKALA02

21.163983

-156.929987

WGS84

Waikolu

FKALA03

21.159446

-156.929134

WGS84

Waikolu

FKALA04

21.146504

-156.921382

WGS84

Waikolu

FKALA06

21.167935

-156.928961

WGS84

Waikolu

FKALA07

21.154313

-156.92413

WGS84

Waikolu

FKALA08

21.141463

-156.91863

WGS84

Waikolu

FKALA09

21.145874

-156.920992

WGS84

115

Appendix 8: Recommended field sampling schedule
Table A.8.1. Aquatic Sampling Schedule at each park for each protocol.
January
February
March
April
May
June
July
August
September
October
November
December

Water Quality
KAHO, KALA, WAPA, AMME
PUHO, PUHE, ALKA
HALE, NPSA
KAHO, KALA, WAPA, AMME
PUHO, PUHE, ALKA
HALE, NPSA
KAHO, KALA, WAPA, AMME
PUHO, PUHE, ALKA
HALE, NPSA
KAHO, KALA, WAPA, AMME
PUHO, PUHE, ALKA
HALE, NPSA

Streams

WAPA
HALE
KALA
NPSA

Groundwater
AMME
KAHO
AMME
KAHO
AMME
KAHO
AMME
KAHO
AMME
KAHO
AMME
KAHO

Benthic Marine

Marine Fish

NPSA
WAPA

NPSA
WAPA

Anchialine Pools

PUHO, KAHO, ALKA, HAVO
KALA

KALA

KAHO

KAHO
PUHO, KAHO, ALKA, HAVO

117

Appendix 9: Data sheets: American Samoa
Data sheets for fish, shrimp, snails, and habitat characterization for streams in American Samoa
are included in this appendix. Given that there is the potential for a lot of data to be collected at
each quadrat and transect, it is recommended that adequate copies, including extra copies, of
each datasheet be made prior to going to the field.

119

121

122

123

124

125

126

127

Appendix 10: Data sheets: Guam
Data sheets for fish, shrimp, snails, and habitat characterization for streams in Guam are included
in this appendix. Given that there is the potential for a lot of data to be collected at each quadrat
and transect, it is recommended that adequate copies, including extra copies, of each datasheet be
made
prior
to
going
to
the
field.

129

131

132

133

135

136

137

Appendix 11: Data sheets: Hawaii
Data sheets for fish, shrimp, snails, and habitat characterization for streams in Hawaii are
included in this appendix. Given that there is the potential for a lot of data to be collected at each
quadrat and transect, it is recommended that adequate copies, including extra copies, of each
datasheet be made prior to going to the field.

139

141

142

143

144

145

Appendix 12: Yearly Project Task List
Table A.12.1 Identification of each task by project stage, indicates who is responsible, and establishes
the timing for each task. Note that the PACN Aquatic Ecologist will serve as the Project Lead, and the
Aquatic Biological Technician will serve as the Field Lead. Protocol sections and SOPs are referred to as
appropriate.
Project Stage
Preparation

Data Acquisition

Data Entry &
Processing

Task Description
Initiate announcements for seasonal
technician positions, begin hiring
Notify data manager and GIS specialist of
needs for the coming season (field maps,
GPS support, training)
Meet (or conference call) to recap past field
season, discuss the upcoming field season,
and document any needed changes to field
sampling protocols or the working database
Ensure all project compliance needs and
permitting are completed for the coming
season
Provide names of field crew to park staff
Plan schedule and logistics, including
ordering any needed equipment and
supplies (SOP #2)
Inform GIS specialist and data manager of
specific needs for upcoming field season
Generate field navigation reports, roster of
sample points and coordinates from the
database (SOP #5)
Prepare and print field maps (SOP #3)
Update and load data dictionary,
background maps, and target coordinates
into GPS units (SOP #5)
Ensure that project workspace is ready for
use and GPS download software is loaded
at each park (SOP #25)
Implement working database copy
Initiate computer access and key requests
(may need park-specific dates)
Provide field crew email addresses and
user logins to data manager
Provide database/GPS training as needed
Train field crew in species identification,
habitat characterization, and safety (SOP
#7)
Examination and certification of field
observer qualifications, enter training
results into database (SOP #7)
Notify park staff and project lead of tour
itinerary
Collect field observations and position data
during field trips
Review data forms after each day
Check in with park staff
Debrief crew on operations, field methods,
gear needs
Download GPS data and email files to GIS
specialist for correction (SOP #5)

147

Responsibility
Project lead (PACN aquatic
ecologist)
Project lead

Project lead, aquatic
biotech (field lead), park
staff, data manager, GIS
specialist
Aquatic biotech, project
lead, park staff
Project lead
Aquatic biotech, assisted
by project lead
Project lead, assisted by
aquatic biotech
Aquatic biotech, assisted
by GIS specialist
Aquatic biotech
GIS specialist

Project lead, data
manager, GIS specialist
Data manager
Aquatic biotech
Aquatic biotech
Data manager and GIS
specialist
Aquatic biotech

Aquatic biotech

Aquatic biotech
Aquatic biotech
Aquatic biotech
Aquatic biotech
Aquatic biotech
Aquatic biotech

Timing

Project Stage

Product
Development
Product Delivery

Quality Review

Metadata

Data Certification &
Delivery

Data Analysis

Reporting &
Product
Development

Task Description
Download and process digital images (SOP
#29)
Enter data into working copy of the
database (SOP #26)
Verification of accurate transcription as
data are entered
Correct GPS data and send screen capture
to field lead and project lead for review
Periodic review of GPS location data and
database entries for completeness and
accuracy
Merge, correct, and export GPS data.
Upload processed and verified coordinates
to database
Complete field season report (SOP #32)

Responsibility
Aquatic biotech

Send field season report to NPS lead, park
biologists, data manager, and GIS
specialist (SOP #30)
Quality review and data validation using
database tools (SOP #27)
Prepare coordinate summaries and/or GIS
layers and data sets as needed for spatial
data review
Joint quality review of GIS data, determine
best coordinates for subsequent mapping
and fieldwork
Identify any sensitive information contained
in the data set (SOP #33)
Update project metadata records (SOP
#31)
Certify the season’s data and complete the
certification report (SOP #27)
Deliver certification report, certified data,
digital photographs, and updated metadata
to Data Manager (SOP #30)
Upload certified data into master project
database, store data files in PACN Digital
1
Library (SOP #34)
Notify Project Lead of uploaded data ready
for analysis and reporting
Update project GIS data sets, layers and
associated metadata records
Finalize and parse metadata records, store
1
in PACN Digital Library (SOP #31)
Check station and stream level data for
normality (see SOP #32).
Create bar graphs of data (see SOP #32).

Project lead

Analyze data for trends over time using yet
to be determined statistical methods (see
SOP #32).
Integrate biotic data with habitat data using
a multivariate approach (see SOP #32).
Export automated summary queries and
reports from database
Produce park-wide and transect-specific
map output for archives

148

Aquatic biotech
Aquatic biotech
GIS specialist
Aquatic biotech

GIS specialist

Aquatic biotech assisted by
project lead

Project lead
GIS specialist

Project lead and GIS
specialist
Project lead and park staff
Project lead and park staff
Project lead
Project lead

Data manager

Data manager
GIS specialist
Data manager and GIS
specialist
Project lead assisted by
aquatic biotech
Project lead assisted by
aquatic biotech
Project lead assisted by
aquatic biotech
Project lead assisted by
aquatic biotech
Data analyst
GIS specialist

Timing

Project Stage

Product Delivery

Posting &
Distribution

Archival & Records
Management

Season Close-out

Task Description
Generate report-quality map output for
reports
Acquire the proper report template from the
NPS website, create annual report
Screen all reports and data products for
sensitive information (SOP #33)
Prepare draft report and distribute to park
biologists for preliminary review
Submit draft I&M report to program
manager for review
Review report for formatting and
completeness, notify project lead of
approval or need for changes
Upload completed report to PACN Digital
1
Library submissions folder, notify data
manager (SOP #30)
Deliver other products according to the
delivery schedule and instructions (SOP
#30)
Product check-in
2
Submit metadata to IRMA Portal
2
Create IRMA Portal record, post reports to
2
the IRMA Portal
2
Update IRMA Portal records according to
data observations
Submit certified data and GIS data sets to
2
IRMA Portal
Store finished products in PACN Digital
1
Library
Review, clean up and store and/or dispose
of project files according to NPS Director’s
3
Order #19
Inventory equipment and supplies
Conference call to discuss recent field
season (close out); discuss who needs to
do what to get data ready for analysis
Discuss and document needed changes to
analysis and reporting procedures

1

Responsibility
GIS specialist

Timing

Data analyst and project
lead
Project lead
Project lead assisted by
aquatic biotech
Project lead
Program manager

Project lead

Project lead

Data manager
Data manager
Data manager
Data manager
Data manager
Data manager
Data manager assisted by
aquatic biotech
Aquatic biotech
Project lead, aquatic
biotech (field lead), park
staff, data manager and
GIS specialist
Project lead, assisted by
aquatic biotech, park staff,
and data manager

The PACN Digital Library is a hierarchical digital filing system stored on the PACN file server. Network
users have read-only access to these files, except where information sensitivity may preclude general
access.
2
The IRMA Portal is a clearinghouse for natural resource data, metadata, bibliographic records, and park
species information (http://irma.nps.gov/App/Portal/Home). Only non-sensitive information is posted to the
IRMA Portal. Refer to the protocol section on sensitive information for details.
3
NPS Director’s Order 19 provides a schedule indicating the amount of time that the various kinds of
records should be retained. Available at: http://data2.itc.nps.gov/npspolicy/DOrders.cfm

149

Appendix 13: Database Documentation
The database for this project consists of four types of tables: core tables describing the “who,
where, and when” of data collection, project-specific tables, lookup tables that contain domain
constraints for other tables, and cross reference tables that link lookup tables with data tables.
Although core tables are based on PACN standards, they may contain fields, domains or
descriptions that have been added or altered to meet project objectives.
The database includes the following standard tables:
tbl_Parks
Sample sites – individual parks
tbl_Locations
Sample locations – streams where sampling is being conducted
tbl_Sites
Sampling unit locations along the stream
tbl_Events
Data collection event for a given location
tbl_Images
Images associated with sample locations
tbl_Db_Meta
Database description and links to I&M metadata tools
tbl_Db_Revisions
Database revision history data
tbl_QA_Results
Data validation results from using the quality review tool

The following are project-specific data tables:
tbl_Fish_Shrimp
Hawaiian fish and crustacean sampling information
tbl_Snails
Mollusc sampling information
tbl_Shrimp
Crustacean sampling information (NPSA)
tbl_Transects
Transect characterization for each stream site
tbl_Site_Geo_Unit
Geomorphic channel unit measurements
tbl_Pebbles
Pebble count for transects
tbl_Points
Transect point measurements
tbl_Canopy
Riparian canopy closure measurements
The following are a few of the more prominent, standard lookup tables:

tlu_Contacts
tlu_Taxa
tlu_Enumerations

Contact data for project-related personnel
Taxon table for sampling events
Enumerated lookup table

The following are a few of the more prominent, standard cross-reference tables:

xref_Event_Contacts
xref_Site_Cover
xref_Site_Geo_Unit
xref_Shrimp_Taxa
xref_Shrimp_Structures
xref_Fish_Shrimp_Taxa

Cross-reference table for event contacts
Cross-reference table for dominant riparian land cover
Cross-reference table for geomorphic channel units
Cross-reference table for crustacean taxa
Cross-reference table for crustacean structures
Cross-reference table for Hawaiian fish and crustacean taxa
xref_Fish_Shrimp_Structures Cross-reference table for Hawaiian fish and crustacean structures
xref_Snails_Taxa
Cross-reference table for mollusc taxa
xref_Snails_Structures Cross-reference table for mollusc structures
xref_Point_Structures
Cross-reference table for point structures
151

152
Figure A.13.1. Data model for the PACN Stream Monitoring database.

Database Tables
tbl_ Parks: Sample sites – individual parks
Field

Primary?

Data Type

Size

Description

Park_ID

Yes

Text

50

Unique identifier for park records

Park_Name

No

Text

100

Unique name or code for a site

Park_Desc

No

Text

255

Park description

Unit_Code

No

Text

4

Four letter Park, Monument or Network code

Park_Notes

No

Memo

-

General notes on the park

tbl_ Locations: Sample locations – streams where sampling is being conducted
Field

Primary?

Data Type

Size

Description

Location_ID

Yes

Text

50

Unique identifier for location records

Park_ID

No

Text

50

Link to tbl_Parks

Loc_Name

No

Text

50

Name of the location (stream name)

Loc_Type

No

Text

10

Location type category (annual or perennial)

Island

No

Text

25

The island on which the stream is located

Unit_Code

No

Text

4

Four letter Park, Monument or Network code

Loc_Notes

No

Memo

-

General notes on the location

tbl_ Sites: Sampling unit locations along the stream
Field

Primary?

Data Type

Size

Description

Site_ID

Yes

Text

50

Unique identifier for site records

Location_ID

No

Text

50

Link to tbl_Locations

Site_Name

No

Text

50

Name of the site (station)

Site_Type

No

Text

25

Site type category

Latitude

No

Number

Double

Lat_Dir

No

Text

25

Longitude

No

Number

Double

Long_Dir

No

Text

25

Longitude direction (east or west)

Datum

No

Text

5

Datum of mapping ellipsoid

Site_Error

No

Number

Double

Estimated GPS error of site coordinates

River_Mouth_Error

No

Number

Double

Estmated GPS error of river mouth coordinates

Accuracy_Notes

No

Text

255

153

Decimal degrees latitude
Latitude direction (north or south)
Decimal degrees longitude

Positional accuracy notes

Site_Desc

No

Memo

-

General description of the site

X_River_Mouth

No

Number

Double

X coordinate of river mouth

Y_River_Mouth

No

Number

Double

Y coordinate of river mouth

River_Mouth

No

Number

Double

Distance to river mouth

Upstream

No

Number

Double

Distance to the reference location from the upstream
end in meters

Downstream

No

Number

Double

Distance to the reference location from the downstream
end in meters

Curv_Reach

No

Number

Double

The curvilinear reach length in meters of the site

Transect_Distance

No

Number

Double

The distance between transect in meters

Marker_Upstream

No

Text

5

Location of the upstream boundary marker; left, right,
both

Marker_Downstream

No

Text

5

Location of the downstream boundary marker; left,
right, both

Site_Notes

No

Memo

-

General notes on the site

Site_Entered_Date

No

Date/Time

-

Date on which data entry occurred for this record

Site_Entered_By

No

Text

50

Person who entered the data for this record

Site_Updated_Date

No

Date/Time

-

Date of the most recent edits to this record

Site_Updated_By

No

Text

50

Site_Verified

No

Boolean

-

Has the record been verified

Site_Verified_Date

No

Date/Time

-

Date that the record was verified

Site_Verified_By

No

Text

50

Person who made the most recent updates to this
record

Person who verified the record

tbl_ Events: Data collection event for a given location
Field

Primary?

Data Type

Size

Description

Event_ID

Yes

Text

50

Unique identifier for event records

Site_ID

No

Text

50

Link to tbl_Sites

Start_Date

No

Date/Time

-

Starting date for the event

End_Date

No

Date/Time

-

Ending date for the event

Start_Time

No

Date/Time

-

Starting time for the event

End_Time

No

Date/Time

-

Ending time for the event

Entered_By

No

Text

50

Entered_Date

No

Date/Time

-

Updated_By

No

Text

50

Updated_Date

No

Date/Time

-

Verified_By

No

Text

50

154

Person who entered the data for this event
Date on which data entry occurred
Person who made the most recent updates
Date of the most recent edits
Person who verified accurate data transcription

Verified_Date

No

Date/Time

-

Date on which data was verified

Verified

No

Boolean

-

Has the data been verified

Certified

No

Boolean

-

Has the data been certified

Certified_By

No

Text

50

Certified_Date

No

Date/Time

-

Date on which data were certified

Event_Notes

No

Memo

-

General notes on the event

Person who certified data for accuracy and
completeness

tbl_ Images: Images associated with sample locations
Field

Primary?

Data Type

Size

Description

Image_ID

Yes

Text

50

Unique identifier for image records

Image_Date

No

Date/Time

-

Date on which the image was created, if
different from the sampling event date

Image_Edit_Notes

No

Memo

-

Comments about the editing or processing
performed on the image

Image_Filename

No

Text

100

Name of the image including extension (.jpg)
but without the image path

Image_Label

No

Text

100

Image caption or label

Image_Notes

No

Memo

-

Image_Project_Path

No

Text

100

Location of the image from the main project
folder or image library

Image_Source

No

Text

50

Name of the person or organization that
created the image

Image_Time

No

Date/Time

-

Time image was taken.

Is_Edited_Version

No

Boolean

-

Indicates whether this version of the image is
the edited (originals = False)

Transect_ID

No

Text

50

Link to tbl_Transects

Root_Path

No

Text

255

The root path for the linked image file. This will change
upon re-linking of database

Base_Path

No

Text

255

The base file path for the linked image file. This will stay
the same no matter where the root folder is

Notes or comments about the image

tbl_ Site_Geo_Unit: Geomorphic channel unit measurements
Field

Primary?

Data Type

Size

Description

Site_Geo_Unit_ID

Yes

Text

50

Unique identifier for geomorphic channel unit records

Site_ID

No

Text

50

Link to tbl_Sites

Start_Date

No

Date/Time

-

Start

No

Text

10

155

Date of data record
Beginning at upstream or downstream

tbl_Transects: Transect characterization for each stream site
Field

Primary?

Data Type

Size

Description

Transect_ID

Yes

Text

50

Unique identifier for transect records

Event_ID

No

Text

50

Link to tbl_Events

Transect_Number

No

Text

50

Transect number

Transect_Loc

No

Number

Double

Transect location in relation to the reference location;
meters upstream from reference location

Channel_Width

No

Number

Double

Wetted channel width in meters

Total_Discharge

No

Text

25

Total discharge for transect point measurements

Flagged

No

Boolean

-

Indicates that the record needs to be reviewed for
accuracy

Root_Path

No

Text

255

The root path for the linked PDF file. This will change
upon re-linking of the database

Base_Path

No

Text

255

The base file path for the linked PDF file. This will stay
the same no matter where the root folder is

PDF_Path

No

Text

255

File location of the PDF

Transect_Notes

No

Memo

-

Transect notes

tbl_Pebbles: Pebble count for transects
Field

Primary?

Data Type

Size

Description

Pebble_ID

Yes

Text

50

Unique identifier for pebble records

Transect_ID

No

Text

50

Link to tbl_Transects

Count

No

Number

Lng Int

Pebble count number

Measure

No

Number

Double

B-axis diameter of pebble (cm)

Tape_Measurement

No

Number

Double

Tape measurement (m)

tbl_ Points: Transect point measurements
Field

Primary?

Data Type

Size

Description

Point_ID

Yes

Text

50

Unique identifier for point records

Transect_ID

No

Text

50

Link to tbl_Transects

Point

No

Text

25

Point name

Tape_Reading

No

Number

Double

Depth

No

Text

25

Depth in meters at the point

Velocity

No

Text

5

Velocity

Shallowness

No

Boolean

-

Is it too shallow for velocity measurement?

Habitat_Type

No

Text

2

Habitat type

156

Measuring tape reading across the transect for the
point, in meters

tbl_ Canopy: Riparian canopy closure measurements
Field

Primary?

Data Type

Size

Description

Canopy_ID

Yes

Text

50

Unique identifier for canopy records

Transect_ID

No

Text

50

Link to tbl_Transects

Facing

No

Text

25

Direction of measurement

Measurement

No

Text

25

Riparian canopy closure measurement

tbl_ Fish_Shrimp: Hawaiian fish and crustacean sampling information
Field

Primary?

Data Type

Size

Description

Fish_Shrimp_ID

Yes

Text

50

Unique identifier for fish and crustacean records

Event_ID

No

Text

50

Link to tbl_Events

Quadrat

No

Text

50

Quadrat for sampling

X

No

Text

50

X section of route taken for the sampling

Y

No

Text

50

Y section of route taken for the sampling

Habitat_Type

No

Text

5

Habitat type

Flagged

No

Boolean

-

Indicates that the record needs to be reviewed for
accuracy.

VX

No

Number

Double

Velocity X of quadrat

VY

No

Number

Double

Velocity Y of quadrat

Depth

No

Number

Double

Depth of quadrat (m)

tbl_ Snails: Mollusc sampling information
Field

Primary?

Data Type

Size

Description

Snail_ID

Yes

Text

50

Unique identifier for mollusc records

Event_ID

No

Text

50

Link to tbl_Events

Quadrat

No

Text

50

Quadrat for sampling

Section

No

Text

25

Section number

X

No

Text

50

X section of route taken for the sampling

Y

No

Text

50

Y section of route taken for the sampling

Spat

No

Number

Double

Number of spat counted

Eggs

No

Number

Double

Number of eggs counted

Habitat_Type

No

Text

5

Habitat type

Flagged

No

Boolean

-

Indicates that the record needs to be reviewed for
accuracy.

VX

No

Number

Double

157

Velocity X of section

VY

No

Number

Double

Velocity Y of section

Depth

No

Number

Double

Depth of section (m)

tbl_ Shrimp: Crustacean sampling information (NPSA)
Field

Primary?

Data Type

Size

Description

Shrimp_ID

Yes

Text

50

Unique identifier for crustacean records

Event_ID

No

Text

50

Link to tbl_Events

Trap

No

Text

100

Trap number or name

Pool

No

Text

50

The pool number the shrimp were sampled in

Collection

No

Text

50

Collection method (net, trap, electrofishing, or visual)

Section

No

Text

25

Section number

Quadrat

No

Text

50

Quadrat for sampling

X

No

Text

50

X section of route taken for the sampling

Y

No

Text

50

Y section of route taken for the sampling

Habitat_Type

No

Text

5

Habitat type

Flagged

No

Boolean

-

Indicates that the record needs to be reviewed for
accuracy.

VX

No

Number

Double

Velocity X of quadrat

VY

No

Number

Double

Velocity Y of quadrat

Depth

No

Number

Double

Depth of quadrat (m)

tbl_ Db_Meta: Database description and links to I&M metadata tools
Field

Primary?

Data Type

Size

Description

Db_Meta_ID

Yes

Text

50

Unique Local primary key

Db_Desc

No

Memo

-

Description of the database purpose

DSC_GUID

No

Text

50

Link to I&M Dataset Catalog desktop
metadata tool

Meta_File_Name

No

Text

50

Name of the metadata file that describes
this NRDT data file (must be in the same
directory as this data file)

Meta_MID

No

Text

255

Link to NPS Data Store

tbl_ Db_Revisions: Database revision history data
Field

Primary?

Data Type

Size

Description

Revision_ID

Yes

Text

50

Unique Database revision (version) number or code

Db_Meta_ID

No

Text

50

Link to tbl_DB_Meta

Revision_Contact_ID

No

Text

50

Link to tlu_Contacts

158

Revision_Date

No

Date/Time

-

Database revision date

Revision_Desc

No

Memo

-

Revision description

Revision_Reason

No

Memo

-

Reason for the database revision

tbl_ QA_Results: Data validation results from using the quality review tool
Field

Primary?

Data Type

Size

Description

Query_Name

No

Text

100

Name of query

Data_Scope

No

Byte

-

Scope of data

Time_Frame

No

Text

30

Time frame of data records

Query_Type

No

Text

20

Type of query

Query_Result

No

Text

50

The number of records returned by the query

Query_Run_Time

No

Date/Time

-

Most recent run time of the query

Query_Description

No

Memo

-

Query description

Query_Expression

No

Memo

-

Expression used to run query

Remedy_Desc

No

Memo

-

Action taken to fix the error

Remedy_Date

No

Date/Time

-

Remedy date

QA_User

No

Text

50

Is_Done

No

Boolean

-

Remedy by
Was the query checked

xref_Site_Cover: Cross-reference table for dominant riparian land cover
Field

Primary?

Data Type

Size

Description

Site_ID

No

Text

50

Link to tbl_Sites

Cover

No

Text

50

Dominant riparian land cover; grassland, shrubs/
woodland, wetland, exposed rock, wet forest, disturbed/
developed

Disturbed_Cover

No

Memo

-

If the dominant riparian land cover is disturbed/
developed, the description of the land cover

Start_Date

No

Date/Time

-

Date of data record

xref_Site_Geo_Unit: Cross-reference table for geomorphic channel units
Field

Primary?

Data Type

Size

Description

Site_Geo_Unit_ID

No

Text

50

Link to tbl_Site_Geo_Unit

Geomorphic_Code

No

Text

2

Two letter abbreviation for the geomorphic channel unit
from tlu_Enumerations

Length

No

Number Double

159

Length in meters of the geomorphic channel units

xref_Fish_Shrimp_Structures: Cross-reference table for Hawaiian fish and crustacean structures
Field

Primary?

Data Type

Size

Description

Fish_Shrimp_ID

No

Text

50

Link to tbl_Fish_Shrimp

Structures

No

Text

25

Structures present

xref_Fish_Shrimp_Taxa: Cross-reference table for Hawaiian fish and crustacean taxa
Field

Primary?

Data Type

Size

Description

Fish_Shrimp_ID

No

Text

50

Link to tbl_Fish_Shrimp

Taxa_ID

No

Text

50

Link to tlu_Taxa

Size

No

Text

50

Size in centimeters

Count

No

Number

Lng Int

Total number of fish or shrimp species counted for the

xref_Snails_Structures: Cross-reference table for mollusc structures
Field

Primary?

Data Type

Size

Description

Snail_ID

No

Text

50

Link to tbl_Snails

Structures

No

Text

25

Structures present
size class

xref_Snails_Taxa: Cross-reference table for mollusc taxa
Field

Primary?

Data Type

Size

Description

Snail_ID

No

Text

50

Link to tbl_Snails

Taxa_ID

No

Text

50

Link to tlu_Taxa

Length

No

Number

Double

Corrosion

No

Boolean

-

Corrosion presence/absence

Estimated

No

Boolean

-

Was the species length estimated?

Length of species in mm

xref_Shrimp_Structures: Cross-reference table for crustacean structures
Field

Primary?

Data Type

Size

Description

Shrimp_ID

No

Text

50

Link to tbl_Shrimp

Structures

No

Text

25

Structures present

xref_Shrimp_Taxa: Cross-reference table for crustacean taxa
Field

Shrimp_ID

Primary?

No

Data Type

Text

Size

50

160

Description

Link to tbl_Shrimp

Taxa_ID

No

Text

50

Length

No

Number

Double

Gravid

No

Text

20

Count

No

Number

Lng Int

Estimated

No

Boolean

-

Link to tlu_Taxa
Length of species
Gravid?
Total number of shrimp species counted
Was the species length estimated?

xref_Point_Structures: Cross-reference table for point structures
Field

Primary?

Data Type

Size

Description

Point_ID

No

Text

50

Link to tbl_Points

Structures

No

Text

50

Structure present

xref_Event_Contacts: Cross-reference table for event contacts
Field

Primary?

Data Type

Size

Description

Contact_ID

No

Text

50

Link to tlu_Contacts

Contact_Role

No

Text

50

The contact's role in the protocol

Event_ID

No

Text

50

Link to tbl_Events

tlu_Contacts: Contact data for project-related personnel
Field

Primary?

Data Type

Size

Description

Contact_ID

Yes

Text

50

Unique identifier for contact records

Address

No

Text

50

Street address

Address_Type

No

Text

50

Address (mailing, physical, both) type

Address2

No

Text

50

Address line 2, suite, apartment number

City

No

Text

50

City or town

Contact_Notes

No

Memo

-

Country

No

Text

50

Country

Email_Address

No

Text

50

E-mail address

First_Name

No

Text

50

First name

Last_Name

No

Text

50

Last name

Middle_Init

No

Text

4

Middle initial

Organization

No

Text

50

Organization or employer

Position_Title

No

Text

50

Title or position description

State_Code

No

Text

8

State or province

Work_Extension

No

Text

50

Phone extension

161

Contact notes

Work_Phone

No

Text

50

Phone number

Zip_Code

No

Text

50

Zip code

tlu_Enumerations: Enumerated lookup table
Field

Primary?

Data Type

Size

Description

Enum_Group

Yes

Text

50

Category for lookup value

Enum_Code

No

Text

50

Code for lookup values

Enum_Description

No

Memo

-

Sort_Order

No

Number

Integer

Lookup value description
Order in which to sort lookup values

tlu_Taxa: Taxon table for sampling events
Field

Primary?

Data Type

Size

Description

Taxa_ID

Yes

Text

50

Unique identifier for species records

Common_Name

No

Text

50

Common name of species

Family

No

Text

50

Taxonomic family

Genus

No

Text

50

Taxonomic genus

Nativity

No

Text

50

Status; native, non-native

Scientific_Name

No

Text

100

Scientific name of species

Species

No

Text

50

Taxonomic species

Kingdom

No

Text

50

Taxonomic kingdom

Phylum

No

Text

50

Taxonomic phylum

TSN

No

Number

4

Taxonomic serial number from ITIS

Class

No

Text

50

Taxonomic class

Order

No

Text

50

Taxonomic order

Hawaiian_Name

No

Text

50

Hawaiian name of species

Range

No

Text

50

Range of nativity

162

Appendix 14: Analysis Log File Checklist
Stream:
Vital Sign

Analysis

Fish, Shrimp, & Snails

Station

Date
Completed

For each species at each station, check for normality of the distribution
for size and abundance.
For each species at each station, generate a table of mean and
standard deviation of size and abundance (add to table that contains
data from previous years). Each table will represent a single station.
For each species at each station, plot mean and standard deviation of
size and abundance (add to plot that contains data from previous
years). Each plot will represent at single station.
Stream
For each species at all stations in the stream, generate a table of mean
and standard deviation of size and abundance over a longitudinal
gradient (add to table that contains data from previous years). Each
table will represent all stations in a stream.
For each species at all stations in the stream, generate a plot of mean
and standard deviation of size and abundance over a longitudinal
gradient (stack with plots that contains data from previous years). Each
plot will represent all stations in a stream.
Trend
To be determined
Habitat
Characteristics

Station
For each habitat characteristic at each station, check for normality of
the distribution of the habitat characteristic.
For each habitat characteristic at each station, generate a table of
mean and standard deviation of the habitat characteristic (add to table
that contains data from previous years). Each table will represent a
single station.

Stream:
Vital Sign

Analysis

Date
Completed

For each habitat characteristic at each station, plot mean and standard
deviation of the habitat characteristic (add to plot that contains data
from previous years). Each plot will represent at single station.
Stream
For each habitat characteristic at all stations in the stream, generate a
table of mean and standard deviation of the habitat characteristic over
a longitudinal gradient (add to table that contains data from previous
years). Each table will represent all stations in a stream.
For each habitat characteristic at all stations in the stream, generate a
plot of mean and standard deviation of the habitat characteristic over a
longitudinal gradient (stack with plots that contains data from previous
years). Each plot will represent all stations in a stream.
Trend
To be determined

163

Appendix 15: Pacific Islands Stream Monitoring Report:
Example Summary of Vital Signs Data
Here we present example results of annual monitoring of abundance data for three fish taxa in
Unknown stream collected in 2007. The data presented here is used for example purposes only
and should not be used as part of actual data analysis activities. The 2007 data is plotted with
data from previous years to demonstrate trends in abundance over time and space. Trends
observed in the plots are discussed in the corresponding figure legends. This data is a subset of a
larger data set that includes annual information on the size and abundance of fish, shrimp, and
snails, as well as habitat characteristics, at multiple sites within each stream being monitored.
Detailed methods and results for all data can be found in the Vital Signs Monitoring Protocol
Annual Report. (Note: Abundance data is presented here for a subset of fish taxa in Unknown
Stream as an example. However, data included in future reports may include size and/or habitat
data for other taxa in other streams, depending on which data is expected to be of interest to park
managers.)

Abundance of Awaous
(Nakea)

2.5

Figure A.15.1. Average abundance of Nakea, Nopili,
and Alamo’o in Unknown Stream at Station D (160
meters from the mouth) from 2000-2007. Error bars
equal one standard deviation. Note the difference in
scale on the y-axes. Nakea has consistently been the
least abundant of the three taxa over the sampling
period with average station abundances less than 1
fish. Given the low abundances of Nakea it is difficult to
extract any meaningful temporal trend information from
this plot. Nopili was the most abundant taxa with station
averages ranging from 1.6-16.3 fish. Nopili has
decreased in abundance from 2001-2005 and
abundances have remained low since 2005. Alamo’o
displayed intermediate abundances with station
averages decrease in abundance of Alamo’o during
2003 and 2004. However, since 2004, abundances
have increased to values similar to those measured
earlier in the decade.

2
1.5
1
0.5

Abundance of Sicyopterus
(Nopili)

0
25
20
15
10
5

Abundance of Lentipes (Alamo'o)

0
6
5
4
3
2
1
0
2000 2001 2002 2003 2004 2005 2006 2007

Year

165

12

2005

10
8
6
4
2

Abundance of Sicyopterus
(Nopili)

0
12
10

2006

8
6
4
2
0
35
30

2007

25
20
15
10
5

30
70
130
160
250
280
330
560
770
1270
1850
1900
2080
2150
2330
2560
2630
2640
3080
3351
3430
3620
3768

0

Distance from mouth (m)

Figure A.15.2. Average abundance of Nopili in Unknown Stream at stations along a longitudinal gradient
from the mouth to the headwaters in 2005, 2006, and 2007. Error bars equal one standard deviation.
Note the difference in scale on the y-axes. In general, there were more Nopili within 100 m of the mouth
as compared to stations further upstream in all three years. The average abundance of Nopili near the
mouth increased from 2005 (~3 fish) to 2006 (~8 fish) and 2007 (~20 fish). In addition to the peak in
abundances near the mouth, there was also a peak in abundance of Nopili between 2000 and 3000
meters upstream of the mouth in 2005 and 2006. This trend was less pronounced in 2007. Fewer than 1
Nopili per station on average were observed at distances greater than 3000 m upstream from the mouth
in all three years. Summary Highlights

1) 160 m upstream from the mouth of Unknown Stream, Nopili has been the most abundant
of the fish species analyzed over the previous 7 years followed by Alamo’o and Nakea.
2) Nopili has decreased in average abundance from 2001-2005 at the 160 m station and
average abundances have remained low since 2005.
166

3) Investigation of longitudinal trends in Nopili indicate that there were more Nopili within
100 m of the mouth as compared to stations further upstream in 2005, 2006, and 2007.
4) The average abundance of Nopili near the mouth increased from 2005 (~3 fish) to 2006
(~8 fish) and 2007 (~20 fish).

167

Appendix 16: Database User’s Guide
Introduction
The Stream Monitoring database is the main storage location for all data related to the Stream
Monitoring protocol. It requires manual data entry for entering survey information.
Database files will be distributed to the project manager at the beginning of the year to facilitate
prompt data entry. At the end of the field season, files will be submitted to the PACN data
management staff for consolidation into the master database file.

Installing the Stream Monitoring Database
The user can copy and paste both front and back end database files to a park server that has
automatic backups. If some parks lack these resources, store the files on a local computer and
employ a backup strategy, such as using an external hard drive. The database application
contains a back up component, which is accessed from the main application Switchboard Form
that opens automatically when the application starts (see “Back Up Data” below). This
component can be programmed to automatically ask the user to create a back up when the
database is opened for a data entry session. This will ensure that the initial data starting point can
be recovered should irreversible errors or problems occur during the data entry session. Back-up
copies are used for the current field season only and will not be archived. The database files
should be stored in the appropriate I&M project folder (recommended directory structure:
streams/database/backups).
To facilitate data entry, the front-end file should be copied to a local workstation if the database
files are stored on a networked server. Opening and using the front-end on the network ‘bloats’
the database file and makes it run more slowly. In some cases, linking to the back-end on the
server will cause the database to run very slowly. In these cases, the back-end file can also be
copied to the local workstation. At the end of the day after data entry, the back end should be
copied back to the server so that it will be backed up. Once these files are copied, users will need
to re-link the front end databases to the correct back-end database file. Important note: Make
sure the front-end database is linked to the correct back-end database. If the back-end was
copied from the server onto a local workstation for data entry, the front-end database will be
linked to the back-end on the server until the link is changed (see “Connect Data Tables” below).

Starting the Stream Monitoring Database
Double-click on streams_FE_v1.mdb to start the application.

Features of the Application Startup Form
The Startup Form is the entry point for the application, and therefore the first thing users will
usually see when opening the application.
Double-clicking “Pacific Island Network” at the top left of the form will open the web site for
the Network. Double-clicking the NPS Arrowhead or the title National Park Service at the top
right of the form will open a browser and navigate to the National Park Service web site
(www.nps.gov).

169

Also at the top right of the form is an exit button which can be used to close the application.
A tabbed menu resides at the lower right corner of the form. It contains tabs for the main menu,
application defaults, and information about the application. Each of the tabs will be examined in
more detail in the sections that follow.
At the bottom center-left of the form is a box that displays the current location of the data file to
which the application is linked.

170

Main Menu
The main menu of the application is what users will see when the application is started. It
provides buttons for entering/editing data and survey sites, entering/editing observers, quality
review checks, data summarization, backing up data, and connecting data tables.

Main Menu

Enter/Edit Data
Clicking the Enter/edit data button will open the Data Gateway Form.
Data Gateway Form
This form displays location and event information for each record, and is designed to help the
user determine which record to edit/view.

171

Data Gateway Form

Filters for Park, Stream Name, Year, and Visit Date can be set by selecting from the drop-down
lists at the top of the form in the Filters box. Filters facilitate finding surveys for certain stream
names; the user will not have to scroll through all records to find the survey they are looking for.
Filters can be removed by clicking the toggle button that says “Filter Is On”. It will toggle up and
say “Filter Is Off” when the filter is removed. When the filter is removed, all records will be
displayed. Optionally, a specific filter can be removed by deleting the text that is currently
displayed in one of the filter controls.
In addition to filters, there are sorting options for the records on the Data Gateway Form.
Double-clicking any of the column headings will cause the records to be sorted in ascending
order by that column value. The column heading will change to a bold italic format to indicate
that it is the column being used to determine sort order. If the same column is double-clicked a
second time, the records will be sorted in descending order by that column value.
Double-clicking a Site Name value will open the Monitoring Site Information Form for that
particular record’s Park and Survey Area (see the Monitoring Site Information Form section that
follows). Double-clicking a Visit Date will open the Data Entry Form (includes Event data; see
the Data Entry Form section below) for that particular record.
To add a new data entry record, click the “Add a new record” button at the top of the Data
Gateway Form.

172

Data Entry Form
The Data Entry Form is used to select/enter a location (Park, Island, Stream Name, Stream Type,
and Site Name), start date, end date, start time, end time, notes, contact information, survey data,
and quality assurance checks.

Data Entry Form

Select a Park from the drop down list. The Island field will be automatically populated based on
your selected Park (does not apply to NPSA; user must choose an island for NPSA). Stream
Names for the selected Park and Island will be available from the drop down list. Stream Type
will also be automatically populated once a Stream Name has been selected. After choosing a
Stream, existing Site Names will be available from the drop down list. To add or edit a
Monitoring Site, click the “Add New” or “Edit” buttons (see “Monitoring Site Information
Form” below).
173

After filling in location information, enter a start date, end date, start time, end time, event notes,
and contact information. The start date and end date must be entered using a month/day/year
format (ex: 5/30/2009). The start time and end time must be entered using an hour/minute format
(ex: 11:45). The user will not be able to enter these items until all of the location information has
been entered. At any time in the data entry process, the buttons located at the top of the page
may be used to go to a new record, delete the current record, or close the form.
Monitoring Site Information Form
To enter a new monitoring site, click the “Add New” button located on the Data Entry Form or
the “Enter/edit sites” button from the Main Menu. To edit an existing monitoring site from the
Data Entry Form, select a Site Name from the drop down list and click the “Edit” button. The
Monitoring Site Information Form will open. To edit an existing monitoring site from the Main
Menu, click the “Enter/edit sites” button and use the Quick Find drop down menu to find a site.

Values entered on this form include:
• Park


Island



Stream Name



Stream Type



Site Name



Site Type



Site Coordinates
-

Decimal Degrees Latitude
Decimal Degrees Longitude
Datum
Error (m)
174



Coordinates of River Mouth
-

X
Y
Error (m)



Distance to River Mouth



Description of Reference Location



Distance to Reference Location
-



Upstream End
Downstream End

Location of Boundary Markers
-

Upstream
Downstream



Curvilinear Reach Length



Distance Between Transects



Notes



Dominant Riparian Land Cover
-



Date
Dominant Riparian Land Cover
Disturbed/Developed – Explain

Geomorphic Channel Units
-

Date
Beginning at
Geomorphic Type
Length (meters)



Entered Date



Entered By



Updated Date



Updated By



Verified



Verified Date



Verified By

175

Monitoring Site Information Form

176

Park, Island, Stream Name, Stream Type, Datum, and UTM Zone will be automatically filled in
based on the information entered in the Data Entry Form. If the Monitoring Site Information
Form was accessed using the Main Menu then these fields will need to be filled in. Dominant
Riparian Land Cover and Geomorphic Channel Units should be recorded annually for each site
(or as often as sites are monitored). This will help track changes over time that may occur at
individual sites. To add a new Dominant Riparian Land Cover or Geomorphic Channel Units
record to a site click the “Add Record” button. To delete a record, click the “Delete Record”
button. The scroll buttons on the bottom can be used to view existing records. In addition, once
Geomorphic Type has reached a total length of 30 meters, no additional records will be accepted.

The Entered Date, Entered By, Updated Date, and Updated By fields are automatically populated
when a record is created or updated. Once all fields have been filled in, the data should be
verified. If a site has been verified the check box next to “Verified” should be marked, and the
“Verified By” and “Date Verified” fields should be completed; these fields are not automatically
populated.
To add or delete a monitoring site record, use the buttons located at the top of the form. The
“Close Form” button will save the site record and return you to the Data Entry Form. A site
name must be entered in order to save the site record. If this field is not filled in a message box
will appear. If no site name is entered, then the record will be deleted.

Contacts Form
To enter a new Contact from the Main Data Entry Form, click “Add Contact”. The View and
Edit Contact Information Form will open. This is where new contact information is entered.
This form can also be accessed from the main menu by clicking on the Enter/Edit Observers
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button. Values entered here include:


First Name, Middle Initial, Last Name



Organization



Position/title



Work Phone and Extension



Email Address



Address Information, including Address Type, Street Address, City, State, Zip Code, and
Country



Comments

Previously entered addresses can be selected from the Address 1 drop-down list, and the
associated Street Address, City, State, Zip, and Country values will automatically be filled in.
The Organization and Position/Title drop-down lists will also allow selection from previously
entered values or new entries.

Contact Information Form (new record)

When the Contact Information Form is in view mode (grey background), individual contacts can
be shown by selecting from the Search drop-down list at the top right of the form.

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Contact Information Form (view mode)

In view mode, records can only be read, not edited. To enable editing for a record, click the Edit
record button.
Transect Surveys Sub-Form
The Transect Surveys Sub-Form is used to enter transect characterization information for
transect surveys in a sampling event. This sub-form is embedded in the Data Entry Form and
values entered here include:


Transect Number



Transect Location (m)



Wetted Channel Width (m)



Total Discharge (m³/sec)



QA/QC Flag



Transect Point Measurements
-



Point
Tape Reading (m)
Depth (m)
Velocity (m/sec)
Too Shallow
Habitat Type
Structure

Pebble Count
-

Count
Measure (cm)
Tape Measure (m)
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Riparian Canopy Closure
-

Facing
Measurement

Transect Survey Sub-Form

Once a transect number, transect location, wetted channel width, and total discharge has been
entered, data should be filled in for Transect Point Measurements, Pebble Counts, and Riparian
Canopy Closure. If a transect number is not entered, these fields will remained locked. To add
additional transect records, click the “Add Transect Survey Record” button, or use the scroll
buttons on the bottom left; to delete a transect record, click the “Delete Transect Survey Record”
button.
Tape Reading, Depth, Velocity, Habitat Type, and Structure should be recorded for transect
point measurements 1, 2, 3, 4, 5, LEW, and REW. To add or delete a transect point measurement
record, click the buttons located at the bottom right of the Transect Point Measurements section.
Total Discharge (located at the top of the Transect Survey Form) applies to Transect Point
Measurements only and should be filled in with the correct discharge number or NA. Pebble
count measurements should measure the b-axis diameter of 20 rocks and provide an accurate
tape measurement in meters. Riparian canopy closure measurements should be taken facing the
left, center and right bank of each stream. If a stream is less than one meter wide, only a center
measurement should be recorded.
If during the transect survey the stream reach is dry, a 0 (zero) should be entered in the following
fields: Wetted Channel Width, Total Discharge, and Depth (Transect Point Measurements
section). It should also be recorded in the Transect Notes section that the stream reach was dry.
The QA/QC Flag checkbox is used to indicate the transect record has been flagged for further
review.
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If flowtracker data is available (as a .pdf), it can be linked to the transect survey by clicking the
“Link Flowtracker Data” button.

Transect Survey Sub-Form

The following dialog box will open. If the flowtracker .pdf file is in the correct location click
“Yes.” If it is not in the correct location click “No”, this will close the dialog box. Use windows
explorer to move the flowtracker .pdf to the appropriate folder before trying to re-link the file
again. In order for the links to work properly in the database, this folder structure must be
maintained.

Once the flowtracker .pdf is in the proper folder location and the “Yes” button is clicked,
navigate to the correct .pdf file and click “Open.” This will automatically link it to the transect
survey. Only one flowtracker .pdf may be linked to each transect survey.

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If there is flowtracker data already linked to a transect, it may be viewed by clicking the “View
Flowtracker Data” button.

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Transect Survey Sub-Form

This will open up the flowtracker .pdf file in a separate window. If there is no data for that
transect, a message box will appear.

Transect Survey Image Form
In order to link images to a transect survey, the Transect Number must be filled in. If a Transect
Number has not been entered a message box will appear.

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To add image records to a Transect click the “Add Image Record” button. A blank Images Form
will open.

Transect Survey Sub-Form

Values entered here include:


File Name



Image Link



Image Caption



Image Date



Image Time



Image Source



Image Quality



Was Image Edited? (Yes or No)



Editing Notes



Additional Comments

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Images Form

To link an image to the record, click the “Insert Image” button in the top left hand corner. If the
image file is in the correct location click “Yes.” If it is not in the correct location click “No”, this
will close the dialog box. Use windows explorer to move the image file to the appropriate folder
before trying to re-link the file again. In order for the links to work properly in the database, this
folder structure must be maintained.

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Once the image file is in the proper folder location and the “Yes” button is clicked, navigate to
the correct image and click “Open.” The image will be linked, and the File Name and Image
Link fields will be automatically populated. This information is taken from the image file name
that is chosen in the dialog box. There is no limit to the number of images that may be linked to a
Transect. To add additional images to a Transect Survey select “New Image Record.” To delete
an Image record or close the Image Form use the control buttons located at the bottom of the
page.

Image Dialog Box

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If an image is already linked to a transect, it may be viewed by clicking the “View Image
Record” button. If there are no images for that Transect record, a message box will appear.

Transect Survey Sub-Form

Mollusc Survey Sub-Form
The Mollusc Survey Sub-Form is used to enter information for mollusc surveys in a sampling
event. This sub-form is embedded in the Data Entry Form and values entered here include:


Quadrat Number



Section Number



(X) Section of Route



(Y) Section of Route



Eggs



Spat <5 mm



Species
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Length (mm)



Estimated



Corrosion



Habitat Type



Structure



Depth (m)



VX (m/sec)



VY (m/sec)



QA/QC Flag

Mollusc Survey Sub-Form

A Quadrat or Section Number must be filled in before species can be entered. The Habitat Type,
Structure, Depth, and Velocity are to be recorded for that specific Quadrat and/or Section and the
QA/QC Flag checkbox is used to indicate the record has been flagged for further review.
To add additional mollusc survey records, click the “Add New Quadrat Record” button, or use
the scroll buttons on the bottom left; to delete a mollusc survey record, click the “Delete Quadrat
Record” button.
Crustacean Survey Sub-Form
The Crustacean Survey Sub-Form is used to enter information for crustacean surveys in a
sampling event. This sub-form is embedded in the Data Entry Form and values entered here
include:

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Collection Method



Trap Number



Section Number



Pool Number



Quadrat Number



(X) Section of Route



(Y) Section of Route



Species



Length (mm)



Estimated



Count



Gravid



Habitat Type



Structure



Depth (m)



VX (m/sec)



VY (m/sec)



QA/QC Flag

Crustacean Survey Sub-Form

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A Quadrat or Section Number must be filled in before species can be entered. The Habitat Type,
Structure, Depth, and Velocity are to be recorded for that specific Quadrat and/or Section and the
QA/QC Flag checkbox is used to indicate the record has been flagged for further review.
To add additional crustacean survey records, click the “Add New Trap Record” button, or use
the scroll buttons on the bottom left; to delete a crustacean survey record, click the “Delete Trap
Record” button.
Fish Survey Sub-Form
The Fish Survey Sub-Form is used to enter information for fish surveys in a sampling event. This
sub-form is embedded in the Data Entry Form and values entered here include:


Quadrat Number



(X) Section of Route



(Y) Section of Route



Species



Size (cm)



Individuals Counted



Habitat Type



Structure



Depth (m)



VX (m/sec)



VY (m/sec)



QA/QC Flag

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Fish Survey Sub-Form

A Quadrat Number must be filled in before species can be entered. The Habitat Type, Structure,
Depth, and Velocity are to be recorded for that specific Quadrat and/or Section and the QA/QC
Flag checkbox is used to indicate the record has been flagged for further review.
To add additional fish survey records, click the “Add New Quadrat Record” button, or use the
scroll buttons on the bottom left; to delete a fish survey record, click the “Delete Quadrat
Record” button.
Quality Assurance Checks
Once all fields and sub-forms on the Data Entry Form have been filled in, the data should be
verified and then certified. If a record has been verified the check box next to “Verified” should
be marked, and the “Verified By” and “Date Verified” fields should be completed; these fields
are not automatically populated. Once a record has been certified, the check box next to
“Certified” should be marked. The “Certified By” and “Date Certified” fields also need to be
completed; these fields are not automatically populated.

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Data Entry Form – Quality Assurance Checks Section

Enter/Edit Sites
The Monitoring Site Information Form may be opened from the Main Menu to add or edit
monitoring sites. See the Monitoring Site Information Form above for details on how the form
works.
Enter/Edit Observers
The Contact Form may be opened from the Main Menu to add or edit contact information. See
the Contact Form above for details on how the form works.
Quality Review Tool
After the season’s field data have been entered into the database, it will need to be reviewed and
certified by the Project Lead for quality, completeness and logical consistency. The quality
review tool contains queries that will help with the validation and certification of data in the
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working project database. These pre-built queries check for data integrity, data outliers and
missing values, and illogical values. The user may then fix these problems and document the
fixes.
The following table shows the automated validation checks that are performed on the data prior
to certification. These queries are designed to return records that need to be fixed, so ideally –
once all data checks have been run and any errors have been fixed – none of the queries will
return records. However, not all errors and inconsistencies can be fixed, in which case a
description of the resulting errors and why edits were not made is then documented and included
in the metadata and certification report.
The queries are named and numbered hierarchically so that high-order data should be fixed
before low-order data. The rationale for this is that one change in a high-order table affects many
downstream records, and so proceeding in this fashion is the most efficient way to isolate and
treat errors.
Query_name
qa_a012_Overview_sites_with_multiple_events
qa_a023_Overview_sampling_event_summary
qa_a033_Quality_assurance_status
qa_a042_Unverified_events
qa_a052_Uncertified_events
qa_b011_Locations_missing_critical_info
qa_b022_Locations_duplicate_sites
qa_b031_Locations_without_coordinates
qa_b043_Locations_missing_sampling_events
qa_b051_Location_illogical_dates
qa_c011_Events_missing_critical_info
qa_c021_Events_duplicates_on_sites
qa_c032_Events_without_observers
qa_c042_Events_missing_QA_info
qa_c051_Events_illogical_dates
qa_d011_Transects_missing_critical_info
qa_d022_Transects_missing_point_measurements
qa_d032_Transects_missing_pebble_counts
qa_d042_Transects_missing_riparian_canopy_closure
qa_d053_Transects_missing_images
qa_d063_Transects_missing_flowtracker_data
qa_e011_Molluscs_missing_species_length
qa_e021_Molluscs_incorrect_species
qa_f011_Crustaceans_missing_species_length
qa_f021_Crustaceans_missing_species_count

Returns records meeting the following criteria
Sites with more than one associated sampling event
Number of sites visited at each park, grouped by island,
stream name, and stream type
Quality assurance status (i.e., unverified, verified, or
updated) of all sampling events in the data set
List of unverified sampling events in the data set
List of uncertified sampling events in the data set
Missing park, island, stream name, stream type, site name
or site type
Duplicate records on park, island, stream name, stream
type, site name, and site type
Sampled sites without coordinate records
Unsampled sites
Updated date prior to created date, or discontinued date
prior to established date
Sampling event records missing Site ID or start date
Duplicate event records on site ID
Events without associated observers
Event records without entered date/by entries, or
incomplete updated date/by or verified date/by entries
Events with end dates prior to start date, or updated or
verified dates prior to the record entry date
Transect surveys missing transect ID, transect number,
transect location, wetted channel width, or total discharge
Transect surveys missing point measurements
Transect surveys missing pebble counts
Transect surveys missing riparian canopy closure
measurements
Transect surveys missing images
Transect surveys missing pdf links to flowtracker data
Mollusc surveys missing species length
Mollusc surveys with species chosen not found in park
Crustacean surveys missing species length
Crustacean surveys missing species count

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Query_name
qa_f031_Crustaceans_incorrect_species
qa_g011_Fish_missing_species_size
qa_g021_Fish_missing_species_count
qa_g031_Fish_incorrect_species

Returns records meeting the following criteria
Crustacean surveys with species chosen not found in park
Fish surveys missing species size
Fish surveys missing species count
Fish surveys with species chosen not found in park

The quality review tool may be accessed from the Main Menu by clicking the Quality Review
Tool button. The Data Validation and Quality Review Tool form will open and display existing
records.

Data Validation and Quality Review Tool Form – Results Summary Tab

The first tab of the Data Validation and Quality Review Tool form is the Results summary. Each
query is sorted by name, type, if it was checked (done), the number of records returned by the
query (N recs), the most recent run time (Last run time), the description, the action taken, who
fixed it (Remedy by), and the date it was fixed (Remedy date). There are also fields to filter by
query type (critical, warning, or information), if a record has been checked (Done), as well as
buttons for refreshing the results (which may need to be done periodically as changes in one part
of the data structure may change the number of records returned by other queries) and viewing a
summary report.
To view the results of an individual query, click on the query name. The View and fix query
results tab will open. At the top of the form is a switch that allows users to put the form in either
view mode (default) or edit mode. Switching to edit mode means that the remedy details can be
entered in the appropriate field (Remedy details). The QA by field will be automatically filled in
once the user types in the remedy details.

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Data Validation and Quality Review Tool Form – View and Fix Query Results Tab (View Mode)

Individual records should be viewed one at a time and errors or inconsistencies fixed as needed.
To view an individual record, highlight the record and then click the Open selected record
button.

Data Validation and Quality Review Tool Form – View and Fix Query Results Tab (Edit Mode)

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This will take you to the appropriate record(s) in the database and allow you to review the record
and make modifications as needed. Once errors have been fixed, click the Requery button to
update the Query results list. All changes should be documented in the Remedy details field.
Keep in mind that not all errors and inconsistencies can or need to be fixed, but should still be
documented in the Remedy details field.

The list of query results can also be exported to an excel spreadsheet by clicking the Export to
Excel button. To return to the results summary click the Results summary tab. Make sure to click
the Done checkbox after a query has been reviewed and fixed for errors. Refreshing the results
will move this query into the done category so you know that it has been checked (the list of
queries that are done can be viewed by changing the Done filter to True at the top of the form).
The Data Validation and Quality Review Tool can also be used to generate summary reports.
These reports include formatted information that lists queries by name, type, number of records,
description, and any remedy details that were typed in by the user. All queries that were run will
be shown in this report regardless if errors were fixed or not.
To generate a summary report click on the “View summary report” button on the Results
summary tab. The Quality assurance report dialog box will open.

Click “Yes” if you would like to limit the report to the specified year. Click “No” to open the
Filter by data time frame dialog box where you can enter a time frame or leave it blank to show
all. Click OK when done.

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Once a time frame is chosen, you will have the option to save the report. Clicking “Yes” will
allow you to choose a location and save the file as a .pdf. Clicking “No” will not save the file,
but still allow you to view it in the database.

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If you have chosen to save the summary report as a .pdf, a dialog box will open to confirm that
the file has been saved. Adobe will also automatically open the file in a new window.

When you are done working with the Data Validation and Quality Review Tool click the Close
button to return to the main menu.

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Data Summary Tool
After the season’s field data have been certified, data will be ready for summarization. The data
summary tool contains queries that summarize and perform basic statistical calculations. These
pre-built queries are developed based on what the project lead needs for their annual reports.
The following table shows the prebuilt queries for the data summary tool. The queries are
named and numbered hierarchically so that data types are grouped together.

Query_name
qs_a011_Sampling_event_summary
qs_a021_Sampling_event_sites
qs_a031_Number_streams_sampled_per_park
qs_a041_Number_sites_sampled_per_stream
qs_b011_Transect_discharge_per_stream
qs_b021_Transect_discharge_per_site
qs_b031_Transect_depth_velocity_per_stream
qs_b041_Transect_depth_velocity_per_site
qs_b051_Transect_habitat_type_per_park
qs_b061_Transect_habitat_type_per_stream
qs_b071_Transect_habitat_type_per_site
qs_b081_Transect_habitat_structure_per_park
qs_b091_Transect_habitat_structure_per_stream
qs_b101_Transect_habitat_structure_per_site
qs_c011_Pebble_count_average
qs_c021_Pebble_count_998
qs_c031_Pebble_count_999
qs_d011_Mollusc_species_per_park
qs_d021_Mollusc_species_count_per_park
qs_d031_Mollusc_species_count_per_stream
qs_d041_Mollusc_species_count_per_site

qs_d051_Mollusc_nativity_count_per_site
qs_d061_Mollusc_habitat_type_per_park
qs_d071_Mollusc_habitat_type_per_stream
qs_d081_Mollusc_habitat_type_per_site
qs_d091_Mollusc_habitat_structure_per_park
qs_d101_Mollusc_habitat_structure_per_stream
qs_d111_Mollusc_habitat_structure_per_site
qs_e011_Crustacean_species_per_park
qs_e021_Crustacean_species_count_per_park
qs_e031_Crustacean_species_count_per_stream
qs_e041_Crustacean_species_count_per_site
qs_e051_Crustacean_nativity_count_per_site
qs_e061_Crustacean_habitat_type_per_park

Returns records meeting the following criteria
Summary of freshwater animal communities, streams monitoring
per park per year.
A list of monitoring sites. Can be filtered on park, island, stream
name, or stream type.
The number of streams visited at each park.
The number of sites visited at each stream.
Total transect discharge by stream.
Total transect discharge by site.
Minimum and maximum depths and velocities of transects by
stream.
Minimum and maximum depths and velocities of transects by site.
A list of transect habitat types found at each park.
A list of transect habitat types found in each stream.
A list of transect habitat types found at each site.
A list of transect habitat structures found at each park.
A list of transect habitat structures found in each stream.
A list of transect habitat structures found at each site.
Average pebble size for each transect (excluding 998 and 998)
Total count of records with a pebble size of 998
Total count of records with a pebble size of 999
A list of mollusc species detected per park. Can be filtered by
nativity and species name
Total number of molluscs (by species) found at each park. Can be
filtered by nativity and species name.
Total number of molluscs (by species) found in each stream. Can
be filtered by nativity and species name
Total number of molluscs (by species) found at each site. Can be
filtered by nativity and species name
Total number of native and non-native molluscs found at each site
A list of mollusc habitat types found at each park
A list of mollusc habitat types found in each stream
A list of mollusc habitat types found at each site
A list of mollusc habitat structures found at each park
A list of mollusc habitat structures found in each stream
A list of mollusc habitat structures found at each site
A list of the crustacean species detected per park. Can be filtered
by nativity and species name
Total number of crustaceans (by species) found at each park. Can
be filtered by nativity and species name
Total number of crustaceans (by species) found in each stream.
Can be filtered by nativity and species name
Total number of crustaceans (by species) found at each site. Can
be filtered by nativity and species name
Total number of native and non-native crustaceans found at each
site
A list of crustacean habitat types found at each park

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Query_name

Returns records meeting the following criteria

qs_e071_Crustacean_habitat_type_per_stream
qs_e081_Crustacean_habitat_type_per_site
qs_e091_Crustacean_habitat_structure_per_park
qs_e101_Crustacean_habitat_structure_per_stream
qs_e111_Crustacean_habitat_structure_per_site
qs_f011_Fish_species_per_park
qs_f021_Fish_species_count_per_park
qs_f031_Fish_species_count_per_stream
qs_f041_Fish_species_count_per_site
qs_f051_Fish_nativity_count_per_site
qs_f061_Fish_species_count_per_quadrat
qs_f071_Fish_habitat_type_per_park
qs_f081_Fish_habitat_type_per_stream
qs_f091_Fish_habitat_type_per_site
qs_f101_Fish_habitat_structure_per_park
qs_f111_Fish_habitat_structure_per_stream
qs_f121_Fish_habitat_structure_per_site

A list of crustacean habitat types found in each stream
A list of crustacean habitat types found at each site
A list of crustacean habitat structures found at each park
A list of crustacean habitat structures found in each stream
A list of crustacean habitat structures found at each site
A list of the fish species detected per park. Can be filtered by
nativity and species name
Total number of fish (by species) found at each park. Can be
filtered by nativity and species name
Total number of fish (by species) found in each stream. Can be
filtered by nativity and species name
Total number of fish (by species) found at each site. Can be
filtered by nativity and species name
Total number of native and non-native fish found at each site
Total number of fish (by species) found at each quadrat. Can be
filtered by nativity and species name
A list of fish habitat types found at each park
A list of fish habitat types found in each stream
A list of fish habitat types found at each site
A list of fish habitat structures found at each park
A list of fish habitat structures found in each stream
A list of fish habitat structures found at each site

Data Summary Tool Form
To access the Data Summary Tool, click on the “Data Summary Tool” button on the
switchboard. The Data Summary Tool form will open (see below).

Data Summary Tool Form

200

The field “Query Type” in the top left hand corner contains a drop down list of the available
query types (see below). Choosing the query type will filter the list of available queries
displayed in the “Select the query” field. Some query types may not have any corresponding
queries. If this is the case, there will be no queries listed in the “Select the query” field.

Query Types

To choose a query and view the results, choose from the list of available queries in the “Select
the query” drop down list. Once a query is chosen, the description of the query will be
displayed under the query name (see below). If the query returns filtered results, the box next
to “Query returns filtered results?” will display “Yes”.

Select a Query

Query Description

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Many queries have the functionality to be queried. The available filters for the query chosen are
listed in the query description. The available queries for the Stream Monitoring Database are:
Location Filters:
• Park


Island – Maui, Molokai, Tau, Tutuila, or Guam. Field will be populated based on the
Park chosen.



Stream Type – Annual or Perennial.



Stream Name –The stream name. Field will be populated based on the Park, Island, and
Stream Type chosen.



Site Type - Fixed or Temporary



Site Name– The site name. Will be populated based on the Park, Island, Stream Type,
Stream Name, and Site Type chosen.

Event Filters:
• Year – all data for the year chosen


From date and To date – all data for the time frame chosen

Data Filters:
• Nativity – Native, Non-native, or Unknown


Species – can filter on any species that is in the species look up table

To use a filter, chose a value from the drop down menu. For Location filters, filters must be
chosen in order, i.e. Park, then Island, Stream Type, Stream Name, etc., as one filter’s drop down
list values are based on the filter value chosen above it. Once a filtered value is chosen, it is
automatically turned on. This is shown by the filter value being displayed in blue, the filter label
font becoming bold, and the toggle button to the right of the filter being turned on, which is
displayed as being sunken (see below). Results in the subform will be requeried and the filtered
results displayed.

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Filters On

There are several options for turning filters off. To leave the chosen values in the filter boxes,
but turn off the filters, click the “Filters off” button. The filters will be turned off, the filter
values will be displayed in black, the filter labels will no longer be bold, and the toggle buttons
turned off, which is displayed as being raised (see below).

Filters Off

To turn off individual filters, click on the toggle button to the right of the filter. The filter will be
turned off, the filter value will be displayed in black, the filter label will no longer be bold, and
the toggle button turned off (see below). To turn the filter back on, click the toggle button again.

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Individual Filter Turned Off

To turn off all the filters and clear the filters of their values, click on the “Clear filters” button.
All filters will be cleared and the query subform will be requeried to display all results.

Clear All Filters

The last filter to turn on or off is the “Include uncertified data?” filter. The default is set to “No”.
This ensures that only certified data is displayed in the query results. To view all data, including
uncertified data, click the “Yes” checkbox. If these queries are being used for annual data
summaries or analysis, only certified data should be used.

Certified Data Filter

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There are options to view or export data in the top right corner of the Data Summary Tool form
(see below). Clicking on an individual button will do the following actions.

Data Viewing Options

- View the selected query in chart view
- View the selected query in pivot table view
- Open the selected query in a new window
- Export the selected query to Excel
- Export the selected query to a text file
- View the selected query in design view
Clicking the “Open data gateway” form will open the Data Gateway Form where data can be
viewed and or edited.
Back Up Data
Clicking the “Back up data” button will pop up a Yes/No box asking if you would like to make a
backup copy of the data. If you select Yes, you will be prompted to select a folder in which to
place the backup copy, which has a default name of streams_BE_v1_yyyymmdd_hhmm.mdb.
You can rename the file if you would prefer a different name. Clicking the Save button creates
the backup file and displays a success message.
Connect Data Tables
The application has a separate front-end (user interface) and back-end (data tables). In order for
the application to work properly, the front-end file must be connected to the correct back-end
file.
Clicking the “Connect data tables” button opens the Update Data Table Connections Form,
which can be used to establish the link from the front-end to the back-end.

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Update Data Table Connections Form

For each back-end file linked to the front-end, a record will be displayed on the Update Data
Table Connections Form. The name, path, and file name of the current back-end file are
displayed. To change the back-end file connection, click the “Browse” button, select a new backend file, and click the “Open” button. You will be returned to the Update Data Table
Connections Form and the New file and Path text boxes will be filled in. To make the new
connection, click the “Update links” button. If the connection is made, a success message will be
shown and you will be returned to the main menu.
Defaults
The Defaults menu provides check boxes for automatic backups on startup, backups on exit, data
file compaction on backup, link verification on startup, and a field for time frame.

206

Defaults

Automatic Backups
The application can be set to automatically prompt for backups every time it is started and/or
every time it is closed using the “Exit” button on the main form. Making backups before and
after data entry sessions is a good habit to get into, in case of database corruption or data entry
mistakes. Backups can also be run manually by clicking the “Back up data” button on the Main
menu.
Compact Back-End on Exit
Compaction is a process whereby Microsoft Access optimizes the organization of the file,
making it smaller and quicker to access data. If you check the option to Compact back-end on
exit (recommended), the application will compact the data file that is linked to the front-end
when the application is closed using the “Exit” button on the main form.

207

Verify Table Links on Startup
The application is structured with a front-end (user interface) and a back-end (data tables). In
order for the application to work properly, the front-end must be linked to the tables in the backend. If this check box is checked (recommended), the link to the back-end file(s) will be checked
when the application is started.
Time Frame
The time frame field will only need to be filled in once at the start of the field season. This field
is necessary for the QA Queries to run properly and should be filled in with the date range of that
field season (i.e., 2009-2010).
About
The About menu presents information about the application, including:


Version number



Application author



Author organization



Author phone



Author email (click to email)

Buttons for viewing release history and reporting bugs are also provided on the About menu.

208

Defaults

Release History
Clicking the “View release history” button opens the Application Releases Form. This form
provides information about all of the different versions of the application that have been
released. It is filled in by the application developer before the application is distributed and is
therefore read-only.
Included in the Application Releases Form are title, version, and release information about the
application, information about the author of the application, and bug information.

209

Application Releases Form

Report a Bug
Clicking the “Report a bug” button will prompt the user to contact the application developer with
the details of the bug. Developer contact information is located above the Report a bug button.
The following information is useful when reporting a bug:


application name



application version
210



name of the form/report you were on when the bug happened



action, if any, you took right before the bug occurred



screen capture of any error messages

211

Appendix 17: Revision history log
Master Version Table Revision History Log
Version
key#

Date of
change

Narrative

SOP
#1

SOP
#2

SOP
#3

SOP
#4

Version
key#

Date of
change

SOP
#11

SOP
#12

SOP
#13

SOP
#14

SOP
#15

SOP
#16

SOP
#17

SOP
#18

SOP
#19

SOP
#20

SOP
#21

SOP
#22

Version
key#

Date of
change

SOP
#23

SOP
#24

SOP
#25

SOP
#26

SOP
#27

SOP
#28

SOP
#29

SOP
#30

SOP
#31

SOP
#32

SOP
#33

SOP
#34

Version
key#

Date of
change

SOP
#35

213

SOP
#5

SOP
#6

SOP
#7

SOP
#8

SOP
#9

SOP
#10

Standard Operating Procedures
The following section consists of 35 Standard Operating Procedures (SOPs) that provide
comprehensive instructions for all aspects of conducting a monitoring program for stream
macrofauna (fish, shrimp, and snails) and habitat characteristics of Pacific Island Network
(PACN) National Parks. Included are SOPs on pre-season preparation; field surveys of fish,
shrimp, and snails; habitat characterization; data management, data analysis and report
preparation; and post-season activities. Appendices related to these SOPs include site maps,
species identification guides, and data sheets for each monitoring activity.
Page
Standard Operation Procedure (SOP) #1: Safety Protocol ........................................................ 219
Standard Operation Procedure (SOP) #2: Preparation for the Field Sampling ........................ 223
Standard Operation Procedure (SOP) #3: Locating Sampling Stations ..................................... 229
Standard Operation Procedure (SOP) #4: Using Garmin Global Positioning System
(GPS) Units ................................................................................................................................. 235
Standard Operation Procedure (SOP) #5: Downloading and uploading data between
Garmin GPS and ArcGIS ............................................................................................................ 243
Standard Operation Procedure (SOP) #6: Using the Ricoh GPS Camera ................................. 251
Standard Operation Procedure (SOP) #7: Training Field Personnel ........................................ 253
Standard Operation Procedure (SOP) #8: Conducting Surveys on Tau, American
Samoa.......................................................................................................................................... 255
Standard Operation Procedure (SOP) #9: Conducting Surveys on Tutuila, American
Samoa.......................................................................................................................................... 257
Standard Operation Procedure (SOP) #10: Conducting Surveys in Guam ................................ 259
Standard Operation Procedure (SOP) #11: Conducting Surveys in Hawaii .............................. 261
Standard Operation Procedure (SOP) #12: Fish Surveys on Tau, American Samoa ................. 263
Standard Operation Procedure (SOP) #13: Shrimp (ula vai) Surveys on Tau, American
Samoa.......................................................................................................................................... 267
Standard Operation Procedure (SOP) #14: Snail (sisi vai) Surveys on Tau, American
Samoa.......................................................................................................................................... 269

215

Standard Operating Procedures (continued)
Page
Standard Operation Procedure (SOP) #15: Shrimp (ula vai) Surveys on Tutuila,
American Samoa ......................................................................................................................... 271
Standard Operation Procedure (SOP) #16: Snail (sisi vai) Surveys on Tutuila,
American Samoa ......................................................................................................................... 273
Standard Operation Procedure (SOP) #17: Fish (atot) Surveys in Guam .................................. 275
Standard Operation Procedure (SOP) #18: Shrimp (uhang) Surveys in Guam ......................... 279
Standard Operation Procedure (SOP) #19: Snail (akaleha) Surveys in Guam .......................... 281
Standard Operation Procedure (SOP) #20: Fish (oopu) and shrimp (opae) surveys in
Hawaii ......................................................................................................................................... 283
Standard Operation Procedure (SOP) #21: Snail (hihiwai) Surveys in Hawaii ......................... 287
Standard Operation Procedure (SOP) #22: Electrofishing for fish and crustaceans ................. 289
Standard Operation Procedure (SOP) #23: Habitat characterization at the reach and
transect scales ............................................................................................................................. 291
Standard Operation Procedure (SOP) #24: After Field Activities .............................................. 297
Standard Operation Procedure (SOP) #25: Workspace Setup and Project Records
Management ................................................................................................................................ 301
Standard Operation Procedure (SOP) #26: Data Entry and Verification .................................. 307
Standard Operation Procedure (SOP) #27: Post-season Data Quality Review and
Certification ................................................................................................................................ 311
Standard Operation Procedure (SOP) #28: Field Form Handling Procedures ......................... 313
Standard Operation Procedure (SOP) #29: Managing Photographic Images ........................... 315
Standard Operation Procedure (SOP) #30: Product Delivery Specifications ............................ 321
Standard Operating Procedure (SOP) #31: Metadata Development.......................................... 327
Standard Operating Procedure (SOP) #32: Data Analysis and Reporting ................................ 329

216

Standard Operating Procedures (continued)
Page
Standard Operating Procedure (SOP) #33: Sensitive Information Procedures ......................... 345
Standard Operating Procedure (SOP) #34: Product Posting and Distribution ......................... 351
Standard Operating Procedure (SOP) #35: Revising the protocol ............................................. 355

217

Standard Operation Procedure (SOP) #1:
Safety Protocol
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure explains the safety protocol for the operations using
the Pacific Islands Stream Monitoring Protocol: Fish, Shrimp, Snails, and Habitat
Characterization protocol and associated SOPs for the Pacific Island Network. This
document outlines safety considerations for conducting any aspect of the protocol. All
observers should be familiar with this SOP in order to identify and use the most current
procedures and ensure optimum safety.
A master equipment list for the entire Freshwater Animal Communities: Stream Vital
Sign Monitoring Protocol can be found in SOP #2: “Preparation for the Field Sampling.”
The master equipment list should be updated simultaneously if any SOP requiring an
equipment list is revised.
General Preparation and Review
Prior to conducting field work, observers are required to review this entire freshwater
stream monitoring protocol, including all SOPs listed in this protocol. In particular, all
participants should be thoroughly familiar with the NPS Occupational Safety and Health
Policies, scuba and watercraft manuals, various environmental and chemical safety
guidelines, procedures outlined in SOP #7: “Training Field Personnel,” as well as in SOP
#2: “Preparation for the Field Sampling.”
The
USGS
National
Field
Manual
(http://water.usgs.gov/owq/FieldManual/Chap9/content.html) is another recommended
reference for safety procedures.
219

Federal employees, volunteers, partners, or cooperators are required to know and follow
safety policies and requirements documented in Reference Manual 50 B Occupational
Safety
and
Health
Program
(http://inside.nps.gov/waso/custommenu.cfm?lv=2&prg=46&id=5898). Boat operators
should
refer
to
Reference
Manual
9
Watercraft
Safety
(http://
inside.nps.gov/waso/custommenu.cfm?lv=3&prg=704&id=2863) for safety guidelines. In
addition, individual parks also have park specific safety procedures, and operational
protocols.
Safety Policies, Regulations and Requirements
Ensure that all field personnel obtain First Aid and CPR training. Supervisory staff
should ensure that all field staff are well trained in the safety guidelines and policies
outlined below.
Weather
Sampling during inclement weather is of particular concern in the aquatic environments.
Streams can swell drastically without warning and weather can change rapidly on the
ocean, creating hazardous conditions in a relatively short time period. Prior to departure,
it is the responsibility of all personnel to be aware of the appropriate local weather, tide,
and current forecast for the day and to decide whether sampling should commence.
Sampling should be conducted during periods of little rain, mild wind, and small ocean
swell. If thunder is heard or lightning seen while boating, sampling will be suspended and
personnel should return to shore for at least 30 minutes. Do not stay on the water during a
lightning storm. During intense rainfall events, visibility may drop and appropriate
precautions should be taken to ensure that the boat does not ground. At any point during
sampling, any personnel involved have the right and responsibility to abort a sampling
trip if hazardous conditions develop.
Environmental Conditions
Individual parks have occupant emergency plans which cover safety procedures for
medical emergencies, earthquakes, floods, fires, and tsunamis. Be familiar with the
procedures and emergency contact numbers of your duty station park as well as other
parks you may visit during field sampling activities.
Rough, steep, and slippery terrain will be encountered when conducting field work
necessary for this protocol. Appropriate footwear should be worn to protect field
personnel from injuries. Felt soled shoes should be worn in around streams. Sturdy hiking
shoes should be worn while accessing field sites. Field conditions in the region are likely
to expose crews to intense tropical sunlight, wind, and rain. Flash flooding should always
be a concern when working near streams. High topographical relief in the region
combined with the episodic nature of rainfall in the tropics leads to extreme flood events
with little or no warning. Collecting freshwater stream data will require hiking over very
rough and unstable terrain in hot and arid conditions. Appropriate precautions should be
taken to protect field personnel from injuries as well as dehydration and exposure in these
220

environments. Personnel should be prepared with adequate sun protection equipment
(hats, sunscreen, etc) and plenty of drinking water. Access to certain field sites may
require hiking long distances (up to 8 miles) over uneven terrain carrying heavy
equipment (up to 50lbs). Camping in potentially inclement weather in backcountry sites
may be required. Appropriate preparations and safety precautions should be taken.
Contaminated Water
Aquatic areas being sampled may be contaminated with pathogens or harmful chemicals
although this situation is rare in the PACN. Consuming untreated or unfiltered freshwater
may result in the contraction of bacterial diseases or parasites (e.g. Leptospirosis,
Giardia.) Personnel should not work in water with open wounds to minimize exposure to
parasites.
Animal Hazards and Disease Vectors
Any open cut has a high likelihood of becoming infected and all cuts should be carefully
tended and monitored. It is the responsibility of all personnel to be familiar with the local
hazardous flora and fauna and to understand the appropriate treatment methods.
Field Trip Preparations and Emergency Contacts
Table S.1.1 contains information a list of basic field survival equipment. No sampling
activities will be conducted without all necessary safety equipment present and in proper
working condition.
Table S.1.1 List of basic field survival equipment for the freshwater stream protocol.
Equipment (#/quantity)
Water
Water Filter
First Aid Kit
Sunscreen
Insect repellant
Sunglasses (polarized)
Headlamp
Headlamp batteries (usually AAA) (6 )
Appropriate raingear, clothing and
footwear (including stream shoes)
Tent, sleeping bag (1/staff)
Personal items

Preparation & Maintenance
Ensure that the proper quantities are available.
Ensure this equipment is available.
Keep stocked
Ensure that the proper quantities are available.
Ensure that the proper quantities are available.
Ensure that this equipment is available.
Ensure this equipment is available.
Label and charge.
Ensure this equipment is available.
Ensure this equipment is available.
Ensure this equipment is available.

Emergency Procedure
In the event of an emergency, the first action is ALWAYS to take care of the injured
person and seek help. Once help is on the way and the situation is under control, the team
leader or crew member should contact, or have someone else contact, the supervisor to
inform them of the incident.

221

Standard Operation Procedure (SOP) #2:
Preparation for the Field Sampling
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes pre-field season procedures for monitoring
stream fish, shrimp, and snails in PACN parks. The procedures described here are
primarily the responsibility of the Field Lead (this role is filled by the Aquatic Biological
Technician) who may be assisted in some tasks by the Project Lead (the PACN Aquatic
Ecologist). Included in this SOP are a description of general preparations, field season
scheduling considerations, and a list of necessary supplies and equipment for sampling.
The procedures described here should begin no later than three months prior to a
sampling trip.
Procedures
General Preparations and Review
1) Review the protocol (monitoring narrative and all SOPs). The Project Lead and
the Field Lead should both be thoroughly familiar with the objectives of PACN
stream protocol. They should also have a solid working knowledge of all field
sampling methods and techniques.
2) Season specific plans. The Project Lead and Field Lead should review sampling
goals, including scheduling and crew member responsibilities. A timeline of tasks
and actual field sampling should be established (see Appendix 12 for details). The
field lead should also review the previous season’s field notes.

223

3) Permits. Obtaining all necessary permits is the responsibility of the Aquatic
Biological Technician, who may be assisted by park staff or the Project Lead.
Permits can be especially time-consuming to obtain and therefore, applications for
these permits should be submitted well before the season begins. A minimum of
90 days is typically required. Scientific collecting permits need to be obtained
from the appropriate state or territory agency, and each individual park where
sampling will occur (Note: contact information regarding permits will be
provided). Note that at least initially it may be necessary to fill out paperwork
ahead of time but actually sign the collecting permits for Guam and American
Samoa once you get there. For the National Park Service, there is a website
http://science.nature.nps.gov/research Research Permit and Reporting System
(RPRS) where permit applications are filed
4) Park contacts. At least two months prior to starting fieldwork, appropriate persons
in the park should be contacted (Chief of Resource Management, Chief Ranger,
other applicable staff that may be required to assist). Details are provided in
Appendix #5: “Logistics”.
5) Travel arrangements. Airline flights, boats (American Samoa), possible helicopter
(to Waikolu), ground transportation, and lodging (hotel, park accommodations, or
camping) should all be arranged well in advance. Details are provided in
Appendix #5: “Logistics”.
6) Supplies and equipment. All of the necessary supplies for the season should be
located and inspected to ensure that they are in adequate condition. This includes,
for example, field guides, data forms, GPS units, maps, preservative, and all
sampling equipment. For additional details see the list of supplies and equipment
(Table S.2.1) and associated data collection SOPs (SOPs #8-23). Supplies should
be grouped together in containers according to sampling activity, and each
container should have an attached checklist of all of the necessary supplies. Each
field season a new set of data forms will need to be photocopied onto waterproof
paper.
All field equipment should be available and organized at least one month before
fieldwork is scheduled to begin. All equipment should also be examined for
functionality and completeness before fieldwork begins. For example, sampling
traps should be clean and free of holes, and a sufficient supply of replacement
batteries and pencils should be available. Wetsuits and waders should be
inspected to ensure that they are clean and free of tears.
It is very important that all gear (including personal items such as boots or tabis)
be thoroughly cleaned to avoid inadvertently transporting introduced species to a
new location. It is recommended that the field crew should have a different set of
gear (including personal items such as boots) for each island group (Hawaii,
Guam, and American Samoa). Details on preventing the transport on introduced
species (aquatic hitchhikers) are provided in Appendix 5 (the logistics Appendix).
224

7) Location of sites. Prior to the field season, the Aquatic Biological Technician
should check all GPS units to ensure that the location coordinates of sampling
sites have been uploaded to each unit. Any unnecessary coordinates from the
previous year should be deleted. A printout of all sampling location coordinates
should accompany each unit as a backup reference for crew members. Laminated
topographic maps with sampling locations marked on them should also
accompany each GPS unit. Access points of difficult to reach areas should be
marked on the maps and if possible, the coordinates of these points should be
saved in the GPS units. Road or trail logs, in addition to site descriptions and
contact information for landowners, park managers, or others should be
maintained in a notebook.
Scheduling Fieldwork
1) Sampling schedule outline. A sampling timeframe has been established for each
park (see Appendix#8: “Recommended Field Sampling Schedule”). This is
coordinated with water quality monitoring, and has been selected to avoid the
times of likely stream flooding.
2) Create a tentative schedule. A tentative schedule should be constructed for the
entire field season, taking into account all logistical considerations. Ultimately,
the sampling scheduling should provide a plan for the entire season, but flexibility
for unforeseen circumstances should be built into the schedule.

225

Table S.2.1. Field supplies.
Personal Gear
Felt-soled boots
Wetsuit
Hood
Dive gloves
Rain jacket
Sun hat
Snorkeling survey/grid survey

Backpack
Drinking water
Food
Flashlight
Batteries
Field notebook

Mask
Snorkel
Fish quadrat wire
Snail quadrat wire
Calipers
SOPs
Data sheets
Random coordinates for quadrats
Electrofishing
Waders
Electricians’ gloves
Electrofisher
Charged batteries
Buckets
Sampling nets
Dip nets
Flagging tape
Tape measure
Aerators
Batteries
Trapping

Clipboards
Pencils
Flagging tape
Waterproof pens
Identification keys
Fingerless gloves
Ziploc bags for datasheets
Transect lines

Traps
Bait
Rope and clips
Buckets
Sampling nets
Dip nets
Flagging tape
Rugged gloves

Ruler
Measuring board
Calipers
Data sheets
Clipboards
Pencils
Waterproof pens
Identification keys
Ziploc bags for datasheets
Polarized sunglasses

Ruler
Measuring board
Calipers
Data sheets
Clipboards
Pencils
Waterproof pens
Identification keys
Ziploc bags for datasheets

Reach layout
Flagging tape
Waterproof pens
Tape measure

226

Table S.2.1. Field supplies (continued).
Habitat measurements (**rapid assessment)
Flow meter**
Wading rod**
Yardstick
Tape measure**
Ruler**
Densiometer

Data sheets**
Clipboards**
Pencils**
Flagging tape**
Waterproof pens**
Ziploc bags for datasheets**

Site information folder
Camera
Underwater camera
Sample jars
GPS
small multi-tool

Laminated site map
Permits
Equipment list
Park/emergency contacts
Field notebook

General Gear

Safety gear
First-aid kit
Sunscreen
Ear drops
Insect repellant
Cell phone
Radio/satellite phone
Drinking water
Spare snacks
Alcohol-based hand wash
Other
Charger for electrofisher
Charger for camera batteries
Laptop
Waterproof paper data sheets

227

Standard Operation Procedure (SOP) #3:
Locating Sampling Stations
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure describes the location of sampling stations. Logistics specific
to each island are in Appendix #5: “Logistics.” Table S.3.1 lists the equipment needed to locate
and document sampling sites.
Procedures
Directions to field sites in the National Park of American Samoa.
Tutuila Field Sites
Leafu stream is accessed by traveling the main road to Pago Pago and the road over the mountain
to the village of Vatia. Note there are no official road names in American Samoa. Roads are
distinguished by the villages they connect. Village chiefs and the mayor must be notified prior to
arrival in the village. This should take place several days to preferably at least a week in
advance. FTUT01 is accessed through a villager’s backyard. Consult homeowners before
sampling. It is helpful to have employees that speak Samoan assist in communication efforts.
FTUT02 and FTUT03 are accessed by a trail that follows on the banks of the stream. Permission
is needed from the mayor of the Vatia to access these sites. Again notification of the mayor in
advance is required. Trail is marked with blue flagging tape.
Fagatutui Stream (FTUT04-FTUT06) is accessed by traveling the road from Pago Pago towards
the village of Fagasa. Park at the Mount Alava trail head; proceed up trail two miles until
specified GPS point. Local staff know how to access these sites. It is helpful to have local
knowledge. Trail is a very steep slope down and marked with pink flagging tape though there
may be other trails in the area that can cause confusion. There are many streams in the area that

229

look quite similar. It is extremely important to have accurate GPS coordinates when accessing
the stream via trail. This stream can also be accessed via boat on days with calm sea conditions.
The boat can is launched from the Fagasa boat ramp and driven 3 bays over to Fagatuitui Bay.
Fagatuitui Bay is a distinctive looking bay with two streams that pour into the Bay. The sampled
stream is the one on the right coming in from the ocean. Depending on sea conditions, crew
capabilities, and boat specifications it may be possible to get relatively close to shore. However,
it will be necessary to swim some distance to shore with all sampling gear. A float for the
equipment will be required.
Amalau stream is accessed via the road from Pago Pago towards Vatia to the village of Amalau.
Visitors must ask local villagers for permission to sample in Amalau stream. Permission should
be obtained the day of, as well as several days in advance so they know to expect you. Site
FTUT07 is at the mouth of the stream near the village fales. The site is accessed through private
land. Remember to obtain permission. FTUT08 is easily accessed by walking upstream crossing
highway and following stream until specified GPS point is reached.
In all travels to sites on Tutuila where village access is required, it is vitally important to
recognize that you are traversing private land. When specific dates and times are established for
sampling, these need to be honored. Local villagers get extremely upset when expected
intrusions do not happen as planned. Also, following local customs is required. While sampling
in village areas, dress must necessarily be modest and no work is to be conducted in village areas
on Sundays. Contact park staff for any questions regarding local customs.
Tau field sites
All fixed field sites (FTAU01-FTAU04) are accessed via the beach trail at the end of the 4WD
road. The trail leads over a short sandy beach, a boulder beach, and a relatively smooth forested
trail. The trail then splits to access lower Laufuti and middle/upper Laufuti. Allow 30 minutes to
trail junction. The trail down to lower Laufuti (FTAU01-FTAU02) is a steep, slippery slope that
ends at a rocky beach. The trail was improved and a ladder installed in 2010 to assist hikers.
Follow the coast along sandy and boulder beaches until the mouth of Laufuti stream. This takes
approximately 2 hours from the split due to the rough terrain and heavy gear. To access the
middle and upper sections of Laufuti (FTAU03-FTAU04), the trail follows the ridgeline up a
steep climb. This trail can be extremely overgrown and may take extra time to cut through the
vegetation with machetes. It is helpful to ask NPSA staff to cut the trail in advance. This saves
hours of hacking through the jungle. Notify staff of intended arrival at least 2 months prior to
facilitate trail clearing. The trail is flagged with blue and pink flagging tape though they may not
be entirely visible if overgrown. The trail climbs through mostly fern forest. Many large
boulders, exposed roots, moss covered lava rocks, and thick vegetation present hazards. Pants,
long sleeve shirts, and mosquito repellant are essential. VIP Tuiluiga Simolea and NPSA Marine
Technician Bert Fuiava know all field sites and access routes.

Directions to field sites in War in the Pacific National Historical Park
All field sites are located on Asan stream in the Asan Unit of War in the Pacific National Park.
From the Airport or Tumon take highway 10A to Marine Corps Drive (Guam Route 1). Turn left
and go approximately 6 miles. Turn left onto Jose Leon Guerrero Street. Park on street near

230

bridge over Asan stream. Access the lower sites by heading upstream in the river. The first fixed
site is approximately 70 meters upstream from the parking location, just immediately past the
overhanging vegetation on the stream. Heading upstream, there is a trail on the left stream bank
(right side when facing upstream) just past the second banana plantation where there are several
limestone rocks in the bend of the stream. This trail can be used to facilitate quicker access to
central river sites up to the dam. All sites can be accessed by hiking upstream in the stream;
however, this is recommended only for sites downstream of FWAPA02 (lower sites).
Middle stream sites can be accessed by turning left onto Guam Route 6 from Marine Corps Drive
toward the Asan Unit Overlook. Turn left onto Mama Sandy Road toward a residential area.
Turn onto the small dirt road labeled J Street. Follow this road over the hill and then take the first
dirt road to the right (it is unmarked as of January 2011). Follow this dirt road downhill until you
reach the lowest cleared lot (the road will turn left and then start heading uphill again). Park in
this cleared lot. At the entrance to the cleared lot, you will find an overgrown access road.
Follow this road along the ridge until it turns to the left. Don’t turn left (This is an extremely
important direction note). Continue hiking over the ridge in front of you (the main ridge). All
middle stream sites can be accessed from points along the main ridge. If luck is on your side, you
will find a hash/pig trail that runs along the top of the main ridge. Follow this trail along the main
ridge and use your GPS to access all sites in the middle portion of the stream. The uppermost
middle site, FWAPA06, can be accessed by crossing this main ridge from the access road and
continuing to head down the side ridge to the stream. You will enter the stream about 100 meters
downstream of the site (this is not the current preferred route as it is presently overgrown with
sword-grass, but it is an access route, and the frequent fires may change the vegetation making it
an excellent access point in the future). As you access the middle trail sites, remember to keep
the main valley to your right. There are several side ridges, which, if taken, will lead you into
sword-grass fields and wasp lairs, which are better avoided. All sites in the middle stream can be
access by heading upstream from the previous location.
Upper sites can be accessed by turning left onto Guam Route 6 from Marine Corps Drive toward
the Asan Unit Overlook. Then turn left onto Mama Sandy Road toward a residential area. Turn
onto the small dirt road labeled J Street and park. Walk through the lower cleared lots to the
furthermost corner of the second cleared lot. There is a short, 15 minute trail down to the stream.
This trail goes directly to the uppermost fixed site on Asan stream, FWAPA16.
Directions to field sites in Haleakala National Park
All field sites are located in the Kipahulu area of Haleakala National Park. From OGG follow the
Hana Hwy/HI-360 (Hana way or north route) to Kipahulu or follow Haleakala Hwy/HI-37 to
Piilani Hwy/HI-31 (south route) to Kipahulu. It takes approximately 3 hours each way from the
airport to Kipahulu.
FHALE01 is located near the mouth of the stream and is accessed via the Seven Sacred Pools
trail from the Kipahulu visitor’s center. FHALE07 is accessed by taking the two mile long
Pipiwai trail then following the rarely used Makahiku Falls trail (marked only by an old sign).
Cross the bridge, and follow trail to the stream. Cross the stream to the right bank and follow the
stream to appointed GPS point. FHALE02, FHALE08, and FHALE03 are located just off the
Pipiwai trail. FHALE02 is at the lower USGS gauging station. FHALE08 is accessed by hiking

231

upstream in Pipiwai Stream just after the confluence of Palikea and Pipiwai. FHALE03 is at the
base of Waimoku falls just upstream of where the trail crosses the stream. FHALE09 is accessed
by hiking in the stream up Palikea just after the confluence of Palikea and Pipiwai. Temporary
sites on Palikea or Pipiwai streams can be accessed via the Pipiwai trail.
FHALE05, FHALE06, and all temporary sites on Alelele are accessed by following highway 31
south from Kipahulu to the Alelele bridge. Park in the pullout near the mouth of the stream.
Follow the trail on the left bank of the stream to access all sites.
Directions to field sites in Kalaupapa National Historical Park
All field sites are located on Waikolu Stream. There are three access options. The first is to hike
from Kalawao (20 minute drive from main Kalaupapa settlement) down to the boulder beach and
across to Waikolu. The trail follows the coast alongside steep sea cliffs. Hardhats are required.
The hike is not advised during periods of heavy rain as this can cause loose rocks to fall from
cliffs. The hike is approximately 1.5 miles over a boulder beach with loose and slippery rocks.
The hike takes 1-1 ½ hours depending on pack weight and weather conditions. The 2nd option is
boat from the settlement around the point to Waikolu. This requires extensive planning with
local staff and calm sea conditions. The drive is approximately 45 minutes. Launching and
loading the boat takes approximately 1 hour. The boat can be anchored in the bay for near shore
gear unloading. Gear unloading takes approximately one hour. Camping is possible at the mouth
of the stream with proper permission. The third option is to drive through the water diversion
tunnel from topside. This allows easier access to sites above the pump house. Prior permission
must be obtained through the Molokai Irrigation System part of the Department of Agriculture.
A 4WD vehicle that meets the tunnels specifications must be obtained. Jeep Wranglers that meet
these specifications are available for rent through Island Kine Rental Car (808-553-5242) located
in Kaunakakai. Arrangements with workers must be made for directions to the tunnel and to
borrow keys to access the tunnel. Contact Oscar Ignacio at 808-336-0587 for tunnel access. The
drive takes approximately 2 ½ hours from Kaunakakai.
Once in Waikolu Valley, all sites below the tunnel can be accessed by hiking up the stream or
from the trail. The trail goes from the mouth of the river to the pump house, and continues as a
road to the tunnel. All sights above the tunnel must be accessed by taking the catwalk that goes
from the tunnel to the diversion dam, and then hiking up stream. Sites near the tunnel and
waterfalls can be accessed by taking the catwalk that crosses the valley to the collection pool at
the base of the waterfalls, and then scrambling down to the stream below. The main trail along
Waikolu stream starts on the left Bank of the lefter most branch of the stream (the extreme right
of the valley facing upstream). Hike to the rocks that form the valley wall and begin walking
upstream. This trail is unmarked in this location so some faith must be taken the trail is there.
You will be touching the cliff as you hike the initial several meters of the trail. The trail then
becomes somewhat more distinct and travels along both sides of the stream crossing in several
places. GPS is useful in locating sites, but not always accurate or dependable as the signal gets
degraded the further upstream you travel. Navigation by topographic maps is advisable, and at
times required to locate the sites.

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How to locate a site:
1) All sites are loaded into the GPS prior to a sampling event and the sampling station
locations are printed on a map of the stream (See SOP 5: Downloading and
Uploading data between Garmin GPS and ArcGIS).
2) Using GPS or a combination of GPS and available maps, the site is approached from
the downstream direction (See SOP 4: Using Garmin Global Positioning System
[GPS] Units).
3) When the GPS or GPS/map combination indicates you have reached the zero station
mark, the lower end of the site is flagged.
4) The site will extend 30 m upstream of the indicated GPS point.
Table S.3.1. Equipment list for locating and documenting sampling site locations.
Equipment (#/quantity)

Preparation & Maintenance

GARMIN Global Positioning System (G.P.S.) unit (1)

Ensure that this equipment is available and set-up appropriately
(according to SOP #4).

AA batteries (6)

Ensure this equipment is available. If rechargeable, ensure fully
charged.

Waterproof case with desiccant and strap (1)

Ensure that this equipment is available. Replace desiccant pack
biannually or if saturated.

Charts and grid layouts
Random number pair list

Ensure that this equipment is available. Store in field binder.
Create document and store in the field binder.

Compass (1)

Ensure that this equipment is available. Store in field binder.

Map of fixed and random sampling sites (2 copies)

Update prior to each trip with GIS specialist. Print in color to
waterproof paper. Label sites. Store in field binder.

Fixed sampling site descriptions (with photo and
compass heading)

Print to waterproof paper and store in field binder. Update If
necessary prior to subsequent field sampling.

Park brochure and general map
ArcMap 10.0® software, Garmin Mapsource software

Store in field binder.
Check for software updates regularly

233

Standard Operation Procedure (SOP) #4:
Using Garmin Global Positioning System (GPS) Units
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure explains how to use an autonomous, non-differential
Garmin (or similar unit) GPS receiver and GPS transfer software. This SOP is written
specifically for Garmin GPSMap76CSx model, but it may be used for any other Garmin
GPS models that can average a waypoint and collect track logs. The GPS transfer process
uses DNR Garmin 5.4.1 and ArcGIS 9.3 software.
Pre-Field Preparation
Equipment
The following equipment should be taken into the field:
• GPS receiver.
• Map.
• Fresh AA batteries (at least 2).
• Compass with declination adjustment (if desired).
• Waypoint(s) preloaded (if necessary).
• Waypoint metadata form and pencil/pen.
• Notebook for recording description of waypoints.

235

Garmin GPS Preparation
1. Read and become familiar with Garmin GPS user manual, hardware, and
software.
2. Load freshly charged batteries and have extra charged sets available. Put extra
batteries in a water tight “dry bag” or a re-sealable plastic bag.
3. Download a fresh Almanac into your Garmin GPS if the unit has not been used
for more than 1 week. Or if the GPS unit has been traveled a distance of 150 miles
or more from the last location (i.e. travel between PACN islands). A fresh
Almanac automatically sets the correct time/date and time zone for your GPS, as
well as other local settings acquired from the satellites. To download an Almanac,
turn on your Garmin GPS and stand in an open area (i.e. away from buildings,
tree canopy, and obstructions) for about 20-30 minutes depends on cloud cover.
4. Get familiar with the Main Menu page and the Set Up page on your Garmin GPS.

5. Make sure your Garmin GPS interface is set correctly. From Main Menu page 
Setup  Interface. Select Garmin for “Serial Data Format” field.
6. Make sure that WAAS is enabled. From Main Menu page  Setup  System.
Set “WAAS” field to Enabled.
7. If necessary, delete old waypoints or tracks from your GPS memory (make sure
data has been downloaded and saved on your computer).
• To delete all waypoints, press FIND  Waypoints. Press ENTER, then press
MENU. Select Delete…and press ENTER. Select All Symbols and press
ENTER.
• To delete all tracks, from Main Menu page  Tracks. Press ENTER, then
press MENU. Select Delete All Saved and press ENTER. Select Yes and press
ENTER.

236

8. If necessary, upload GIS data (e.g. shapefiles) to the GPS unit using DNR Garmin
software (see SOP #5: “Downloading and Uploading Data between Garmin GPS
and ArcGIS” for instructions).
9. If you plan to GPS a line showing where you traverse (i.e. a track), then make
sure to set up the Track Log. From Main Menu page  Tracks  Setup. Check
the box Wrap When Full if you want Track Log records over oldest data with new
data, otherwise leave the box unchecked. Set “Record Method” field to Time. Set
“Interval” (i.e. logging rate for data collection) field to 00:00:05 (5 seconds is
recommended for data collection while walking).
10. Set the coordinate system. From Main Menu page  Setup  Units. For the field
“Position Format”, select either hddd.ddddd, or hdd mm.mmm, or hddd mm ss.s if
you want your waypoints collected in LAT/LONG. Otherwise select UTM UPS.
Note: Standard unit for Distance, Elevation, and Depth is Metric or Meters for all
PACN islands.

237

11. Set the Map Datum. From Main Menu page  Setup  Units. Set “Map Datum”
field to either NAD83 or WGS84 depends on island location. Standard Map
Datum settings for PACN islands are in Table 1 below.
Table S.4.1. Coordinate systems and datum for PACN islands.

Island

Datum

Coordinate
system

Hawaii Island

NAD83

UTM zone_5N

Maui Island

NAD83

UTM zone_4N

Molokai Island

NAD83

UTM zone_4N

Oahu Island

NAD83

UTM zone_4N

Guam

WGS84

UTM zone_55N

Saipan

WGS84

UTM zone_55N

American Samoa (all islands)

WGS84

UTM zone_2S

12. If necessary, check North Reference setting. From Main Menu page  Setup 
Heading. Set “North Reference” field to True.
13. After using Garmin GPS in the field, make sure to put the unit in its carrying pack
and store in a dry location.
GPS Field Procedures
Data Collection Preparation
1. Turn on your Garmin GPS unit. Press PAGE button several times to access the
Satellite page, then press MENU and select Use with GPS On, press ENTER.
2. Hold GPS unit in front of you. Keep it flat and leveled. Wait for the satellites to
appear on the Satellites page. Note: A minimum of 4 satellites is required to
ensure data accuracy.

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IMPORTANT NOTE: Garmin GPS will collect data regardless of how many
satellites being detected or no matter what the GPS positioning quality is,
therefore you must check the Satellites page frequently while collecting data. A
good rule of thumb is ONLY collecting data when the 3D satellite fix mode signal
is shown on the Status bar at the top of the screen of your GPS unit. Avoid
collecting data when Garmin GPS is in 2D fix mode.

Also, check the Location accuracy error from time to time to ensure the GPS
positioning quality when you collect data.

239

Navigating To Waypoints
1. Press FIND  Waypoints, press ENTER.
2. Use the Rocker key (move Up/Down or Left/Right) to enter the name of the
waypoint or just select OK. Scroll down the list and select the waypoint that you
want to navigate to, press ENTER. Select Go To at the bottom of the page and
press ENTER.

3. Map page should open automatically (if not, press PAGE button several times to
access the Map page). Start walking and follow the compass direction on the Map
page to navigate to the waypoint.
Collecting Waypoints
1. Stand still at the location where you want to GPS.
2. Press and hold ENTER/MARK button until the Mark Waypoint page appear.

240

3. At the top of the Mark Waypoint page, enter a waypoint name, using the Rocker
key. Tip: To save time in the field, write down any notes/comments about this
waypoint into a notebook. You may enter this information later back at the office,
after downloading the waypoints into ArcGIS.
4. Select OK at bottom of the page and press ENTER.
5. Go to your next location and repeat the above steps.
Collecting Tracks
1. Turn Track Log to ON. From Main Menu page  Tracks. Select On and press
OK.
Also, from Main Menu page  Tracks  Setup Track Log, make sure the box
Wrap When Full is checked if you want Track Log records over oldest data with
new data (otherwise leave the box unchecked).

2. Begin walking and Track Log will start collecting track points (at an interval of
every 5 seconds as you walk).
3. Turn Track Log to OFF to stop collecting. From Main Menu page  Tracks.
Select Off and press OK.
4. Tip: You may stop Track Log when nearing the beginning point of an area
(polygon) you’ve walked. Track Log will automatically close the polygon even if
a track is left open ended.
Other Data Collecting Tips
1. For more detail information on data collecting with Garmin GPS, check out the
User’s Guide at this link:
2. http://www8.garmin.com/manuals/GPSMAP76CSx_OwnersManual.pdf

241

Standard Operation Procedure (SOP) #5:
Downloading and uploading data between Garmin GPS and ArcGIS
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes how to download/upload GPS data using
DNRGarmin, free software that is the Pacific Islands NPS standard for incorporating
Garmin GPS data into GIS. This SOP is written specifically for Garmin GPSMap76CSx
model, but it may be used for any other Garmin GPS models that can average a waypoint
and collect track logs. The data transfer process uses DNR Garmin 5.4.1 and ArcGIS 9.3
software.
Installation of DNR Garmin Software
1. If you already have DNR Garmin 5.4.1 installed on your computer, go to next
section “Connect Garmin GPS unit to Computer” below.
2. If a previous version of DNR Garmin exists on your computer, start from Step 3.
If there is no previous DNR Garmin software on your computer, start from Step 5.
3. Uninstall any previous versions of DNR Garmin by using the Start  Control
Panel  Add/Remove Programs function.
4. When uninstallation is done, perform a search on local drives for all files named
“dnrgarmin”. If found, delete them. Note: Failure to completely remove any
earlier versions can cause problem running the current DNRGarmin version.
5. Install DNRGarmin: If you have access to I&M server, go to
M:\Software\GPS_Garmin\DNRGarmin5.4.1, then go to Step 6 to install the
software.
If you don’t have access to I&M server, you may download the free DNR Garmin
5.4.1 software from the Minnesota Department of Natural Resources at this link
243

6.
7.
8.
9.

http://www.dnr.state.mn.us/mis/gis/tools/arcview/extensions/DNRGarmin/DNRG
armin.html and then go to Step 6 to install it.
Double click the dnrgarmin54setup.exe file.
Press “Next” at the Welcome Screen, then accept the License Agreement. Press
“Next” to continue.
The program will be installed in a default location “c:/program files/dnrgarmin”.
Press “Next” to continue.
The program will install a desktop shortcut and a DNR Garmin folder will be
added to the Start  All Programs menu. Press “Finish” and view the Readme
file if desired, otherwise close Readme file.

Connect Garmin GPS Unit to Computer
1. Attach the Garmin Cable to either a COM1 serial port or a USB port (depends on
what type of cable that comes with your Garmin GPS unit) in the back of your
computer.
2. Attach the other end of the Garmin Cable to the back of the Garmin GPS.
3. Turn on the GPS by pressing and holding the red lantern button.
4. Press the Menu button and select the “Use With GPS Off”.
5. Press Enter and the Garmin should be in Simulator Mode (GPS unit no longer is
searching for satellites).
6. Press the Page button several times until you get to the Main Menu.
7. Make sure the “Serial Data Format” field is set to Garmin. From Main Menu page
 Setup  Interface.
8. You’re now ready to download or upload data between a Garmin GPS unit and
your computer.
Download GPS Data into ArcGIS
GPS waypoints and tracks collected in the field can be downloaded directly into ArcGIS
as shapefiles.
1. Open ArcMap.
2. Launch DNR Garmin from the desktop shortcut or loading from All Programs 
DNR Garmin. You should see a screen announcing version 5.4.1 and MN-DNR
Garmin window opens with the word “Connected” displayed at the bottom. If you
receive a connection error message or “Not Connected” displayed at the
bottom of the DNRGarmin screen, go to section “Connection
Troubleshooting Guide” at the end of this document for suggested steps to
resolve connection problem.
3. When DNR Garmin opens for the first time on a computer, you will be asked to
accept or change the default projection of UTM -1983, Zone 15. Select NO to
change the default projection.
4. The DNR Garmin Properties dialog box appears.
5. Set projection based on Table 1 below.

244

Table S.5.1. Projection settings for islands in PACN
Island

ESRI (or EPSG) POSC code

Datum

Projection

Hawaii Island

26905

NAD83

UTM zone_5N

Maui Island

26904

NAD83

UTM zone_4N

Molokai Island

26904

NAD83

UTM zone_4N

Oahu Island

26904

NAD83

UTM zone_4N

Guam

32655

WGS84

UTM zone_55N

Saipan

32655

WGS84

UTM zone_55N

American Samoa (all islands)

32702

WGS84

UTM zone_2S

6. When Finished Press OK. These projection settings MUST be checked EACH
time you download GPS data by selecting File  Set Projection.
7. In ArcMap, ensure that the Data Frame is set to the appropriate projection:
- Right click on Data Frame name, select Properties.
- In Data Frame Properties window, select Coordinate System tab. Read the
information in Current Coordinate System box. It should have the same Datum and
Projection as the GPS data you’re about to download. If it is NOT the same or “No
projection” is displayed, then go down to Select a Coordinate System box, click on
Predefined folder and select the appropriate coordinate system (refer to Table 1
above). Download the waypoints (or tracks) into ArcGIS:
First, download waypoints into DNRGarmin by selecting Waypoint (or Track) 
Download. The waypoints (or tracks) will be tabulated and it might take a while.

245

Next, you MUST save the waypoints (or tracks) as a GIS layer by selecting
File  Save To  ArcMap  Shapefile Layer.

Select a location folder and type in a name for the shapefile.
Press the Save Button. The new shapefile will be automatically added into ArcMap.
Upload GIS Data into Garmin GPS
GIS data (point, line, polygon shapefiles) can be uploaded into the Garmin GPS unit to be
used as background map features or locations to navigate to.
1. Connect GPS to computer (see section “Connect Garmin GPS unit to Computer”
above).
2. Launch DNRGarmin.
3. Go to FileSet Projection to change the coordinate system if needed. It should
match the coordinate system of the GIS data you want to upload.
4. Chose either of the 2 methods below to start uploading data.

246

From ArcMap Method
This is an option if you already have an ArcMap project opened and you want to upload a
layer from your map project into the Garmin GPS.
1. In ArcMap Table of Content, highlight the layer you want to upload.
2. In DNRGarmin, select File  Load From  ArcMap  Layer. Data will be
transferred into DNRGarmin. Note: The data are NOT uploaded into your GPS
yet, must perform step 3
3. From the Waypoint (or Track, Route) menu, select Upload and data will be
uploaded into the GPS.
From DNRGarmin Method
1. Go to File  Load From  File. Select Shapefile as Files of Type. Navigate to
where the shapefile is located on your computer and select it. Press Open.
2. An Identify Fields dialog may open. Fill in the appropriate fields if necessary.
Click OK. Data will be transferred into DNRGarmin. Note: The data are NOT
uploaded into your GPS yet, must perform step 3.
3. From the (or Track, Route) menu, select Upload and data will be uploaded into
the GPS.

247

Connection Troubleshooting Guide
Here are some steps to follow if you failed to make a connection between the GPS unit
and your computer:
1. Ensure the GPS is in Garmin Interface Mode. On your Garmin GPS unit, from
Main Menu page  Setup  Interface. Check to make sure the “Serial Data
Format” field is set to Garmin.
2. Check all cable connections to ensure everything is secured tightly. In DNR
Garmin, click GPS Set Port. Make sure Port 1 is checked if you attached the
cable to COM1 serial port. Otherwise, USB should be checked if you attached to a
USB port on your computer.
3. If your computer has two or more serial ports, make sure you are attached to
COM1. If COM1 port is already taken up by another cable (printer, scanner, etc.),
attach the Garmin cable to another available serial port, i.e. COM2, COM3. Then
in DNR Garmin, go to GPS  Set Port and select Port2 or Port 3 accordingly.

4. If you are using a serial port cable, make sure it has 4 prongs on one end (where it
attached to the back of the Garmin GPS unit) and a parallel port on the other end
(attached to a parallel port on your computer).
5. If you are using a USB cable, you may need to install a USB driver to make
this connection work. The driver is available on I&M server. Follow the steps
below to install the USB driver on your computer (you must have administrative
privileges to install):
• Close all running programs.
• Go to M:\Software\GPS_Garmin\USB Driver. Double click on
USBDrivers_221.exe
• Click Run button to start the installation process.
• Click Next.
• Select “I accept the terms in License Agreement”, then click Next.
• Select “No, Not at this time”, then click Next.
• Select “Install the software…(Recommended)”, then click Next.
• Click Finish.
248




Restart your computer when installation is successfully done.
Connect USB cable from Garmin GPS to your computer. Turn on GPS
unit, check to make sure “Use with GPS off” is set and GPS is in Garmin
Interface Mode (refer to section “Connect Garmin GPS to Computer”
above if needed).
• Launch DNRGarmin, go to GPS  Set Port and select USB. Connection
should be established.
6. If you’re using COM1 serial port and DNR Garmin is still not connecting to your
GPS after performing step1-5 above, then follow these additional steps (written
for Windows XP, may be slightly different for other Windows operating systems):
• Close DNR Garmin, ArcGIS and turn off GPS unit. You may leave GPS
unit connected to the COM1 serial port.
• Click on Start  Control Panel  Performance and Maintenance 
Administrative Tools.
• Double-Click Computer Management.
• Double-Click Device Manager.
• Open up Ports and select COM 1.
• Right mouse over COM 1 and select Disable.
• Say yes to really disable this.
• Press OK or Apply all the way out to close all windows.
• Restart your computer.
• When the computer is rebooted, Windows will re-establish the COM1
port. Proceed to step 1 of section “Connect GPS Receiver to
COMPUTER” of this document.
Other Trouble Shooting Tips
3. You must have administrative privileges to install DNRGarmin software in the
C:/Program Files directory on your computer. Contact your system administrator if
installation was stalled because of installation rights.
4. If you have an earlier version of the DNR Garmin program on your machine you
MUST uninstall before installing the new version. Uninstall previous versions by
using the Start  Control Panel  Add/Remove Programs tool.
5. ActiveSync software (for use with Trimble GPS) often conflicts with DNR Garmin or
other software needing access to a serial port. You may need to exit or disable
ActiveSync on your computer first before using DNR Garmin.
6. For other installation errors please refer to Minn. DNR Help page at
http://thoreau.dnr.state.mn.us/mis/gis/tools/arcview/Training/WebHelp/Training.htm#
DNRExt/DNRGarmin4/GPSIntro.htm

249

Standard Operation Procedure (SOP) #6:
Using the Ricoh GPS Camera
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision; identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.

1. Load camera memos onto Ricoh camera prior to sampling trip. Example memos:
Stream Memos for KALA
Park:
KALA
Stream:
Waikolu
Site:
FKALA01
FKALA02
FKALA03
FKALA04
FKALA06
FKALA07
FKALA08
FKALA09
TKALA10
TKALA11
TKALA12
TKALA13
TKALA14
TKALA15
TKALA16
TKALA17
Transect Number:
1
2
3
Direction:
Upstream

251

Downstream
Right Bank
Left Bank
Photographer: Anne Farahi
Tahzay Jones

2. Perform compass calibration procedure each time you move the camera more than
100 miles as instructed in Ricoh Instruction Manual.
3. Turn on Ricoh camera and allow enough time for the GPS receive signals from at
least four satellites. Wait until you see 3D fix displayed on the camera’s display;
this indicates that the GPS is receiving at least four satellite signals and can
accurately map your location. A GPS point of where you are standing when the
photo is taken will automatically be collected when you take a picture.
4. Be careful to not block the GPS receiver when taking photos. The GPS receiver
says “GPS” and has a small antenna that extends beyond the camera body.
5. Photos should be taken from the center of each transect facing upstream,
downstream, and towards the right and/or left bank if noteworthy.
6. Select the appropriate field for each memo by pressing the ad/memo button.
Select ok to set memo.
7. Wait for 3D fix on the camera’s display. Take picture. Repeat for each direction at
each transect.

252

Standard Operation Procedure (SOP) #7:
Training Field Personnel
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision; identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes general qualifications and training
procedures for implementing the Pacific Islands Stream Monitoring: Fish, Shrimp, Snails
and Habitat Characterization protocol. Training may be conducted on a yearly basis by
experienced PACN staff, for example the Aquatic Ecologist. In line with other
monitoring programs, such as the USGS NAWQA program, periodic training (every
three to five years) and review of the SOPs should be conducted in conjunction with
other experts (for example the authors of the protocol).
Review the protocol
The first step of the training procedure is to thoroughly read and understand the protocol
and especially the associated SOPs. All persons doing fieldwork should read the protocol
prior to beginning sampling, and should periodically review it (at a minimum it should be
reread each year). Field crews should always carry a copy of all the SOPs describing the
field activities for the location they will be sampling.
Species identification
For snorkeling surveys, all crew members doing sampling must be able to identify fish by
sight. Because shrimp and snails are collected, identification of these organisms can be
done using field guides. Currently, atyid shrimp in Guam are sent to a laboratory for
identification, so crew members do not need to be able to identify them.
The first step in learning to identify the fish, shrimp, and snails that will be surveyed
occurs in the office. Crew members should familiarize themselves with the entire native
and introduced organisms that they are likely to observe at the sampling site. Appendices
253

#1-4 provide pictures to assist in species identification and training. Waterproof copies of
these appendices should be carried in the field. Initially new crew members should
review the species on their own, and then receive training from an experienced observer
on key characteristics to assist in identification in the field.
The second step occurs in the field. Prior to conducting any surveys, all new crew
members should pair up with an experienced observer and work together on identifying
the species they observe while snorkeling in a reach of the stream that will not be part of
the actual sampling.
Conducting faunal surveys
Steps for conducting surveys are covered in detail in SOPs #8-21. Initially new crew
members should review the SOPs on their own, and then receive training in the office
prior to going to the field. Additional training on conducting surveys should occur at a
field site. Finally, prior to beginning the sampling each year, all steps for conducting
surveys for each taxonomic group should be practiced in a reach of the stream that will
not be part of the sampling. Training for conducting surveys should include not only the
actual surveying of fish, shrimp, and snails, but also proper data entry and field checking
of data sheets.
Conducting habitat assessments
Steps for conducting habitat assessments are covered in detail in SOP #23: “Habitat
Characterization at the Reach and Transect Scales.” Initially new crew members should
review the SOPs on their own, and then receive training in the office prior to going to the
field. Additional training on habitat assessments should occur at a field site. Finally, prior
to beginning the sampling each year, all steps for making habitat measurements should be
practiced in a reach of the stream that will not be part of the sampling. Training for
conducting surveys should include not only the actual habitat measurements, but also
proper data entry and field checking of data sheets.
Data Management
All persons involved with any aspect of data management should review Chapter 4 and
SOPs #25-31. Each year an in-office training should be conducted by the PACN data
manager, to review all data management activities.
Data Analysis and Reporting
All persons involved with any aspect of data analysis and reporting should review
Chapter 4 and SOP #32: “Data Analysis and Reporting”. An example report is provided
in Appendix #15: “Pacific Islands Stream Monitoring Report: Example Summary of Vital
Signs Data.” Assistance with data analysis and reporting efforts can be provided by the
PACN aquatic ecologist and authors of this protocol.
Other training
All crew members should be certified in first aid and CPR. A range of other training is
available nationally; from wilderness first aid and swift water rescue to advanced
statistical techniques for data analysis.
254

Standard Operation Procedure (SOP) #8:
Conducting Surveys on Tau, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
the general sampling order. This SOP will be used in American Samoa on the island of
Tau at NPSA.
Conducting surveys on Tau
1. Mark the reach. Each reach is thirty meters long following the thalweg of the
stream. The start of the reach (0 m) is marked with flagging tape on the bank
where the mark can be easily seen from the stream. Locations are then marked at
15 m and 30 m. At this point, it is also useful to divide the reach into five sections
for the shrimp surveys, therefore, sections will be also be marked at 6 m, 12 m, 18
m, and 24 m. It is important not to enter the stream when marking the reach. If it
is impossible not to enter the stream at any point during this procedure, stop and
wait for the fish and shrimp observers to finish their surveys before continuing to
mark the reach.
2. Mark the location using a Global Positioning System (GPS). See SOP #4: “Using
Garmin Global Positioning System (GPS) Units.”
3. Conduct water quality sampling. See Water Quality Monitoring Protocol. Water
quality nutrient samples and physical parameters are taken at the top of the reach
above the 30 m mark. Nutrient samples are taken only at fixed sampling stations.
Physical parameters are recorded at all fixed and temporary sampling stations.
4. Conduct the fish survey. See SOP #12: “Fish Surveys on Tau, American Samoa.”
It is important that the fish observers are the only people in the water while
conducting a survey in a given area.

255

5. Conduct the shrimp survey. See SOP #13: “Shrimp (ula vai) Surveys on Tau,
American Samoa”. It is important that the shrimp observers are the only people in
the water while conducting a survey in a given area.
6. Conduct the snail survey. See SOP #14: “Snail (sisi vai) Surveys on Tau,
American Samoa.” Snail observers use the same coordinate locations as the fish
observers. They work from downstream to upstream.
7. Conduct the habitat survey. See SOP #23: “Habitat Characterization at the Reach
and Transect Scales.”

256

Standard Operation Procedure (SOP) #9:
Conducting Surveys on Tutuila, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
the general sampling order. This SOP will be used in American Samoa on the island of
Tutuila at NPSA.
Conducting surveys on Tutuila
1. Mark the reach. Each reach is thirty meters long following the thalweg of the
stream. The start of the reach (0 m) is marked with flagging tape on the bank
where the mark can be easily seen from the stream. Locations are then marked at
15 m and 30 m. At this point, it is also useful to divide the reach into five sections
for the shrimp surveys, therefore, sections will be also be marked at 6 m, 12 m, 18
m, and 24 m. It is important not to enter the stream when marking the reach. If it
is impossible not to enter the stream at any point during this procedure, stop and
wait for shrimp observers to finish their surveys before continuing to mark the
reach.
2. Mark the location using a Global Positioning System (GPS). See SOP #4: “Using
Garmin Global Positioning System (GPS) Units.”
3. Conduct water quality sampling. See Water Quality Monitoring Protocol. Water
quality nutrient samples and physical parameters are taken at the top of the reach
above the 30 m mark. Nutrient samples are taken only at fixed sampling stations.
Physical parameters are recorded at all fixed and temporary sampling stations.
4. Snorkel surveys for fish are not conducted on the island of Tutuila. Stream mouths
are not safe for snorkeling due to potential contaminants from surrounding
villages. Upstream regions are too shallow to utilize snorkel surveys. Fish

257

presence is noted on site datasheets; however, fish are only identified and
measured if caught incidentally during shrimp survey.
5. Conduct the shrimp survey. See SOP #15: “Shrimp (ula vai) Surveys on Tutuila,
American Samoa.” It is important that the shrimp observers are the only people in
the water while conducting a survey in a given area.
6. Conduct the snail survey. See SOP #16: “Snail (sisi vai) Surveys on Tutuila,
American Samoa.” Snail observers use the same coordinate locations as the fish
and shrimp observers. They work from downstream to upstream
7. Conduct the habitat survey. See SOP #23: “Habitat Characterization at the Reach
and Transect Scales.”

258

Standard Operation Procedure (SOP) #10:
Conducting Surveys in Guam
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
the general sampling order. This SOP will be used in Guam at WAPA.
Conducting surveys in Guam
1. Mark the reach. Each reach is thirty meters long following the thalweg of the
stream. The start of the reach (0 m) is marked with flagging tape on the bank
where the mark can be easily seen from the stream. The reach is then divided into
five 6 meter sections, therefore, sections will be marked at 6 m, 12 m, 18 m, and
24 m, and 30 m. It is important not to enter the stream when marking the reach. If
it is impossible not to enter the stream at any point during this procedure, stop and
wait for the fish and shrimp observers to finish their surveys before continuing to
mark the reach.
2. Mark the location using a Global Positioning System (GPS). See SOP #4: “Using
Garmin Global Positioning System (GPS) Units.”
3. Conduct water quality sampling. See Water Quality Monitoring Protocol. Water
quality nutrient samples and physical parameters are taken at the top of the reach
above the 30 m mark. Nutrient samples are taken only at fixed sampling stations.
Physical parameters are recorded at all fixed and temporary sampling stations.
4. Conduct the fish survey. See SOP #17: “Fish (atot) Surveys in Guam.” It is
important that the fish observers are the only people in the water while conducting
a survey in a given area.
5. Conduct the shrimp survey. See SOP #18: “Shrimp (uhang) Surveys in Guam.” It
is important that the shrimp observers are the only people in the water while
conducting a survey in a given area.
259

6. Conduct the snail survey. See SOP #19: “Snail (akaleha) Surveys in Guam.” Snail
observers use the same coordinate locations as the fish observers. They work from
downstream to upstream.
7. Conduct the habitat survey. See SOP #23: “Habitat Characterization at the Reach
and Transect Scales.”

260

Standard Operation Procedure (SOP) #11:
Conducting Surveys in Hawaii
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
the general sampling order. This SOP will be used in Hawaii on the island of Maui at
HALE and on the island of Molokai at KALA.
Conducting surveys in Hawaii
1. Mark the reach. Each reach is thirty meters long following the thalwag of the
stream. The start of the reach (0m) is marked with flagging tape on the bank
where the mark can be easily seen from the stream. Locations are then marked at
15m and 30m. It is important not to enter the stream when marking the reach. If it
is impossible not to enter the stream at any point during this procedure, stop and
wait for the fish and shrimp observers to finish their surveys before continuing to
mark the reach.
2. Mark the location using a Global Positioning System (GPS). See SOP #4: “Using
Garmin Global Positioning System (GPS) Units.”
3. Conduct water quality sampling. See Water Quality Monitoring Protocol. Water
quality nutrient samples and physical parameters are taken at the top of the reach
above the 30m mark. Nutrient samples are taken only at fixed sampling stations.
Physical parameters are recorded at all fixed and temporary sampling stations.
4. Conduct the fish and shrimp survey. See SOP #20: “Fish (oopu) and Shrimp
(opae) Surveys in Hawaii.” It is important that the fish and shrimp observers are
the only people in the water while conducting a survey.
5. Conduct the snail survey. See SOP #21: “Snail (hihiwai) Surveys in Hawaii.”
Snail observers use the same coordinate locations as the fish and shrimp
observers. They work from downstream to upstream. The fish and shrimp
261

observer must be in a location where the snail observers will not disturb the fish.
For instance, the snail observers cannot begin their survey until the fish and
shrimp observer has finished their survey in a pool where the water would be
disturbed with another person in the water.
6. Conduct the habitat survey. See SOP #23: “Habitat characterization at the Reach
and Transect Scales.”

262

Standard Operation Procedure (SOP) #12:
Fish Surveys on Tau, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snorkeling survey for fish using a quadrat sampling design. This SOP will
be used in American Samoa on the island of Tau at NPSA.
Overview of sampling procedure
This procedure must be done first before other observers enter the water so as to
minimize disturbance to fish prior to sampling. Sampling moves from downstream to
upstream. A total of ten quadrats per reach will be surveyed. With two available
observers, two observers will conduct surveys simultaneously, one sampling six quadrats
and the other sampling four quadrats. With one observer available, the observer moves
upstream to sample all ten quadrats. Observer(s) identify and size/count all fish in the
quadrat in three minutes. Datasheets are included in Appendix #9: “Data Sheets:
American Samoa.”
Conducting a survey for fish
Within each reach ten random number pairs are generated using the Cartesian coordinate
system. The Y coordinate represents the distance in meters upstream between 0 and 30
(see Figure S.12.1). The X coordinate represents the distance in meters across the stream
and varies depending on the maximum width of the stream. This is done to avoid over
sampling the edges of the stream. X coordinates for the stream on Tau should be between
0 and 4. Coordinates should be ordered (Y, X) starting with Y=0 to facilitate movement
upstream. When facing upstream, 0 begins on the left bank. For example, a quadrat
location of (4,2) would be paced four meters upstream and two meters to the right of the
left bank when facing upstream. To count fish, an observer unobtrusively paces off the
263

meters to the appropriate quadrat location. Always approaching from downstream, the
observer carefully and quietly lowers into the water and, using mask and snorkel, moves
slowly toward the quadrat location. A one-meter-long thin metal wire is used to
determine the exact boundaries of the quadrat. The observer should lie as still as possible
for two minutes prior to beginning the survey in order to allow fish to return to the
quadrat. The observer records all fish within the quadrat during a three-minute time
period, noting species and size (total length from tip of nose to tip of tail) in cm. Observer
then proceeds to the next coordinate location by snorkeling slowly through the water.
Repeat procedure until all ten locations have been sampled.

Figure S.12.1: Snorkel survey sampling procedure on Tau.

264

Both native and introduced species should be noted within a quadrat. Additionally, if an
introduced species is seen in the stream, but is not in a quadrat it should be identified and
noted on the datasheet in a separate location. In general, introduced fish should be
collected and removed from the stream. If the species is not previously known from that
area it should be vouchered. If an introduced species is not able to be identified observers
should catch the specimen for expert identification.

265

Standard Operation Procedure (SOP) #13:
Shrimp (ula vai) Surveys on Tau, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason for
Change

Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a sectional shrimp survey. This SOP will be used in American Samoa on the
island of Tau in NPSA.
Overview of procedure
Sampling moves from downstream to upstream. The 30 m reach will be divided into five
sections each measuring six m. Sampling requires two observers collecting shrimp using
dip nets and/or opae nets as available. The same observers, or other observers if
available, measure and identify shrimp and record data. Datasheets are included in
Appendix #9: “Data Sheets: American Samoa.”
Conducting a survey for shrimp
The 30 m reach is divided into five six meter sections. Two observers utilize dip nets
and/or opae nets to catch as many shrimp as possible within a fifteen minute time period
in a given section. Observers can use a variety of strategies to catch shrimp depending on
the environment. One strategy would be to place the net downstream of a cascade and stir
up the substrate upstream of the net to dislodge smaller shrimp. Another strategy is to
pick up smaller rocks and leaves, as smaller atyid shrimp tend to hide under debris, and
guide shrimp into nets. Larger crustaceans can also be found in deeper pools. Observers
should sample a variety of substrate types to maximize the species diversity sampled.
Observers will need to carefully inspect each piece of debris (rock, leaf, stick, etc)
scooped up by the net in order to find shrimp. Shrimp can be as small as three cm and
relatively clear, therefore, net contents must be inspected thoroughly. Shrimp caught
within a section should be placed in a bucket with water from the site. Larger crustaceans
267

(Macrobrachium sp) and other shrimp that can be readily identified should be measured
in terms of total length (from tip of the rostrum to the tip of the tail). Once identified and
measured, shrimp should be returned to the stream. All other atyid shrimp that cannot be
confidently identified in the field are to be collected and placed in a marked sample jar
containing ethanol for later lab identification and analysis.
Introduced species
Introduced species should be noted on the datasheet. In general, introduced fish should be
collected and removed from the stream. If the species is not previously known from that
area it should be vouchered. If an introduced species is not able to be identified observers
should catch the specimen for expert identification.

268

Standard Operation Procedure (SOP) #14:
Snail (sisi vai) Surveys on Tau, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snail survey using a quadrat sampling design. This SOP will be used in
American Samoa on the island of Tau at NPSA
Overview of procedure
Sampling moves from downstream to upstream. A total of ten quadrats per reach will be
surveyed. Sampling requires one observer collecting snails, and a second observer
measuring snails and recording data. The observers first count egg capsules in a ¼ m2
area. The observers then proceed to collect and measure all snails, and count all postlarval snails called spat that measure less than 5 mm in the 1 m2 quadrat. Datasheets are
included in Appendix #9: “Data Sheets: American Samoa.”
Conducting a survey for snails
Within each reach, ten random number pairs are generated using the Cartesian coordinate
system. These number pairs are the same coordinates used to conduct the fish surveys.
The Y coordinate represents the distance in meters upstream between 0 and 30. The X
coordinate represents the distance in meters across the stream and varies depending on
the maximum width of the stream. X coordinates for streams on Tau should be between 0
and 4. Coordinates should be ordered using the Y coordinate starting with 0 to facilitate
movement upstream. When facing upstream, 0 begins on the left bank. To count snails
each observer paces off the meters to the appropriate quadrat location based on the
coordinate system and uses a thin one meter long metal wire to determine the exact
boundaries of the 1 m2 quadrat. The observer first counts all the eggs visible or under
rocks in the bottom left ¼ of the plot frame. Wearing a face mask and snorkel, the
269

observer collects all snails (visible or located between and beneath boulders) within the
quadrat and measures them with calipers. As demonstrated in Figure S.14.1, shell lengths
are measured to the nearest millimeter, as the longest distance between the apex (origin
of whorl) and the anterior margin (Ford 1979). All loose gravel, cobble, and rocks are
then removed and additional snails found within the quadrat are collected and measured.
Snails are returned to the stream after being measured. Place the snail so that it can
reattach to the substrate; don’t just toss it back in or it may be eaten by a prawn. The
number of post-larval snails [any snail < 5 mm (Ford 1979; Hodges 1992)] within each
quadrat is also recorded (counted).
Apex

Figure S.14.1. Measure the snail as the longest distance from the apex of the shell to the anterior
margin (indicated by the pink line).

270

Standard Operation Procedure (SOP) #15:
Shrimp (ula vai) Surveys on Tutuila, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a sectional shrimp survey. This SOP will be used in American Samoa on the
island of Tutuila in NPSA.
Overview of procedure
Sampling moves from downstream to upstream. The 30 m reach will be divided into five
sections each measuring 6 m. Sampling requires two observers collecting shrimp using
dip nets and/or opae nets. The same observers, or other observers if available, measure
and identify shrimp and record data. Datasheets are included in Appendix #9: “Data
Sheets: American Samoa.”
Conducting a survey for shrimp
The 30 m reach is divided into five 6 m sections. Two observers utilize dip nets and/or
opae nets to catch as many shrimp as possible within a fifteen minute time period in a
given section. Observers can use a variety of strategies to catch shrimp depending on the
environment. One strategy would be to place the net downstream of a cascade and stir up
the substrate upstream of the net to dislodge smaller shrimp. Another strategy is to pick
up smaller rocks and leaves, as smaller atyid shrimp tend to hide under debris, and guide
shrimp into nets. Larger crustaceans can also be found in deeper pools. Observers should
sample a variety of substrate types to maximize the species diversity sampled. Observers
will need to carefully inspect each piece of debris (rock, leaf, stick, etc) scooped up by
the net in order to find shrimp. Shrimp can be as small as 3 mm and relatively clear,
therefore, net contents must be inspected thoroughly. Shrimp caught within a section

271

should be placed in a bucket with water from the site. Larger crustaceans
(Macrobrachium sp) and other shrimp that can be readily identified should be measured
in terms of total length (from tip of the rostrum to the tip of the tail). All other atyid
shrimp that cannot be confidently identified in the field are to be collected and placed in a
marked sample jar containing ethanol for later lab identification and analysis. Note
quantity of shrimp placed in sample jar on datasheet.

272

Standard Operation Procedure (SOP) #16:
Snail (sisi vai) Surveys on Tutuila, American Samoa
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snail survey using a quadrat sampling design. This SOP will be used in
American Samoa on the island of Tutuila at NPSA
Overview of procedure
Sampling moves from downstream to upstream. A total of ten quadrats per reach will be
surveyed. Sampling requires one observer collecting snails, and a second observer
measuring snails and recording data. The observers first count egg capsules in a ¼ m2
area. The observers then proceed to collect and measure all snails, and count all postlarval snails called spat that measure less than 5 mm in the 1 m2 quadrat. Datasheets are
included in Appendix #9: “Data Sheets: American Samoa.”
Conducting a survey for snails
Within each reach, ten random number pairs are generated using the Cartesian coordinate
system. The Y coordinate represents the distance in meters upstream between 0 and 30.
The X coordinate represents the distance in meters across the stream and varies
depending on the maximum width of the stream. X coordinates for streams on Tutuila
should be between 0 and 4. Coordinates should be ordered using the Y coordinate starting
with 0 to facilitate movement upstream. When facing upstream, 0 begins on the left bank.
To count snails each observer paces off the meters to the appropriate quadrat location
based on the coordinate system and uses a thin one meter long metal wire to determine
the exact boundaries of the 1 m2 quadrat. The observer first counts all the eggs visible or
under rocks in the bottom left ¼ of the plot frame. Wearing a face mask and snorkel, the

273

observer collects all snails (visible or located between and beneath boulders) within the
quadrat and measures them with calipers. As demonstrated in Figure S.16.1, shell lengths
are measured to the nearest millimeter, as the longest distance between the apex (origin
of whorl) and the anterior margin (Ford 1979). All loose gravel, cobble, and rocks are
then removed and additional snails found within the quadrat are collected and measured.
Snails are returned to the stream after being measured. Place the snail so that it can
reattach to the substrate; don’t just toss it back in or it may be eaten by a prawn. The
number of post-larval snails [any snail < 5 mm (Ford 1979; Hodges 1992)] within each
quadrat is also recorded (counted).
Apex

Figure S.16.1. Measure the snail as the longest distance from the apex of the shell to the anterior
margin (indicated by the pink line).

274

Standard Operation Procedure (SOP) #17:
Fish (atot) Surveys in Guam
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snorkeling survey for fish using a quadrat sampling design. This SOP will
be used in Guam at WAPA.
Overview of sampling procedure
This procedure must be done first before other observers enter the water so as to
minimize disturbance to fish prior to sampling. Sampling moves from downstream to
upstream. A total of ten quadrats per reach will be surveyed. With two available
observers, two observers will conduct surveys simultaneously, one sampling six quadrats
and the other sampling four quadrats. With one observer available, the observer moves
upstream to sample all ten quadrats. Observer(s) identify and size/count all fish in the
quadrat in three minutes. Datasheets are included in Appendix #10: “Data Sheets:
Guam.”
Conducting a survey for fish
Within each reach ten random number pairs are generated using the Cartesian coordinate
system. The Y coordinate represents the distance in meters upstream between 0 and 30
(see Figure S.17.1). The X coordinate represents the distance in meters across the stream
and varies depending on the maximum width of the stream. This is done to avoid over
sampling the edges of the stream. X coordinates for the stream on Tau should be between
0 and 4. Coordinates should be ordered (Y, X) starting with Y=0 to facilitate movement
upstream. When facing upstream, 0 begins on the left bank. For example, a quadrat
location of (4,2) would be paced four meters upstream and two meters to the right of the

275

left bank when facing upstream. To count fish, an observer unobtrusively paces off the
meters to the appropriate quadrat location. Always approaching from downstream, the
observer carefully and quietly lowers into the water and, using mask and snorkel, moves
slowly toward the quadrat location. A one-meter-long thin metal wire is used to
determine the exact boundaries of the quadrat. The observer should lie as still as possible
for two minutes prior to beginning the survey in order to allow fish to return to the
quadrat. The observer records all fish within the quadrat during a three-minute time
period, noting species and size (total length from tip of nose to tip of tail) in cm. Eels
(asuli) as well as introduced fish should also be identified, sized, and noted on the
datasheet. Observer then proceeds to the next coordinate location by snorkeling slowly
through the water. Repeat procedure until all ten locations have been sampled.

Figure S.17.1. Conducting fish surveys in Guam.

276

Introduced species
Both native and introduced species should be noted within a quadrat. Additionally, if an
introduced species is seen in the stream, but is not in a quadrat it should be identified and
noted on the datasheet in a separate location. In general, introduced fish should be
collected and removed from the stream. If the species is not previously known from that
area it should be vouchered. If an introduced species is not able to be identified observers
should catch the specimen for expert identification.

277

Standard Operation Procedure (SOP) #18:
Shrimp (uhang) Surveys in Guam
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a sectional shrimp survey. This SOP will be used in Guam at WAPA.
Overview of procedure
Sampling moves from downstream to upstream. The 30 m reach will be divided into five
sections each measuring 6 m. Sampling requires an observer collecting shrimp using an
opae net or dip net as available. Another observer measures and identifies larger
crustaceans (Macrobrachium lar) and counts smaller atyid shrimp and places them in
marked sample jars filled with ethanol for later identification. Datasheets are included in
Appendix #10: “Data Sheets: Guam.”
Conducting a survey for shrimp
The 30 m reach is divided into five 6 m sections. One observer utilizes an opae net and/or
dip net to catch shrimp using three targeted scoops per section. A targeted scoop is
directed towards an area that appears to be suitable shrimp habitat. Generally, stream
edges near areas with roots, leaves, and tree trunks tend to provide good hiding places for
shrimp. Another strategy would be to place the net downstream of a cascade or riffle and
stir up the substrate upstream of the net to dislodge smaller shrimp. Also, observers can
pick up pebbles and leaves, as smaller atyid shrimp tend to hide under debris, and guide
shrimp into nets. Larger crustaceans can also be found in deeper pools. Observers should
sample a variety of substrate types to maximize the species diversity sampled. Observers
will need to carefully inspect each piece of debris (rock, leaf, stick, etc) scooped up by
the net in order to find shrimp. Shrimp can be as small as 3 cm and relatively clear,

279

therefore, net contents must be inspected thoroughly. Shrimp caught within a section
should be placed in a bucket with water from the site. Larger crustaceans
(Macrobrachium lar) that can be readily identified should be measured in terms of total
length (from tip of the rostrum to the tip of the tail) and returned to the stream. All other
shrimp that cannot be confidently identified in the field are to be collected and placed in a
marked sample jar containing ethanol for later lab identification and analysis.

280

Standard Operation Procedure (SOP) #19:
Snail (akaleha) Surveys in Guam
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snail survey using a quadrat sampling design. This SOP will be used in
Guam at WAPA.
Overview of procedure
Sampling moves from downstream to upstream. Five 6 m sections will be surveyed for
snails. This method is a full sectional search. Sampling requires one or two observers
collecting snails, and another observer onshore measuring snails and recording data. The
observers count egg capsules, collect snails, and count all post-larval snails (spat) that
measure less than 5 mm in each 6 m section. The onshore observer identifies and
measures snails and records data. Datasheets are included in Appendix #10: “Data
Sheets: Guam.”
Conducting a survey for snails
Each of five 6 m sections will be completely surveyed for snails. Ideally two observers
would be available to perform in-water counting and collecting simultaneously. One
observer can search the right bank to the center of the stream and the other can search the
left bank to the center of the stream in order to completely cover the stream. The in-water
observers count egg capsules found on and between rocks using mask and snorkel if
necessary. Observers should also pick up smaller rocks and count egg capsules that can
often be found underneath rocks. Observers tell the onshore recorder the number of egg
capsules counted per section. The in-water observers also count the number of post-larval
snails [any snail < 5 mm (Ford 1979; Hodges 1992)] within each section and inform the

281

onshore data recorder. Wearing a face mask and snorkel, the observer collects all snails
(visible or located between and beneath boulders) within the section and hands them to
the onshore recorder to identify and measure them with calipers. As demonstrated in
Figure S.19.1, shell lengths are measured to the nearest millimeter, as the longest distance
between the apex (origin of whorl) and the anterior margin (Ford 1979). All loose gravel,
cobble, and rocks are then removed and additional snails found within the section are
collected and measured. Snails are returned to the stream after being measured. Place the
snail so that it can reattach to the substrate; you may have to hold it in place for a short
time, don’t just toss it back in or it may be eaten by a prawn.
Apex

Figure S.19.1. Measure the snail as the longest distance from the apex of the shell to the anterior
margin (indicated by the pink line).

282

Standard Operation Procedure (SOP) #20:
Fish (oopu) and shrimp (opae) surveys in Hawaii
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snorkeling survey for fish and shrimp using a quadrat sampling design. This
SOP will be used at in Hawaii on the island of Maui at HALE and on the island of
Molokai at KALA.
Overview of sampling procedure
This procedure must be done first before other observers enter the water so as to
minimize disturbance to fish and shrimp prior to sampling. Sampling moves from
downstream to upstream. A total of ten quadrats per reach will be surveyed. With two
available observers, two observers will conduct surveys simultaneously, one sampling six
quadrats and the other sampling four quadrats. With one observer available, the observer
moves upstream to sample all ten quadrats. Observer(s) identify and size/count all fish
and shrimp in the quadrat in three minutes. Datasheets are included in Appendix #11:
“Data Sheets: Hawaii.”
Conducting a snorkel survey for fish and shrimp
Within each reach ten random number pairs are generated using the Cartesian coordinate
systems. The Y coordinate represents the distance in meters upstream between 0 and 30
(See Figure S.20.1). The X coordinate represents the distance in meters across the stream
and varies depending on the maximum width of the stream. This is done to avoid
oversampling the edges of the stream. X coordinates for streams in Hawaii should be
between 0 and 7. Coordinates should be ordered using the Y coordinate starting with 0 to
facilitate movement upstream. When facing upstream, 0 begins on the left bank. For

283

example, a quadrat location of (4,2) would be paced four meters upstream and two meters
to the right of the left bank when facing upstream. To begin the snorkel survey, an
observer unobtrusively paces off the meters to the appropriate quadrat location. Always
approaching from downstream, the observer carefully and quietly loers into the water
and, using mask and snorkel, moves slowly toward the quadrat location. A one-meterlong thin metal wire is used to determine the exact boundaries of the quadrat. The
observer should lie as still as possible to beginning the survey in order to allow fish to
return to the quadrat. The observer records all fish and crustaceans within the quadrat
during a three-minute period, noting species and size (total length from tip of nose to tip
of tail) in centimeters. Atyoida bisulcata (Opae kala ole) are recorded as a total number of
individuals with each quadrat

Figure S.20.1: Snorkel survey sampling procedure in Hawaii.

284

Conducting a survey in a pool
When a large pool is too deep or murky to see to the bottom, the edges are sampled. In
this case, use the y coordinates of the already selected points to determine the location
along the edge of the pool (see Figure S.20.2). Points should be as evenly divided
between both sides of the pool as possible. If the pool encompasses the entire reach, then
sample 5 quadrats on one side and 5 quadrats on the other. In this case, it is useful to have
two observers though one observer can sample all locations if necessary. A one-meterlong thin metal wire is placed at the edge of the pool so that the survey location is a one
meter square quadrat away from the edge. The observer enters the pool wearing mask and
snorkel as quietly as possible to approach the first location. The observer should lie as
still as possible for two minutes prior to beginning the survey in order to allow fish to
return to the quadrat. The observer records all fish and crustaceans within the quadrat
during a three-minute period, noting species and size (total length from tip of nose to tip
of tail) in centimeters. Atyoida bisulcata (`O`pae kala`ole) are counted and recorded as a
total number of individuals within each quadrat. If the pool does not encompass the entire
reach, all points after the end of the pool are treated normally. For example, if the pool is
twenty meters long and sites with a y coordinate greater than 20 would be sampled as
stated in the above paragraph.

Figure S.20.2. Snorkel survey in deep pool in Hawaii.

285

Introduced species
Both native and introduced species should be noted within a quadrat. Additionally, if an
introduced species is seen in the stream, but is not in a quadrat it should be identified and
noted on the datasheet in a separate location. In general, introduced fish should be
collected and removed from the stream. If the species is not previously known from that
area it should be vouchered. If an introduced species is not able to be identified observers
should catch the specimen for expert identification.

286

Standard Operation Procedure (SOP) #21:
Snail (hihiwai) Surveys in Hawaii
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes setting up a sampling station (reach) and
conducting a snail survey using a quadrat sampling design. This SOP will be used in
Hawaii on the island of Maui at HALE and on the island of Molokai at KALA.
Overview of procedure
Sampling moves from downstream to upstream. A total of 10 quadrats per reach will be
surveyed. Sampling requires one observer collecting snails, and a second observer
measuring snails and recording data. The observers first collect and measures all snails,
and count all post-larval snails called spat that measure less than 5mm then proceed to an
adjacent area to count egg capsules. Datasheets are included in Appendix #11: “Data
Sheets: Hawaii.”
Conducting a survey for snails
Within each reach ten random number pairs are generated using the Cartesian coordinate
system. These number pairs are the same coordinates used to conduct the fish and shrimp
surveys. The Y coordinate represents the distance in meters upstream between 0 and 30.
The X coordinate represents the distance in meters across the stream and varies
depending on the maximum width of the stream. X coordinates for streams in Hawaii
should be between 0 and 7. Coordinates should be ordered using the Y coordinate starting
with 0 to facilitate movement upstream. When facing upstream, 0 begins on the left bank.
To count snails each observer paces off the meters to the appropriate quadrat location
based on the coordinate system and places a thin wire ¼ m2 quadrat plot frame on the
stream bed. Wearing a face mask and snorkel, the observer collects all snails (visible or

287

located between and beneath boulders) within the quadrat and measures them with
calipers. As demonstrated in Figure S.21.1, shell lengths are measured to the nearest
millimeter, as the longest distance between the apex (origin of whorl) and the anterior
margin (Ford 1979). All loose gravel, cobble, and rocks are then removed and additional
snails found within the quadrat are collected and measured. Snails are returned to the
stream after being measured. Place the snail so that it can reattach to the substrate; don’t
just toss it back in or it may be eaten by a prawn. The number of post-larval snails [any
snail < 5 mm (Ford 1979; Hodges 1992)] within each quadrat is also recorded (counted).
After all snails in each quadrat are measured, the quadrat is flipped upstream and to the
right once in order to count unhatched egg capsules in an undisturbed 156 cm2 quadrat
(one-quarter of the plot frame).
Apex

Figure S.21.1. Measure the snail as the longest distance from the apex of the shell to the anterior
margin (indicated by the pink line).

288

Standard Operation Procedure (SOP) #22:
Electrofishing for fish and crustaceans
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes methods for using electrofishing to sample
fish and crustaceans on Tutuila (NPSA) and at WAPA. This is an optional activity, and
its use will be determined by the PACN Aquatic Ecologist. At this time, electrofishing is
not being used for monitoring following this protocol. Also, for this protocol, no
electrofishing will occur on Tau or in Hawaii.
Overview of procedure
Electrofishing requires a crew trained in both sampling techniques and safety procedures.
At least one crew member is required to have official training and certification for
electrofishing. All crew members must be certified in first aid and CPR. One person
wears the electrofisher, and two people collect fish and shrimp with large nets. Sampling
moves from downstream to upstream. The sampling reach for electrofishing is the same
reach where all other monitoring activities will occur. Additional information about
electrofishing is available in the Western EMAP protocol (Peck et al. 2006) and in the
Fisheries Techniques book (Nielsen and Johnson 1983). It is recommended that all crew
members who will electroshock read the chapter on Electrofishing by James Reynolds in
the Fisheries Techniques book. Information in this SOP comes primarily from Peck et al.
2006. The objective of this type of survey is to collect a representative sample of all
except very rare species in the assemblage. It is not to collect all individuals within the
reach. Sampling effort is allocated along the entire length of the reach. Backpack
electrofishers are used as the sampling gear.

289

Importance of safety during electrofishing
The use of electrofishing gear to collect fish and shrimp requires training to do it safely
and correctly to reduce the potential for injury or mortality to both humans and the
animals being collected. Primary responsibility for safety while electrofishing rests with
the sampling team leader. Electrofishing units can deliver a fatal electrical shock. While
electrofishing, avoid contact with water unless sufficiently insulated against electrical
shock. Use chest waders with nonslip soles and heavy rubber “linesmen” gloves. If you
perspire heavily, wear polypropylene or other wicking and insulating clothing instead of
cotton. If it is necessary for a team member to reach into the water to pick up something
that was dropped, do so only after the electrical current is off and the anode is removed
from the water. Crew members should keep each other in constant view or
communication while electrofishing.
Conducting an electrofishing survey
All people in the water should have on waders and gloves. One person wears the
electrofisher and two persons carry long-handled nets (made specifically for
electrofishing) to collect the fish. The netters position themselves one on each side, and
about ½ meter downstream of the person wearing the electrofisher. If additional crew
members are available they can help by carrying the buckets. Otherwise the netters are
also responsible for the buckets. Each bucket is filled halfway with stream water. Once a
bucket begins to get crowded with fish or shrimp a new bucket is used.
Begin sampling at the downstream end of the reach, and proceed in an upstream
direction. Start the electrofisher, set the timer, and depress the switch to begin collecting
organisms. It is important the settings on the electrofisher are adjusted properly to sample
effectively and minimize injury and mortality. Be sure to sample all habitats. In these
small streams a reach can be adequately sampled in about 30 minutes. Record voltage
settings, pulse rate, and time of sampling on a data sheet (this information is all available
on the electrofisher).
As fish and shrimp are temporarily stunned, the crew members scoop them up and place
them in a bucket. While the organisms are being transferred to the bucket, the
electrofisher should be off. Once the entire reach has been sampled, all of the fish and
shrimp in the buckets are identified and measured, and then returned to the stream
unharmed.
We do not recommend two or three pass sampling. One pass through the reach should be
adequate to characterize the fauna and estimate population abundance.

290

Standard Operation Procedure (SOP) #23:
Habitat characterization at the reach and transect scales
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase
incrementally by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major
revisions should be designated with the next whole number (e.g., version 2.0, 3.0, 4.0).
Record the previous version number, date of revision, author of the revision, identify
paragraphs and pages where changes are made, who approved the revision, and the
reason for making the changes along with the new version number.
Purpose
This Standard Operating Procedure describes the conducting of habitat characterization
work in each reach and transect. This protocol is consistent with previously established
habitat assessment techniques used by the national NAWQA and EMAP programs, and
users can refer to those documents for additional information. See Fitzpatrick et al. 1998
for NAWQA protocols; (http://water.usgs.gov/nawqa/protocols/bioprotocols.html), and
Section 7 in Peck et al. CITATION for EMAP protocols; (http://
www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/ewwsm_s7.pdf).
Datasheets are included in Appendices #9-11.

291

Figure S.23.1. Measuring habitat characteristics.

Procedures
The reach should capture the full sequence of geomorphic channel units that are present
in the stream segment. Reach length corresponds to the sampling reach for the fauna (30
meters). If possible, all physical habitat measurements should be made at each site on the
same day that faunal samples are conducted. Within each reach, six equally spaced
transects will be established perpendicular to the direction of flow (Figure S.23.1).
Habitat will be measured at three transects (transects 1, 3, and 5) in American Samoa, at
all six transects in Guam, and at three transects (transects 1, 3, and 5) in Hawaii. Physical
measurements of bank and riparian features and in-stream characteristics will be made at
each transect.
Curvilinear reach length
The reach should capture the full sequence of geomorphic channel units that are present
in the stream segment. Total reach length should be 30 meters. The curvilinear reach
length is measured by following the path of the thalweg (the part of the stream with the
deepest water and most flow). If there is no distinct thalweg, then follow the center of the
channel. In order not to disturb the fish and shrimp, it is important to set up the reach
following snorkeling surveys. If electrofishing is to occur in the reach, set up the reach
from the bank (do not enter the water prior to the electrofishing survey).
Distance between transects (complete characterization)
Three equidistant transects are spaced evenly within each reach in American Samoa and
Hawaii, whereas six equidistant transects are spaced evenly within each reach in Guam.

292

The distance between transects is the reach length (curvilinear reach length) divided by
two in American Samoa and Hawaii and five in Guam. The distance between transects is
measured by following the thalweg of the channel. If no thalweg is observable, follow the
center of the channel. Mark each transect with flagging tape or flag.
Geomorphic channel units (GCU)
Measure and record the length and identity of all geomorphic channel units (See
Appendices #9-11 for channel unit descriptions) along the length of the reach. Note on
the field sheet the measurement units used to determine GCU lengths, and whether you
started at the upstream or downstream end of the reach. This is typically the last step (to
avoid unnecessarily disturbing the reach) in physical habitat characterization.
At each transect record:
1) Habitat type. Dominant geomorphic channel unit across the transect.
2) Wetted channel width. Record the distance between the left and right edges of the
water.
3) Transect point measurements. Stretch a metric tagline or measuring tape from the
left bank to the right bank, perpendicular to the direction of flow, and secure each
end to the ground using a stake. Depth and velocity are recorded at the thalweg
(deepest part of the channel) and four additional equidistant points along the
transect.
a. Distance from left edge of water. The distance from the transect point to
the left edge (facing downstream) of water is recorded.
b. Depth. The depth of the stream is recorded at each transect point. The
depth is determined by measuring the distance between the water surface
and the bed substrate. Depth is measured using a wading rod. Note
whether the wading rod is in metric or English units.
c. Velocity. The velocity at the sampling location is measured using a flow
meter to record the 40-second average velocity of the water column.
Record type of flow meter used on the data sheet. Velocity is recorded at
60% depth when the depth is less than one meter. When depths are greater
than or equal to one meter, two velocity measurements are taken. One
measurement is taken at 20% depth and the other at 80% depth. The two
velocity measurements are then averaged.
4) Riparian canopy closure. Riparian canopy closure is measured at the bank on each
side of the stream using a concave spherical densiometer (Figure S.23.2). The
densiometer is modified by drawing a right angle on the mirror surface with an
indelible marker At the stream edge, the densiometer is held on the transect line
facing the bank, 30 cm from and 30 cm above the water’s edge. The measurement
is made by counting the number of point intersections (maximum is 17) covered
by vegetation (Figure S.23.3). Record this number on the data sheet. At transects
that are less than one meter in wetted width, one reading is made is the center of

293

the stream. For the center measurements, the densiometer is held 30 cm above the
water surface, halfway between the left and right edges of the water, while facing
upstream.
It is extremely important to keep the densiometer in the same position for each
reading. You may wish to use the measuring tape as a guide to maintain the
densiometer in the same position relative to the water’s edge as you rotate. It is
also important to keep the densiometer level using the bubble level and to view
the densiometer from the same angle with each reading. This can be accomplished
by positioning yourself so that the top of your forehead appears in the top-center
of the mirror as you make the reading.

Figure S.23.2. Using a spherical densiometer to measure riparian canopy closure.

Figure S.23.3. A concave spherical densiometer.

294

Note the tape marking the right angle (above which points are counted) on the
bubble level, and 17 points of intersection. Closed circles represent line
intersections where vegetation is present and consequently counted in
measurement of canopy closure, resulting in 11 out of 17 points (Fitzpatrick at el.
1998).
5) Pebble Count. The modified Wolman pebble count is a quantitative
measurement of channel-substrate particle size. Across each transect, 20 pebbles
should be collected and measured.
a. Begin the pebble count at each transect at the wetted edge on the left bank
and proceed to the wetted edge on the right bank.
b. Divide the width of the transect by the number of pebbles to be measured
to determine the interval length between points at which pebbles will be
counted. If the channel is narrow, you may traverse the transect multiple
times until twenty pebbles are measured; however, you must measure
pebbles across the entire channel with each traverse.
c. Using the measuring tape as a guide, aim your finger down vertically at
each sampling point and pick up the first pebble that you touch. If the
pebble is smaller than 0.1 cm, a value of “< 0.1cm” is recorded. If
possible, differentiate between sand and silt.
d. To reduce sampling bias, look across and not down at the channel bottom
when retrieving the pebble.
e. Measure each pebble across the longest axis.

295

Standard Operation Procedure (SOP) #24:
After Field Activities
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure describes procedures for the Project Lead Biological
Technician to follow after the field season. There are four subsections of this SOP: (1) returning
field equipment; (2) data sheets and data management; (3) summarizing field notes; and (4)
reporting scientific collecting activities. Note that additional information regarding data
management is provided in SOPs #25-34.
Procedures
Returning Field Equipment
1) Clean all equipment and gear before storage. Any problems with equipment or gear
should be reported to the crew leader.
2) Sign in and store field equipment. The crew leader should sign in all gear that was issued
at the beginning of the season. Any damaged equipment should be set aside to be repaired
or replaced; all other equipment should be properly stored.
3) Repair or replace damaged equipment. When possible, damaged equipment should be
repaired. Otherwise, damaged equipment should be replaced. The Project Lead is
responsible for making sure that all necessary equipment is functional and accounted for
before the next field season.

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Data Sheets
Proofread data sheets. Proofread the data sheets to ensure that they are complete and legible.
Although all data sheets should be reviewed for completeness in the field, some errors may not
be identified until later.
1) Mark corrections on copied data sheets with red pen. Corrected errors and changes made
on a data form should be circled using a red marker and initialed. A short explanation of
the change should be included in the margin of that form.
2) Photocopy data sheets. Ensure that all original datasheets have been photocopied and that
the originals and copies are stored in separate places.
3) Proofread copied data sheets. Proofread the copied datasheets to ensure that they are
complete and legible.
4) Indicate corrections from originals on copied data sheets with red pen. Corrected errors
and changes made on a data form should be circled using a red marker and initialed. A
short explanation of the change should be included in the margin of that form.
5) Archive original data sheets. Organize and file data sheets by sampling location.
6) Create or update database log. Include the date and name of the technician entering data.
Use the database log to keep notes on data entry, including suggestions for updates, errors
encountered, and who entered or proofread the data.
7) Finish entering any remaining data into the appropriate database.
8) Proofread data entry. After the data have been entered, a different person should
proofread the data from that year. Enter errors or changes into the database log.
9) Back up data entry files on an external drive that is periodically uploaded/exchanged by
the data manager.
Summarizing Field Notes
1) Identify and store all photos from field season.
2) Photocopy the field notes from all crew members. Store the copies of the field notes with
the original data sheets.
3) Compile trip reports from the sampling season. The crew leader should compile all
sampling reports that were written during the sampling season.
Preparing samples for transport
1) Decant each specimen jar after 24 hours in 95% alcohol.
2) Refill specimen jar with 95% alcohol. You only need enough alcohol to cover the
specimens (not the entire sample jar).
3) Decant each specimen jar a second time after 24 hours

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4) Refill specimen jar with 95% alcohol and leave in alcohol until shipping is ready to
begin. You only need enough alcohol to cover the specimens (not the entire sample jar).
5) Obtain export permit from the Fish and Wildlife Service. You will need to know
approximately how many specimens of each type you will have.
6) Obtain a certificate of origin from the local government natural resources division.
7) Make copies of the collection permit, the FWS export permit, and the certificate of
origin.
8) Call the lab specimens are being shipped to, so they can prepare to receive them. It is
important to know how many samples, how many boxes, and when the samples will be
expected to arrive.
9) Decant alcohol from the specimen jar and place cotton damp with alcohol in the
specimen jar to gently fill the void.
10) Place in shipping box(s) along with collection permit, certificate of origin, and FWS
export permit.
11) Call FWS to let them know the samples are being transported.
12) Mail package. It needs to arrive within 1 week from the last decanting. Lab will refill
with alcohol and process.
Reporting Scientific Collecting Activities
1) Prepare and submit reports. Prepare and submit reports for all scientific collecting
activities via the NPS Research Permit and Reporting System (RPRS) website
http://science.nature.nps.gov/research. In addition, prepare and submit a report for the
appropriate state or territorial agency.

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Standard Operation Procedure (SOP) #25:
Workspace Setup and Project Records Management
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure describes how to set up a project workspace, and describes
the PACN Digital Library which is used for archival of finished Pacific Islands Stream
Monitoring Protocol: Fish, Shrimp, Snails, and Habitat Characterization products.
Set up project workspace
A section of the networked PACN file server is reserved for this project, and access permissions
are established so that project staff members have access to needed files within this workspace.
Prior to each season, the Project Lead should make sure that network accounts are established for
each new staff member, and that the Data Manager is notified to ensure access to the project
workspace and databases. If network connections are too slow for efficient data entry and
processing, individual staff members may set up a workspace on their own workstation, with
periodic data transfer to the PACN server. Daily back ups of the workstation to an external hard
drive will ensure that no data is lost.
The recommended file structure within this workspace is shown in Figure 1. Certain folders –
especially those for GPS data and images – should be retained in separate folders for each
calendar year as shown in Figure S.25.1. This will make it easier to identify and move these files
to the project archives at the end of each season (see Chapter 4: Season Close-out).

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Figure S.25.1. Recommended file structure for the Freshwater Animal Communities, Streams project
workspace.

.
Images that are to be linked to the database have to be in the folders as designated in Figure 2.
This will insure that when the images and database are moved that the links to the files will be
updated in the database. The database must be in the data folder for the links to work.
Within the Database folder there should be a folder called “Database_images”. Within this folder
should be a folder for the current monitoring year. The year folder will have a folder for each
park. Images that are to be linked to the database should be organized into folders by date of
sampling event and placed in the appropriate folder for the year and park. All other images
should go into the image folder in the main directory.
Flowtracker data that will be linked to the database should be placed in the folder called
“Flowtracker_pdfs” (see Figure S.25.2). Within this folder should be a folder for the current
monitoring year. Each of the year folders will have a folder for each park. The flowtracker .pdf
files should be organized into folders by date of sampling event and placed in the appropriate

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folder for the year and park. Make sure these files are placed in the correct folders before linking
to the database.
Following these steps will ensure that the files will be re-linked to the database upon moving as
long as the structure is maintained.

Figure S.25.2. Required file structure for images and flowtracker data linked to the Freshwater Animal
Communities, Streams database.

Each major subfolder is described as follows:
1) Analysis – Contains working files associated with data analysis.

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2) Data – Contains subfolders to categorize project data and the working database file
for the season. The master database for the project is stored in the PACN Digital
Library.
3) Documents – Contains subfolders to categorize documents as needed for various
stages of project implementation.
4) Images – For storing images associated with the project (refer to SOP #29:
“Managing Photographic Images”). Note that this folder contains subfolders to
arrange files by year.
5) Spatial info – Contains subfolders that arrange files relating to visualizing and
interacting with GIS data by year and layers. Yearly folders are broken down into the
following
subfolders
a. ArcMap documents – Map products.
b. GIS data – New working shapefiles and geodatabases specific to the project.
c. GPS data – Contains GPS data dictionaries, and raw and processed GPS data
files.
d. File naming conventions for files in this folder are as follows:
 YYYYMMDD_Park Code_site type_temp (temp stations, plots, etc)
Example: 20100121_WAPA_stream_temp.mxd
 Park Code_site type_fixed (fixed stations, plots, etc.) Example:
KAHO_marine_fixed.shp
Naming Conventions
Folder Naming Standards
In all cases, folder names should follow these guidelines:
1) No spaces or special characters in the folder name.
2) Use the underbar (“_”) character to separate words in folder names.
3) Try to limit folder names to 20 characters or fewer.
4) Dates should be formatted as YYYYMMDD.
File Naming Standards
In all cases, file names should follow these guidelines:
1) No spaces or special characters in the file name.
2) Use the underbar (“_”) character to separate file name components.
3) Try to limit file names to 30 characters or fewer, up to a maximum of 50 characters.
4) Dates should be formatted as YYYYMMDD.

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5) Correspondence files should be named as YYYYMMDD_AuthorName_subject.ext.
Archival and records management
All project files should be reviewed, cleaned up, and organized by the Project Lead on a regular
basis (e.g., annually in January). Decisions on what to retain and what to destroy should be made
following guidelines stipulated in NPS Director’s Order 19 7, which provides a schedule
indicating the amount of time that the various kinds of records should be retained. Although
many of the files for this project may be scheduled for permanent retention, it is important to
isolate and protect these important files and not lose them in the midst of a large, disordered
array of miscellaneous project files. Because this is a long-term monitoring project, good records
management practices are critical for ensuring the continuity of project information. Files will be
more useful to others if they are well organized, well named, and stored in a common format. In
addition, it is important that files containing sensitive information be stored in a manner that will
enable quick identification. Refer to SOP #33: “Sensitive Information Procedures” for more
information.
To help ensure safe and organized electronic file management, PACN has implemented a system
called the PACN Digital Library, which is a hierarchical digital filing system stored on the
PACN file servers. The typical arrangement is by project, then by year to facilitate easy access.
Network users have read-only access to these files, except where information sensitivity may
preclude general access. Submission of certified products occurs in the PACN Digital Library by
uploading the certified products in the “Submissions” folder and notifying the Data Manager.
As digital products are delivered for long-term storage according to the schedule in SOP #30:
“Product Delivery Specifications”, they will be catalogued in the PACN project tracking
database and filed within the PACN Digital Library by the Data Manager. The master versions of
all digital files relating to the Freshwater Animals Communities, Streams protocol are stored
within the PACN Digital Library, with regular file back-ups accomplished automatically.
Presently, the master protocol files include the protocol narrative, the SOPs, and the Freshwater
Animal Communities, Streams database files. Analog (non-digital) materials are to be handled
according to current practices of the individual park collections.
Archived Data Maintenance
Any editing of archived data is accomplished jointly by the Project Lead or designee and PACN
Data Manager. Prior to any major changes of a dataset, a copy is stored with the appropriate
version number to allow for tracking of changes over time. Likewise, any time a revision of the
protocol requires a revision to the database, a complete copy of the database will be made and
stored in an archive directory. In addition to this copy in its native database format, all tables will
be archived in a comma-delimited ASCII format that is platform-independent by using the
Access_to_ascii.mdb utility developed by Northern Colorado Plateau Network.
Versioning of archived datasets is handled by adding a three digit number to the file name, with
the first version being numbered 001 (e.g.,
freshwater_animal_streams_be_2008_validated_v001, for the first version of a back-end data file
7

http://www.nps.gov/refdesk/DOrders/DOrder19.html

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validated by the Project Lead and Data Manager at the end of the 2008 field season). The two
text files generated by the Access_to_ascii.mdb utility, FieldDef.txt and TableDef.txt, will be
stored in a similarly named folder (e.g.,
freshwater_animal_streams_be_2008_validated_v001_text). Each additional version is assigned
a sequentially higher number. Frequent users of the data are notified of the updates, and provided
with a copy of the most recently archived version.
Every change must be documented in the edit log and accompanied by an explanation that
includes pre- and post-edit data descriptions. All data collected using this protocol are subject to
the following three caveats:
1) Only make changes that improve or update the data while maintaining data integrity.
2) Once archived, document any changes made to the data set through an edit log. At end of
each fiscal year, the database manager will update the central database and will post readonly versions.
3) Mistakes can be made during editing so updates must be compared with the original data
form prior to validating the data.

306

Standard Operation Procedure (SOP) #26:
Data Entry and Verification
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document describes the general procedures for entry and
verification of field data in the working project database. Refer to protocol sections Overview of
Database Design and Data Entry and Processing for related guidance and a clarification of the
distinction between the working database and the master database.
Data Entry
The following are general guidelines to keep in mind:
1) Data entry will be conducted by the Field Lead at his or her duty station.
2) Data entry should occur as soon after data collection as possible so that field crews keep
current with data entry tasks, and catch any errors or problems as close to the time of data
collection as possible.
3) The working database application will be found in the project workspace. The project
workspace may be on the user’s computer if the connection to the networked server is too
slow (see SOP #25: “Workspace Setup and Project Records Management”), with periodic
uploads to the network server. If the workspace resides on the networked server, it is
recommended that users copy the front-end database onto their workstation hard drives
and open it there for enhanced performance. This front-end copy may be considered
“disposable” because it does not contain any data, but rather acts as an interface with data
residing in the back-end working database.

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4) Each data entry form is patterned after the layout of the field form, and has built-in
quality assurance components such as pick lists and validation rules to test for missing
data or illogical combinations. Although the database permits users to view the raw data
tables and other database objects, users are strongly encouraged only to use the pre-built
forms as a way of ensuring the maximum level of quality assurance.
5) As data are being entered, the person entering the data should visually review each data
form to make sure that the data on-screen match the field forms. This should be done for
each record prior to moving to the next form for data entry.
6) After each data entry session, the Field Lead should upload the working copy of the
database onto the networked server if the database has been stored on their computer.
Data Verification
Data verification checks that the digitized data match the source data. The following guidelines
regarding data verification should be followed:
1. Project leaders are responsible for specifying in the project protocol one or more of the
data verification methods available and ensuring proper execution. At the discretion of
the project leader, additional verification methods may be applied.
2. Data verification is carried out by staff thoroughly familiar with data collection and entry.
3. All records (100%) should be verified against original source data using the method
below.
a) Visual review after data entry: Upon completion of data entry, all records are printed
and compared with the original values from the hard copy. Errors are clearly marked
and corrected in the database as soon after data entry as possible. Reliability increases
if someone other than the person keying the data performs the review. Alternatively,
two technicians (one reading from the original data and one checking the entered
data) can perform this review.
4. A subset of randomly selected records (10%) should be reviewed after initial verification
by the project leader. If errors are found, the entire data set should be verified again.
5. A record of the verification process for each data set, including number of iterations and
results, will be prepared by the project leader as part of formal metadata generation.
6. Spatial data collected as part of the project will be viewed in a GIS and visually inspected
for accuracy (e.g., points located outside park boundaries, upland locations occurring in
water).
Database Instructions
The first action to take is to make sure the data entry workspace is set up properly, either on a
networked drive or the user’s computer (if networked server connections are too slow for
efficient data entry). If you are unclear about where the data entry workspace should be, contact
the Data Manager (see SOP #25: “Workspace Setup and Project Records Management” for more
information).
1) Store the back-end database file in the database folder in the project workspace. The
back-end file has “_be_” as part of its name.

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2) The user’s copy of the front-end database should also be stored in the same folder.
3) If it doesn’t already exist, also create a folder in the same folder named “backups” for
storing daily backups of the back-end database file.
4) Open the front-end database. The first thing it will do is to ask to update the links to the
back-end database file. This will only need to be done once for each new issue of the
front-end database.
Important Reminders for Daily Database Use
1) A copy of the front-end will need to be copied to your workstation if the project
workspace is set up on the networked server. Do not open up and use the front-end on the
network as this ‘bloats’ the database file and makes it run more slowly.
2) The front-end application will automatically prompt you to make a backup upon initially
opening the application.
3) To save drive space and network resources, backup files should be compacted by rightclicking on the backup file in Windows Explorer and selecting the option: “Add to Zip
file”. Older files may be deleted at the discretion of the Field Lead.
4) New issues of the front-end application may be released as needed through the course of
the field season. If this happens, there should be no need to move or alter the back-end
file. Instead, the front-end file may be deleted and replaced with the new version, which
will be named in a manner reflecting the update (e.g.,
freshwater_animal_streams_be_2008_v2.mdb).
5) If the front-end database gets bigger and slower, compact it periodically by selecting
Tools > Database Utilities > Compact and Repair Database.
Working Database Functions
The working front-end application has the following functional components, which are accessed
from the main application switchboard form that opens automatically when the application starts:
Data Entry and Review
1) Data entry/edit: After verifying default settings (e.g., park, coordinate datum) the data
gateway form will open. From here, data for a particular sampling date and location can
be reviewed and edited if necessary. By choosing the option “Add a New Record” the
data entry form will open and new data may be entered.
2) Quality assurance tools: opens a form that shows the results of pre-built queries that
check for data integrity, missing data, and illogical values, and allows the user to fix these
problems and document the fixes. See SOP #27: “Post-season Data Quality Review and
Certification.”

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Other Functions
1) Manage lookups: opens a tool for managing the lookup values for the project data set
(e.g., species list, list of project personnel)
2) View database window: allows the user to view the database objects (tables, queries and
forms)
3) Back up data: creates a date-stamped copy of the back-end database file
4) Connect back-end database: Verifies the connection to the back-end working database
file, and provides the option to redirect or update that connection
5) Set system defaults: for example, user name, declination, current park, coordinate datum
6) View release history: opens a form describing known bugs and changes made to the
front-end database since its first release
General Use Instructions
To view detailed instructions for entering and editing data, see Appendix X: Freshwater Animal
Communities, Streams Monitoring Database User’s Guide.

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Standard Operation Procedure (SOP) #27:
Post-season Data Quality Review and Certification
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document describes the procedures for validation and
certification of data in the working project database. Refer also to protocol sections in Chapter 4
(Overview of Database Design, Quality Review, and Data Certification and Delivery) for related
guidance and a clarification of the distinction between the working database and the master
database.
After the season’s field data have been entered and processed, they need to be reviewed and
certified by the Project Lead for quality, completeness and logical consistency. Data validation is
the process of checking data for completeness, logical consistency, and structural integrity. The
working database application facilitates this process by showing the results of pre-built queries
that check for data integrity, data outliers and missing values, and illogical values. The user may
then fix these problems and document the fixes.
Data Quality Review
At the end of each field season, the Project Lead and the PACN data management staff are
collectively responsible for finalizing a validated dataset for that field season. The Project Lead
will complete all data validation. Some validation (ensuring that the data make sense) methods
have been incorporated into the Stream Macrofauna database. Other, more specific validation
routines will be worked out with the Project Lead and/or project staff and incorporated into the
database as appropriate. These modifications will be described in the edit log and the
functionality of the validation routines will be explained in detail in the Stream Macrofauna
Database User Guide.

311

Completing Data Certification
Data certification is a benchmark in the project information management process that indicates:
1) the data are complete for the period of record, 2) the data have undergone and passed the
quality assurance checks, and 3) that the data are appropriately documented and in a condition
for archiving, posting and distribution as appropriate. Certification is not intended to imply that
the data are completely free of errors or inconsistencies which may or may not have been
detected during quality assurance reviews.
To ensure that only quality data are included in reports and other project deliverables, the data
certification step is an annual requirement for all tabular and spatial data. Once the data have
been through the validation process and metadata have been developed for them, they are to be
certified by completing the PACN Project Data Certification Form 8, available on the PACN
website. The Project Lead is primarily responsible for completing this form. The completed
form, certified data, and updated metadata may then be delivered to the Data Manager according
to the timeline in Appendix #12: “Yearly Project Task List”. Refer to SOP #30: “Product
Delivery Specifications” for delivery instructions.

8

http://www1.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Project_Data_Certification_Form.doc

312

Standard Operation Procedure (SOP) #28:
Field Form Handling Procedures
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure describes how to process field data forms.
Field form handling procedures
As the field data forms are part of the permanent record for project data, they should be handled
in a way that preserves their future interpretability and information content. If changes to data on
the forms need to be made either during or after field data acquisition, the original values should
not be erased or otherwise rendered illegible. Instead, changes should be made as follows:
1) Draw a horizontal line through the original value, and write the new value adjacent to the
original value with the date and initials of the person making the change.
2) All corrections should be accompanied by a written explanation in the appropriate notes
section on the field form. These notes should also be dated and initialed.

3) If possible, edits and revisions should be made in a different color ink to make it easier
for subsequent viewers to be able to retrace the edit history.
4) Edits should be made on the original field forms and on any photocopied forms.
These procedures should be followed throughout data entry and data revision. After each tour,
data sheets are to be scanned as PDF documents and placed in the project workspace folder
assigned to data forms (see SOP #25: “Workspace Setup and Project Records Management” for

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more details). These digital files will be archived with the certified data according to SOP #30:
“Product Delivery Specifications”. The PDF files may then serve as a convenient digital
reference of the original if needed.

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Standard Operation Procedure (SOP) #29:
Managing Photographic Images
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document describes how to process photographic images
collected by project staff or volunteers during the course of conducting project-related activities.
Images that are acquired by other means – e.g., downloaded from a website or those taken by a
cooperating researcher – are not project records and should be handled separately.
Care should be taken to distinguish data photos from incidental or opportunistic photos taken by
project staff. Data photos are those taken for at least one of the following reasons:
1) to document a particular feature or perspective for the purpose of site relocation
2) to capture site habitat characteristics and possibly to indicate gross structural changes
over time
3) to document a species detection that is also recorded in the data
Data photos are linked to specific records within the database, and are stored in a manner that
permits the preservation of those database links. Other photos—e.g., of field crew members at
work, or photos showing fish, shrimp, or snails—may also be retained but are not necessarily
linked with database records.
Effectively managing hundreds of photographic images requires a consistent method for
downloading, naming, editing, and documenting. The general process for managing data photos
proceeds as follows:

315

1) File Structure Setup – Set up the file organization for images prior to acquisition
2) Image Acquisition
3) Download and Process
a. Download the files from the camera
b. Rename the image files according to convention
c. Copy and store the original, unedited versions
d. Review and edit or delete the photos
e. Move into appropriate folders for storage
4) Establish Database Links
5) Deliver Image Files for Final Storage
File Structure Setup
Prior to data collection for any given year, project staff will need to set up a new folder under the
Images folder in the project workspace as follows:
[Year]
_Processing
_Ricoh_memos
[Park code]
[Park code]
Data
[Site_code]
[Date]
Miscellaneous
[Site_code]
[Date]
Originals
[Site_code]
[Date]
Ricoh_Camera

The appropriate year – 2008, 2009, etc.
Processing workspace
Memos to be loaded onto the Ricoh GPS camera
Arrange files by park – HAVO, NPSA, etc.
Arrange files by park – HAVO, NPSA, etc.
Data images
Arranged by sampling locations, or
by date, for images not taken at sampling locations
Non-data images taken by project staff
Arranged by sampling locations, or
by date, for images not taken at sampling locations
Renamed but otherwise unedited image file copies
Arranged by sampling locations, or
by date, for images not taken at sampling locations
Arranged by sampling locations and date

This folder structure permits data images to be stored and managed separately from non-record
and miscellaneous images collected during the course of the project. It also provides separate
space for image processing and storage of originals. Note: For additional information about the
project workspace, refer to SOP #25: “Workspace Setup and Project Records Management.”
Folder Naming Standards
In all cases, folder names should follow these guidelines:
1) No spaces or special characters in the folder name
2) Use the underscore (“_”) character to separate words in folder names

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3) Try to limit folder names to 20 characters or fewer
4) Dates within folder names should be formatted as YYYYMMDD (for better sorting)
Image Acquisition
Capture images at an appropriate resolution that balances space limitations with the intended use
of the images. Although photographs taken to facilitate future navigation to the site do not need
to be stored at the same resolution as those that may be used to indicate gross environmental
change at the site, it may be more efficient to capture all images at the same resolution initially.
A recommended minimum raw resolution is 1600 x 1200 pixels (approximately 2 megapixels).
Download and Processing Procedures
1) Download the raw, unedited images from the camera into the appropriate “_Processing”
folder.
2) Rename the images according to convention (refer to the image file naming standards
section below). If image filenames were noted on the field data forms, be sure to update
these to reflect the new image filename prior to data entry. See SOP #28: “Field Form
Handling Procedures.”
3) Process the images in the “_Processing” folder. At a minimum, the following processing
steps should be performed on all image files:
a. Copy the images to the “Originals” folder and set the contents as read-only by
right clicking in Windows Explorer and checking the appropriate box. These
originals are the image backup to be referred to in case of unintended file
alteration or deletion.
b. Delete any poor-quality photos, repeats, blurred or otherwise unnecessary photos.
Low-quality photos might be retained if the subject is highly unique, or the photo
is an irreplaceable data photo.
c. Rotate the image to make the horizon level.
d. Photos of people should have red eye glare removed.
e. Photos should be cropped to remove edge areas that grossly distract from the
subject.
4) When finished, move the image files that are to be retained and possibly linked in the
database to the appropriate folder – data images under the Data folder, other images
under the Miscellaneous folder. Photos of interest to a greater audience should be copied
to the PACN Digital Library\Photo Archive folder. Metadata associated with the image
should be entered into the ThumbsPlus application. To minimize the chance for
accidental deletion or overwriting of needed files, no stray files should remain in the
processing folder between downloads.
5) Depending on the size of the files and storage limitations, contents of the Originals folder
may be deleted if all desired files are accounted for after processing.
Large groups of photos acquired under suboptimal exposure or lighting can be batch processed to
enhance contrast or brightness. Batch processing can also be used to resize groups of photos for
use on the web. Batch processing may be done in ThumbsPlus, Extensis Portfolio or a similar
image software package.

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Image File Naming Standards
In all cases, image names should follow these guidelines:
1) No spaces or special characters in the filename
2) Use the underscore (“_”) character to separate file name components
3) Try to limit filenames to 30 characters or fewer, up to a maximum of 50 characters
4) Park code and year should either be included in the filename or conclusive by the
directory structure
The image file name should consist of the following parts:
1) The date of data capture (formatted as YYYYMMDD)
2) The sampling location (if recorded at a sampling location)
3) Optional: a brief descriptive word or phrase
4) Optional: a sequential number if multiple images were captured
5) Optional: time (formatted as HHMM)
Examples:
1) 20070621_Waihanau_habitat_001.jpg: The habitat at Waihanau Valley taken on June 21,
2007
2) 20070518_training_004.jpg 4th photo taken during training on May 18, 2007
In cases where there are few photos it is practical to individually rename these files. However,
for larger numbers it may be useful to rename files in batches. This may be done in ThumbsPlus,
Extensis Portfolio or a similar image software package. A somewhat less sophisticated
alternative is to batch rename files in Windows Explorer, by first selecting the files to be
renamed and then selecting File > Rename. The edits made to one file will be made to all others,
although with the unpleasant side effect of often adding spaces and special characters (e.g.,
parentheses) which will then need to be removed manually.
Renaming photos may be most efficient as a two-part event—one step performed as a batch
process which inserts the date and transect number at the beginning of the photo name, and a
second step in which a descriptive component is manually added to each filename.
Establish Database Links
During data entry and processing, the database application will provide the functionality required
to establish a link between each database record and the appropriate image file(s). To establish
the link, the database prompts the user to indicate the root project workspace directory path, the
specific image folder within the project workspace, and the specific file name. This way, the
entire workspace may be later moved to a different directory (i.e., the PACN Digital Library) and

318

the links will still be valid after changing only the root path. Refer to SOP #25: “Workspace
Setup and Project Records Management” and SOP #26: “Data Entry and Verification” for
additional details on setting up the database images structure and establishing these links.
Note: It is important that the files keep the same name and relative organization once these
database links have been established. Users should not rename or reorganize the directory
structure for linked image files without first consulting with the Data Manager.
Deliver Image Files for Final Storage
Please refer to SOP #30: “Product Delivery Specifications.”
At the end of the season, and once the year’s data are certified, data images for the year may be
delivered along with the working copy of the database to the Data Manager on an external
drive.To do this, simply copy the folder for the appropriate year(s) and all associated subfolders
and images onto the disk. These files will be loaded into the project section of the PACN Digital
Library, and the database links to data images will be updated accordingly.
Prior to delivery, make sure that all processing folders are empty. Upon delivery, the delivered
folders should be made read-only to prevent unintended changes.

319

320

Standard Operation Procedure (SOP) #30:
Product Delivery Specifications
Version 1.01
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document provides details on the process of submitting
completed data sets, reports, and other project deliverables. Prior to submitting digital products,
files should be named according to the naming conventions appropriate to each product type (see
below for general naming conventions).
All digital file submissions that are sent by email should be accompanied by a Product
Submission Form 9, which briefly captures the following information about the products:
1) Submission date
2) Name of the person submitting the product(s)
3) Name and file format of each product
4) Indication of whether or not each product contains sensitive information (see SOP #33:
“Sensitive Information Procedures” for more detail).
The Product Submission Form 10 can be obtained from the Data Manager or from the PACN
website. Upon notification and/or receipt of the completed products, the Data Manager or GIS
Specialist will check them into the PACN project tracking application.
9

http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Product_Submissions_Form.doc
http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Product_Submissions_Form.doc

10

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Table S.30.1. Product delivery schedule and specifications.

Deliverable Product
Field season report

Primary
Responsibility
Project Lead

Raw GPS data files

Field Lead

September 15 of the
same year

Processed GPS data files

GIS Specialist

Digital photographs

Project Lead

September 15 of the
same year
November 30 of the
same year

Certified working database
Certified geospatial data

Project Lead
Project Lead with
GIS Specialist
Project Lead
Project Lead
Data Manager and
GIS Specialist

November 30 of the
same year

Annual I&M report

Project Lead

5-year analysis report

Field data forms

Project Lead, Data
Analyst
Project Lead, Data
Analyst
Project Lead

April 30 of the
following year
Every 5 years by
April 30
as completed

Other records

Project Lead

Data certification report
Metadata interview form
Full metadata (parsed XML)

Other publications

Target Date
September 15 of the
same year

March 15 of the
following year

Every 5 years by
April 30

review for retention
every January

Instructions
Upload digital file in MS Word
1
format to the PACN Digital Library
submissions folder.
Zip and send all digital files to the
GIS Specialist who will post them to
1
the PACN Digital Library .
Zip and upload files to the PACN
1
Digital Library .
Organize, name and maintain
photographic images in the project
workspace according to SOP #29:
“Managing Photographic Images.”
Refer to the following section on
delivering certified data and related
materials. Data will be uploaded to
2
the IRMA Portal , and stored in the
1
PACN Digital Library .
Upload the parsed XML record to
2
the IRMA Portal , and store in the
1
PACN Digital Library .
Refer to the following section on
reports and publications. Final
reports will be entered in IRMA
2
Portal , and stored in the PACN
1
Digital Library .
Scan original, marked-up field
forms as PDF files and upload
1
these to the PACN Digital Library
submissions folder. Originals go to
the park curator for archival.
Organize and send analog files to
park curator for archival. Digital files
that are slated for permanent
retention should be uploaded to the
PACN Digital Library. Retain or
dispose of records following NPS
3
Director’s Order #19 .

1

The PACN Digital Library is a hierarchical digital filing system stored on the PACN file servers. Network users
have read-only access to these files, except where information sensitivity may preclude general access.
2
The IRMA Portal is a clearinghouse for natural resource data, metadata, bibliographic records, and park species
information (http://irma.nps.gov/App/Portal/Home). Only non-sensitive information is posted to the IRMA Portal.
Refer to the protocol section on sensitive information for details.
3 NPS Director’s Order 19 provides a schedule indicating the amount of time that the various kinds of records
should be retained. Available at: http://data2.itc.nps.gov/npspolicy/DOrders.cfm

Specific Instructions for Delivering Certified Data and Related Materials
Data certification is a benchmark in the project information management process that indicates
that: 1) the data are complete for the period of record; 2) they have undergone and passed the
quality assurance checks; and 3) that they are appropriately documented and in a condition for

322

archiving, posting and distribution as appropriate. To ensure that only quality data are included
in reports and other project deliverables, the data certification step is an annual requirement for
all tabular and spatial data. For more information refer to SOP #27: “Post-Season Data Quality
Review and Certification.”
The following deliverables should be delivered as a package:
1) Certified working database – Database in MS Access format containing data for the
current season that has been through the quality assurance checks documented in SOP
#27: “Post-Season Data Quality Review and Certification.”
2) Certified geospatial data – GIS themes in ESRI coverage or shapefile format.
3) Data certification form – A brief questionnaire in MS Word that describes the certified
data product(s) being submitted. A template form is available on the PACN website
(http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Project_Data_Certifica
tion_Form.doc).
4) Metadata interview form – The metadata interview form is an MS Word questionnaire
that greatly facilitates metadata creation. This form is available on the PACN website
(http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Metadata_Interview_F
orm.doc). For more details, refer to SOP #31: “Metadata Development.”
After the quality review is completed, the Project Lead should package the certification materials
for delivery as follows:
1) Open the certified back-end database file and compact it (in Microsoft Access, Tools >
Database Utilities > Compact and Repair Database). This will make the file size much
smaller. Back-end files are typically indicated with the letters “_be” in the name (e.g.,
stream_macrofauna_be_2007.mdb).
2) Rename the certified back-end file with the project name (“stream_macrofauna”), the
year or span of years for the data being certified, and the word “certified”. For example:
stream_macrofauna_2007_certified.mdb.
3) Create a compressed file (using WinZip or similar software) and add the back-end
database file to that file. Note: The front-end application does not contain project data
and as such should not be included in the delivery file.
4) Add the completed metadata interview and data certification forms to the compressed
file. Both files should be named in a manner consistent with the naming conventions
described elsewhere in this document.
5) Add any geospatial data files that aren’t already in the possession of the GIS Specialist.
Geospatial data files should be developed and named according to PACN GIS Naming
Conventions.

323

6) Upload the compressed file containing all certification materials to the submissions folder
of the PACN Digital Library. If the Project Lead does not have access to the PACN
Digital Library, then certification materials should be delivered as follows:
a. If the compressed file is less than 5 megabytes in size, it may be delivered directly
to the Data Manager by email.
b. If the compressed file is larger than 5 megabytes, it should be copied to an
external drive and delivered in this manner.
7) Notify the Data Manager by email that the certification materials have been uploaded or
otherwise sent.
Upon receiving the certification materials, the Data Manager will:
1) Review them for completeness and work with the Project Lead if there are any questions.
2) Notify the GIS Specialist if any geospatial data are submitted. The GIS Specialist will
then review the data, and update any project GIS data sets and metadata accordingly.
3) Check in the delivered products using the PACN project tracking application.
4) Store the certified products together in the PACN Digital Library.
5) Upload the certified data to the master project database.
6) Notify the Project Lead that the year’s data have been uploaded and processed
successfully. The Project Lead may then proceed with data summarization, analysis and
reporting.
7) Develop, parse and post the XML metadata record to the NPS Data Store.
8) After a holding period of 2 years, the Data Manager will upload the certified data to the
NPS Data Store. This holding period is to protect professional authorship priority and to
provide sufficient time to catch any undetected quality assurance problems. See SOP
#34: “Product Posting and Distribution.”

Specific Instructions for Reports and Publications
Annual reports and trend analysis reports will use the NPS Natural Resource Publications
template, a pre-formatted Microsoft Word template document based on current NPS formatting
standards. Annual reports will use the Natural Resource Report 11 template, and trend analysis
and other peer-reviewed technical reports will use the Natural Resource Technical Report 12
template. Instructions for acquiring a series number and other information about NPS publication

11
12

http://www.nature.nps.gov/publications/nrpm/docs/templates/NRR_Template_v3.dot
http://www.nature.nps.gov/publications/nrpm/docs/templates/NRTR_Template_v3.dot

324

standards can be found at the NPS Natural Resources Publications website 13. In general, the
procedures for reports and publications are as follows:
1) The document should be formatted using the NPS Natural Resource Publications
template. Formatting according to NPS standards is easiest when using the template from
the very beginning, as opposed to reformatting an existing document.
2) The document should be peer reviewed at the appropriate level. For example, I&M
Annual Reports should be reviewed by other members of the appropriate project work
group. The Program Manager will also review all annual reports for completeness and
compliance with I&M standards and expectations.
3) Upon completing the peer review, acquire a publication series number from the NPS Peer
Review Manager (currently the Regional I&M Program Manager).
4) Upload the file in PDF and MS Word formats to the PACN Digital Library submissions
folder.
5) Send a printout to each park curator.
6) The Data Manager or a designee will create a bibliographic record and upload the PDF
document to NRInfo according to document sensitivity.
File naming conventions
In all cases, digital file names should follow these guidelines:
1) No spaces or special characters in the filename
2) Use the underscore (“_”) character to separate filename components
3) Try to limit filenames to 30 characters or fewer, up to a maximum of 50 characters
4) As appropriate, include the project name (e.g., “stream_macrofauna”), network code
(“PACN”) or park code, and year in the filename.
Examples:
1) PACN_stream_macrofauna_2008_Annual_report.pdf
2) PACN_stream_macrofauna_2008_Field_season_report.doc

13

http://www.nature.nps.gov/publications/NRPM/index.cfm

325

Standard Operating Procedure (SOP) #31:
Metadata Development
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document describes the guidelines for documenting data and
how it should be accomplished.
Metadata Documentation
Data documentation is a critical step toward ensuring that data sets are usable for their intended
purposes well into the future. This involves the development of metadata, which can be defined
as structured information about the content, quality, condition and other characteristics of a given
data set. Additionally, metadata provide the means to catalog and search among data sets, thus
making them available to a broad range of potential data users. Metadata for all PACN
monitoring data will conform to Federal Geographic Data Committee (FGDC) guidelines and
will contain all components of supporting information such that the data may be confidently
manipulated, analyzed and synthesized.
Updated metadata is a required deliverable that should accompany each season’s certified data.
For long-term projects such as this one, metadata creation is most time consuming the first time
it is developed – after which most information remains static from one year to the next. Metadata
records in subsequent years then only need to be updated to reflect changes in contact
information and taxonomic conventions, to include recent publications, to update data
disposition and quality descriptions, and to describe any changes in collection methods, analysis
approaches or quality assurance for the project.

327

Specific procedures for creating, parsing, and posting the metadata record are found in PACN
Metadata Development Guidelines 14. The general flow is as follows:
1. After the annual data quality review has been performed and the data are ready for
certification, the Project Lead (or a designee) updates the PACN Metadata Interview
Form 15.
a. The metadata interview form greatly facilitates metadata creation by structuring the
required information into a logical arrangement of 15 main questions, many with
additional sub-questions.
b. The first year, a new copy of the metadata interview form should be downloaded.
Otherwise the form from the previous year can be used as a starting point, in which
case the Track Changes tool in MS Word should be activated in order to make edits
obvious to the person who will be updating the XML record.
c. Complete the metadata interview form and maintain it in the project workspace.
Much of the interview form can be filled out by cutting and pasting material from
other documents (e.g., reports, protocol narrative sections, and SOPs).
d. The Data Manager can help answer questions about the metadata interview form.
2. Deliver the completed interview form to the Data Manager according to SOP #30:
Product Delivery Specifications.”
3. The Data Manager (or GIS Specialist for spatial data) will then extract the information
from the interview form and use it to create and update an FGDC- and NPS-compliant
metadata record in XML format. Specific guidance for creating the XML record is
contained in PACN Metadata Development Guidelines.
4. The Data Manager will post the record and the certified data to the IRMA Portal3, and
maintain a local copy of the XML file for subsequent updates
5. The Project Lead should update the metadata interview content as changes to the protocol
are made, and each year as additional data are accumulated.
Identifying sensitive information
Part of metadata development includes determining whether or not the data include any sensitive
information, which is partly defined as the specific locations of rare, threatened or endangered
species. Prior to completing the metadata interview form, the Project Lead should identify any
sensitive information in the data after first consulting SOP #33: “Sensitive Information
Procedures.” Findings may be documented and communicated to the Data Manager through the
metadata interview form.

14
15

http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Metadata_Guidelines.pdf
http://science.nature.nps.gov/im/units/pacn/data/data_sop/PACN_Metadata_Interview_Form.doc

328

Standard Operating Procedure (SOP) #32:
Data Analysis and Reporting
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure describes methods for data analysis and reporting of stream
macrofauna and habitat surveys. Data analyses for the abundance and size of fish, shrimp, and
snails, as well as geomorphologic habitat characteristics, are outlined with examples to show
data structure, statistical tests, and graphical plots. This SOP outlines two initial steps of data
analysis at each of the station, stream, and trend assessment levels. These steps summarize and
determine the range-of-variation for some parameters. A third step which integrates habitat
characteristics with biological data is also included at the trend assessment level. Report types
are identified according to the categories in the PACN monitoring plan, with most reporting
occurring on an annual basis. Specifically, station level and stream level size, abundance, and
habitat characteristic summarization and range of variation data is reported on an annual basis.
Statistical trend analyses are conducted on abundance data on an annual basis (after five years of
data have been collected). Trend analysis of size and habitat data, as well as integration of
biological data with habitat characteristics, is included in the five year reports. Additional, multivital sign integration, synthesis, analysis, and reporting is not addressed in this SOP at present.
The use of products identified in this protocol does not imply endorsement, effectiveness, or
warranty by NPS.
A master equipment list for the entire Pacific Islands Stream Monitoring Protocol can be found
in Table S.2.1 of SOP #2: “Preparation for the Field Sampling.” The master equipment list
should be updated simultaneously if any SOP requiring an equipment list is revised.

329

Analysis Overview
Data analysis is defined here as the steps by which observations of the environment are
processed for interpretation and synthesis into meaningful information that is accessible to
managers. Data analysis also includes quality assurance and control efforts that occur in the field,
during exploratory analysis, in summarization, during interpretation, and when drawing
conclusions.
Analytical Approach
Two basic initial steps are identified in data analysis for all Pacific Islands Stream monitoring
data: summarization and establishing the range of variation. These steps are encompassed in the
larger construct of data management and data stewardship which is discussed in SOPs #25-31.
We identify four basic levels of analytical methods for our monitoring data: station level, stream
level, trend assessment level, and synthesis (Table S.32.1). Quadrant (Hawaii and American
Samoa) or segment (Guam) level macrofauna abundance and size data is used to calculate
summarization and range of variation data (mean and standard deviation) for each station.
Similarly, transect data is used to calculate summarization and range of variation data for habitat
characteristics (e.g. velocity, substrate characteristics, etc.). The station level data includes mean
and standard deviation abundance, size, and habitat characteristic data at a given station over
time. The stream level data includes mean and standard deviation abundance, size, and habitat
characteristic data at all stations in a stream at a given time. The trend assessment level integrates
station or stream level abundance, size, and habitat characteristic summarization and range of
variation data over time to detect change. For example, some form of regression may be used to
identify the slope or trend. In addition, a third step is included in the trend assessment level that
uses multivariate statistics to integrate station and stream level macrofauna abundance and size
data with habitat characteristics. Finally, synthesis examines relationships between temporal and
spatial trends in stream macrofauna size and abundance and water quality data. Station level,
stream level, and trend assessment level are addressed here. Synthesis will be addressed within
and across multiple Vital Signs and is therefore left for network level or broader scientific
consideration in the future.

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Table S.32.1. Three approaches for analyzing Pacific Islands Stream Vital Sign monitoring data.
Analysis

Description

Responsible Party

Station Level

Quality assurance and control routines and calculation of statistics from
monitoring data (abundance, size, habitat):
Step 1 (Summarization): Measures of mean, median, variation, and
other basic statistics. Include graphical presentation of data.
Step 2 (Range of Variation): Establish historical or expected range of
values, relation to relevant regulatory levels, confidence estimates.

Stream Level

Quality assurance and control routines and calculation of statistics from
monitoring data (abundance, size, habitat):
Step 1 (Summarization): Measures of mean, median, variation, and
other basic statistics. Include graphical presentation of data.
Step 2 (Range of Variation): Establish historical or expected range of
values, relation to relevant regulatory levels, confidence estimates.

Trend Assessment

Biological technician
with oversight by
aquatic ecologist and
with assistance from
park leads

Biological technician
with oversight by
aquatic ecologist and
with assistance from
park leads

Step 1: Integration of station and stream level summarization over time
using some form of regression analysis.
Step 2: Integration of station and stream level variation results over
time using some form of regression analysis. Includes establishing a
direction and rate of change of variation that may be used to provide
early warnings of trends in resources condition. Confidence levels of
documenting trend will be established.

PACN aquatic
ecologist and
researchers from
other institutions
(e.g. USGS)

Step 3: Integration of station and stream level abundance and size
data with habitat characteristics using a multivariate approach.

These analytical approaches will be applied to each of the components of Vital Signs (e.g. size
and abundance of fish, shrimp, and snails and habitat characteristics).
Analysis Procedures
Analysis procedures are to be documented, for each stream on an annual basis as well as on a
five year basis, in a compiled document (such as an MS Word® file), referred to hereafter as an
analysis log file. This file would essentially be a ‘log’ of all the quantitative and qualitative steps
taken, such as various transformations tested, and screen shots of data visualizations. A check list
for the steps is provided in Appendix #14: “Analysis log file checklist.” Each year, seven such
files (one for each stream that is slated for initial implementation of the Pacific Islands Stream
monitoring protocol) will be generated. On Tutuila (American Samoa) it is possible that
additional streams will be selected for the yearly random sampling. These analysis log files are
internal working documents, that while not subject to explicit peer-review for most reporting
other than protocol and programmatic reviews, will serve as the documentation and foundation
for analyses for reports which are peer-reviewed. Table S.32.2 summarizes these analytical
procedures and frequency of analysis (annually or every five years) for the parameters measured
in each stream.

331

Table S.32.2. Summary of analytical procedures including parameters measured at the stream level.
Level of
Analysis

Data Analysis Approach

Frequency of
Analysis

Responsible
Party

Station

Summarization and range-ofvariation for annual macrofauna
size, abundance, and habitat
characteristics at a given station
over time

Annually

Aquatic ecologist

Stream

Summarization and range-ofvariation for annual macrofauna
size, abundance, and habitat
characteristics at a given time over
stream longitudinal distribution.

Annually

Aquatic ecologist

Trend
Assessment

Multi-year change in macrofauna
abundance for both station and
stream level data.

Annually (after five
years of data have
been collected)

Aquatic ecologist
and researchers
from other
institutions (e.g.
USGS)

Multi-year change in macrofauna
size and habitat characteristics for
both station and stream level data.

Every five years

Aquatic ecologist
and researchers
from other
institutions (e.g.
USGS)

Integration of station and stream
level abundance and size data with
habitat characteristics using a
multivariate approach.

Every five years

PACN aquatic
ecologist and
researchers from
other institutions
(e.g. USGS)

Station and Stream Level Analyses: These analyses are conducted annually for macrofauna size,
abundance, and habitat characteristic summarization and range of variation data. The data sets
are analyzed for normality of the distribution. Text and graphic plots of mean and standard
deviation at each station over time (station level analysis) and at each time over stream
longitudinal distribution (stream level analysis) are created. If multiple observers have been
collecting data, the summaries should be grouped by observer to evaluate potential observer bias.
Trend Assessment Analyses: These analyses are conducted annually for macrofauna abundance
data after the first five years of data have been collected. These analyses are conducted on a five
year recurrence interval for macrofauna size data and habitat characteristic data. However, if an
unusual change in abundance is detected, trend analyses for size and habitat characterization
should be conducted annually. Text and graphic plots of mean and standard deviation of
abundance, size, or habitat characteristics at each station over time (station level analysis) and at
each time over stream longitudinal distribution (stream level analysis) are created. Change
detection over time can be analyzed using a variety of statistical techniques, including repeated
measures ANOVA or regression. Integration of stream and station level abundance and size data
with habitat characteristics will be accomplished every five years using canonical
correspondence analysis (CCA).

332

Example Procedure for Stream Macrofauna Abundance
It should be noted that the following analytical procedures should only be conducted by an
individual with advanced statistical training. In addition, many of the procedures described
below may change over time due to advancements and updates in statistical tests, perspectives,
techniques and software. Consequently, this example merely serves to illustrate the desirable
sequence of steps necessary to examine and present the data. The data presented in these sections
is used for example purposes only and should not be used as part of actual data analysis
activities.
Example #1: Checking for normality of the distribution.
Step 1: Copy annual quadrant (or segment in Guam) data for a station from a Microsoft Access®
query into Microsoft Excel®. Keep in mind that data copied from Access® is treated as text and
must usually be converted into value format. Programs like Excel® can do the value conversion.
In this example, abundance of Sicyopterus stimpsoni in Unknown Stream from ten quadrants at
Station A in 2006 is pasted into the Example 1.xls file (Figure S.32.1).

®

Figure S.32.1. Abundance data structure at the station level in Microsoft Excel .

333

Step 2: Check the normality of the distribution of the abundance data by selecting “Data
Analysis” under the “Data” tab. Choose “Descriptive Statistics” and define the abundance data as
the input range. Select a blank cell as the output range and check the “Summary statistics” box.
If the absolute value of the skewness statistic is greater than two standard errors of skewness you
can assume that the distribution is significantly skewed (non-normal). The standard error of
6

skewness can be estimated as �𝑁 (Tabachnick and Fidell, 1996). In this example, the absolute
value of skewness is 0.3, which is less than the standard error of skewness (0.77). Therefore, the
data can be considered normally distributed.
Step 3: Repeat this procedure for each species in each segment in each stream for the macrofauna
abundance and size data as well as the habitat characteristics data each year.
Example #2: Station level analysis of fish abundance data.
Step 1: Copy annual quadrant (or segment in Guam) data for a station from a Microsoft Access®
query into Microsoft Excel®.
Step 2: Using quadrant (or segment in Guam) data calculate the average abundance and standard
deviation in a segment on a given date for each species. In this example, the 2007 annual average
abundance and standard deviation data of S. stimpsoni for Unknown Stream at Station D in
Unknown Stream is pasted into the Example 2.xls file which already contains data from 20002006 (Figure S.32.2).

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Figure S.32.2. Average abundance and standard deviation data structure at the station level in Microsoft
®
Excel .

Step 3: Create a plot that shows the change in average station abundance and standard deviation
over time (Figure S.32.3). This plot represents station level summarization and range of variation
data for S. stimpsoni at Station D in Unknown Stream.

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Average Abundance of S. stimpsoni at
Station D in Unknown Stream

25
20
15
10
5
0
2000

2001

2002

2003

2004

2005

2006

2007

Year
Figure S.32.3. Average station level abundance +/- 1 standard deviation of S. stimpsoni at Station D in
Unknown Stream.

Step 4: Repeat this procedure for each species in each segment of each stream for the
macrofauna size, abundance, and habitat characteristics data on an annual basis.
Example #3: Stream level analysis of fish abundance data.
Step 1: Copy annual quadrant (or segment in Guam) data for a station from a Microsoft Access®
query into Microsoft Excel®.
Step 2: Using quadrant (or segment in Guam) data calculate the average abundance and standard
deviation in each segment on a given date for each species. In this example, the 2000 annual
average abundance and standard deviation data of S. stimpsoni for Unknown Stream at Stations
A-W in Unknown Stream is pasted into the Example 3.xls (Figure S.32.4).

336

Figure S.32.4. Average abundance and standard deviation data structure at the stream level in Microsoft
®
Excel .

Step 3: Create a plot that shows the change in average station abundance and standard deviation
over longitudinal distance from the mouth of the stream (Figure S.32.5). This plot represents
stream level summarization and range of variation data for S. stimpsoni at stations A-W in
Unknown Stream in 2000.

337

35
30
25
20
15
10
5
0
30
70
130
160
250
280
330
560
770
1270
1850
1900
2080
2150
2330
2560
2630
2640
3080
3351
3430
3620
3768

Average Abundance of S. Stimpsoni in
year 2000 at Unknown Stream

40

Distance from Mouth (m)
Figure S.32.5. Average stream level abundance +/- 1 standard deviation of S. stimpsoni at in year 2000
at Unknown Stream.

Step 4: Repeat this procedure for each species in each stream for the macrofauna size,
abundance, and habitat characteristics data on an annual basis.
Reporting Overview
Report Types
Unlike the analysis log files which will generate individual files for each park and each of the
three analysis strategies (station, stream, and trend assessment levels), reporting documents will
integrate both parks and analysis strategies. Table S.32.3 identifies product types, purposes,
targeted audiences, responsible parties, production frequency, and review processes. We have
identified a cohesive suite of seven product categories: (1) program and protocol reviews, (2)
monitoring protocol and project reports, (3) status and trends reports, (4) scientific writing and
presentations, (5) management briefings, (6) website communication, and (7) interpretation and
outreach.

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Table S.32.3. Summary of anticipated products, grouped by type and frequency.

Type of Report

Purpose of Report

Targeted
Audience

Initiated by

Frequency of
Reporting

Review Process

Program and Protocol
Reviews
Protocol Review Reports

Document where actual procedures fall short or
exceed expectations, recommend necessary
changes, document changes since last protocol
review report; document overall quality of
protocol – particularly in terms of protocol
objectives and implementation, effectiveness,
and data management.

Superintendents,
park resource staff,
I&M staff, servicewide program
managers, external
scientists, partners

PACN aquatic
ecologist

Within 1-3 years of
implementation, 5year intervals
thereafter

Peer review at
network and
regional level

Vital Signs Monitoring
Protocol Reports

Document and archive annual monitoring
activities and data, describe current resource
condition and core analysis results, document
related data management activities, document
changes in monitoring protocol, communicate
monitoring efforts to resource managers. During
protocol development stages, will emphasize
progress made and challenges encountered.

Park resource staff,
PACN staff,
external scientists,
partners

PACN aquatic
ecologist

Annually, compiled
each March

Peer review at
network level

Summary of Vital Sign
Monitoring Protocol
Reports

Same as annual “Vital Sign Monitoring Protocol
Reports” above, but highlights key points for nontechnical audiences

Superintendents,
NPS interpreters,
public, partners

PACN aquatic
ecologist

Annually, compiled
each March

Peer review at
network level

Pilot Projects and
Monitoring Research
Reports

Provide background and methods of monitoring
protocol development and other methods related
investigations

Park resource
managers, PACN
staff, external
scientists, partners

PACN aquatic
ecologist

Variable with annual
status reporting, as
necessary

Peer review at
network level plus
review appropriate
to final product

Monitoring Protocol
and Project Reports

339
Status and Trends
Reports

Table S.32.3. Summary of anticipated products, grouped by type and frequency (continued).
Targeted
Audience

Initiated by

Frequency of
Reporting

Purpose of Report

Trend Analysis and
Synthesis Reports

Describe and interpret patterns/trends of
monitored resources, identify new characteristics
of resources and correlations among monitored
resources, identify relationships between
drivers/stressors and responses, recommend
changes to management of resources (adaptive
management feedback).

Park resource
managers, PACN
staff, external
scientists, partners

Aquatic ecologist,
park leads

3-5 year intervals.
Abbreviated annual
edition, as necessary
for PACN Vital Signs
Program

Peer review at the
network and
regional level

Summary of: Trend
Analysis and Synthesis
Report

Executive summary of “Trend Analysis and
Synthesis Report” above with key points on one
page for non-technical audiences. Usually this is
a bulleted list.

Superintendents,
NPS interpreters,
public, partners

Aquatic ecologist

Commensurate with
reporting activity of
“Trend Analysis and
Synthesis Report”

Peer review at the
network level

PACN contribution to
NPS-wide “State of the
Parks” Report

Describes current conditions of park resources,
reports interesting trends and highlights of
monitoring activities, identifies resource issues of
concern, explores future issues and directions

Congress, budget
office, NPS
leadership,
superintendents,
general public

Compiled by the
Washington
Support Office
(WASO) from
data provided by
networks

Annual

Peer review at
national level

PACN Vital Signs
Monitoring Conference

Review and summarize information on this Vital
Sign, help identify emerging issues and generate
new ideas

Park resource staff,
network staff,
external scientists,
partners

PACN aquatic
ecologist

Biennial (around time
PACN “Status and
Trends Report” is
published)

Peer review at
national level

Scientific journal articles
and book chapters

Document and communicate advances in
knowledge, provides a broader perspective on
quality assurance and peer review

External scientists,
park resource
managers, and
professional staff

Aquatic ecologist,
others

Variable

Peer review
according to
journal or book
standards

Other symposia,
conferences and
workshops

Review and summarize information on this Vital
Sign, help identify emerging issues and generate
new ideas

External scientists,
professional staff,
park resource
managers, and
other resource
managers.

Aquatic ecologist,
others

Variable (e.g., Hawaii
Conservation
Conference, George
Wright Society)

Peer review at
network level; for
papers may also
be peer reviewed

340

Type of Report

Review Process

Scientific Writing and
Presentations

Table S.32.3. Summary of anticipated products, grouped by type and frequency (continued).
Type of Report

Purpose of Report

Targeted
Audience

Initiated by

Frequency of
Reporting

Review Process

Management
Briefings

341

Protected area managers
briefing

Communicate highlights and potential
management action items, with 1-2 page briefing
statements for each protocol

Park resource staff,
Network staff,
agency, academic
scientists, other
Federal, State, and
Territorial Protected
Area managers,
discipline
specialists,
interpretive staff

Network program
manager,aAquatic
ecologist

Annually, likely in
conjunction with
Board of Directors
administrative
meetings

Peer review by
network, PICRP,
and monitoring
staff

Executive briefings

Update superintendents and other VIPs on parkspecific findings and potential resource issues;
suggest action items where appropriate

Individual
Superintendents
and other VIPs

Aquatic ecologist,
network program
manager, park
leads

As needed

Peer review by
network, PICRP
and monitoring
staff

Centralized repository of all final reports to
ensure products are easily accessible in
commonly-used electronic formats; other
synthesized information on the PACN

Superintendents,
park resource staff,
PACN staff,
service-wide
program managers,
external scientists,
partners, students,
public

Variable, typically
network
webmaster

As media is
completed

Peer review at
network level to
NPS web
standards as
finalized, reviewed
products

Website Posting
Web-based media

Table S.32.3. Summary of anticipated products, grouped by type and frequency (continued).
Type of Report

Purpose of Report

Targeted
Audience

Initiated by

Frequency of
Reporting

Review Process

Interpretation and
Outreach

342

Science Days

Communicate main monitoring findings as well as
underlying data; discuss potential significance for
management, further monitoring, potential
additional research needs, and for outreach

Superintendents,
park resource staff,
PACN staff,
protocol managers,
partners, public

Aquatic ecologist,
biological
technician, and
others as needed

Variable by park,
annual when possible

Meeting /
presentation itself
is a form of review

Interpretive
Conversations

Interactive conversations with park interpretive
staff to discuss main monitoring findings as well
as underlying data; discuss potential significance
for management, further monitoring, potential
additional research needs, and for outreach

Park interpretive
staff, environmental
educators, PACN
staff

Aquatic ecologist,
biological
technician, and
others as needed

Variable by park, at
least annual when
possible

Meeting /
presentation itself
is a form of review

Park Interpretive /
outreach sessions

Review and summarize information on PACN
Vital Signs; engage and involve greater
participation in monitoring efforts

Park staff, public,
partners

Aquatic ecologist,
biological
technician, and
others as needed

Variable

Peer review by
network, PICRP
staff

Park staff meetings
(results synthesis)

Communicate results to non-technical audiences,
discuss potential significance for management,
receive feedback on resource and monitoring
issues in park operations

All park staff,
volunteers, and
partners, especially
those not typically
encountered in I&M
program, RM,
science operations

Aquatic ecologist,
biological
technician, and
others as needed

Annually for each
network park

Peer review by
network, PICRP
staff

Figure S.32.6. Image example of one site of actual field data collection upon which reports should be
based.

Report Preparation Process
Reports identified in Table S.32.3 are to be based on collected data (Figure S.32.6) and other
science-based documentation. An example summary report of vital signs data that could be
presented to park superintendents is included in Appendix 15: “Pacific Islands Stream
Monitoring Report: Example Summary of Vital Signs Data.” These reports will provide context
and explanations for the results presented, as well as include any additional analyses that may
result from initial investigations. The ‘analysis log’ files will serve as the basis for most of the
reporting results. The biological technician for this Vital Sign is identified as the primary
individual responsible for updating the analysis log files and will also be pivotal in preparation of
subsequent reports. It is anticipated that the aquatic ecologist or another statistically trained
individuals will be responsible for the statistical analyses.
Drafts of the reporting products will be organized according to the categories outlined above,
with key versions and review comments archived, and final versions clearly communicated to
PACN network staff to ensure distribution via websites and other channels.
References
Tabachnick, B. G., and L. S. Fidell. 1996. Using multivariate statistics (3rd ed.). New York:
Harper Collins, New York, New York, USA.

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Standard Operating Procedure (SOP) #33:
Sensitive Information Procedures
Version 1.01
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
Although it is the general NPS policy to share information widely, the NPS also realizes that
providing information about the location of park resources may sometimes place those resources
at risk of harm, theft, or destruction. This can occur, for example, with regard to caves,
archeological sites, tribal information, and rare plant and animal species. Therefore, information
will be withheld when the NPS foresees that disclosure would be harmful to an interest protected
by an exemption under the Freedom of Information Act (FOIA). The National Parks Omnibus
Management Act, Section 207, 16 U.S.C. 5937, is interpreted to prohibit the release of
information regarding the “nature or specific location” of certain cultural and natural resources in
the national park system. Additional details and information about the legal basis for this policy
can be found in the NPS Management Policies 16 (National Park Service 2006), and in Director’s
Order #66 17.
These guidelines apply to all PACN staff, cooperators, contractors, and other partners who are
likely to obtain or have access to information about protected NPS resources. The Project Lead
has primary responsibility for ensuring adequate protection of sensitive information related to
this project.
The following are highlights of our strategy for protecting this information:

16
17

http://www.nps.gov/policy/mp/Index2006.htm
http://data2.itc.nps.gov/npspolicy/DOrders.cfm

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1) Protected resources, in the context of the PACN Inventory and Monitoring Program,
include species that have state or federal status, and other species deemed rare or
sensitive by local park taxa experts.
2) Sensitive information is defined as information about protected resources which may
reveal the “nature or specific location” of protected resources. Such information must not
be shared outside the National Park Service, unless a signed confidentiality agreement is
in place.
3) In general, if information is withheld from one requesting party, it must be withheld from
anyone else who requests it, and if information is provided to one requesting party
without a confidentiality agreement, it must be provided to anyone else who requests it.
4) To share information as broadly as legally possible, and to provide a consistent, tractable
approach for handling sensitive information, the following shall apply if a project is
likely to collect and store sensitive information:
a. Random coordinate offsets of up to 2 km for data collection locations, and
b. Removal of data fields from the released copy that are likely to contain sensitive
information.
What Kinds of Information Can and Cannot Be Shared?
Do not share: Project staff and cooperators should not share any information outside NPS that
reveals details about the “nature or specific location” of protected resources, unless a
confidentiality agreement is in place. Specifically, the following information should be omitted
from shared copies of all data, presentations, reports, or other published forms of information.
1) Exact coordinates – Instead, public coordinates are to be generated that include a random
offset azimuth and distance. These offset coordinates can be shared freely.
2) Other descriptive location data – Examples may include travel descriptions, location
descriptions, or other fields that contain information which may reveal the specific
location of the protected resource(s).
3) Protected resource observations at disclosed locations – If specific location information
has already been made publicly available, the occurrence of protected resources at that
location cannot be shared outside NPS without a confidentiality agreement. For example,
if the exact coordinates for a monitoring station location are posted to a website or put
into a publication, then at a later point in time an endangered fish species is observed at
that monitoring station, that monitoring station location in reference to the endangered
fish species cannot be mentioned or referred to in any report, presentation, data set, or
publication that will be shared outside NPS.
Do share: All other information about the protected resource(s) may be freely shared, so long
as the information does not reveal details about the “nature or specific location” of the protected
resource(s) that aren’t already readily available to the general public in some form (e.g., other
published material). Species tallies and other types of data presentations that do not disclose the

346

precise locations of protected resources may be shared, unless by indicating the presence of the
species the specific location is also revealed (i.e., in the case of a small park).
Details for Specific Products
Whenever products such as databases and reports are being generated, handled, and stored, they
should be created explicitly for one of the following purposes:
1) Public or general use: These products are intended for general distribution, sharing with
cooperators, or posting to public websites. These databases or reports may be derived
from products that contain sensitive information so long as the sensitive information is
either removed or otherwise rendered in a manner consistent with other guidance in this
document.
2) Internal NPS use: These are products that contain sensitive information and should be
stored and distributed only in a manner that ensures their continued protection. These
products should clearly indicate that they are solely for internal NPS use by containing
the phrase: “Internal NPS Use Only—Not For Release.” These products can only be
shared within NPS or in cases where a confidentiality agreement is in place. They do not
need to be revised in a way that conceals the location of protected resources.
Data Sets
To create a copy of a data set that will be posted or shared outside NPS:
1) Make sure the public offset coordinates have been populated for each sample or
observation location in “tbl_Locations.”
2) Delete any database objects that may contain specific, identifying information about
locations of protected resources.
The local, master copy of the database contains the exact coordinates and all data fields. The
Data Manager and/or GIS Specialist can provide technical assistance as needed to apply
coordinate offsets or otherwise edit data products for sensitive information.
Maps and Other GIS Output
General use maps and other geographic representations of observation data that will be released
or shared outside NPS should be rendered using offset coordinates, and should only be rendered
at a scale that does not reveal their exact position (e.g., 1:100,000 maximum scale).
If a large-scale, close-up map is to be created using exact coordinates (e.g., for field crew
navigation, etc.), the map should be clearly marked with the following phrase: “Internal NPS Use
Only—Not For Release.”
The Data Manager and/or GIS Specialist can provide technical assistance as needed to apply
coordinate offsets or otherwise edit data products for sensitive information.
Presentations and Reports
Public or general use reports and presentations should adhere to the following guidelines:

347

1) Do not list exact coordinates or specific location information in any text, figure, table, or
graphic in the report or presentation. If a list of coordinates is necessary, use only offset
coordinates and clearly indicate that coordinates have been purposely offset to protect the
resource(s) as required by law and NPS policy.
2) Use only general use maps as specified in the section on maps and other GIS output.
If a report is intended for internal use only, these restrictions do not apply. However, each page
of the report should be clearly marked with the following phrase: “Internal NPS Use Only—Not
For Release.”
Voucher Specimens
Specimens of protected taxa should only be collected as allowed by law. Labels for specimens
should be clearly labeled as containing sensitive information by containing the following phrase:
“Internal NPS Use Only—Not For Release.” These specimens should be stored separately from
other specimens to prevent unintended access by visitors. As with any sensitive information, a
confidentiality agreement should be in place prior to sending these specimens to another nonNPS cooperator or collection.
Procedures for Coordinate Offsets
1) Process GPS data, upload into the database, and finalize coordinate data records.
2) Set the minimum and maximum offset distances (project-specific, typically up to 2 km).
3) Apply a random offset and random azimuth to each unique set of coordinates.
4) Coordinates may then be either rounded or truncated so the UTM values end in zeros to
give a visual cue that the values are not actual coordinates.
5) Do not apply independent offsets to clustered or otherwise linked sample locations (e.g.,
multiple sample points along a transect). Instead, either apply a single offset to the cluster
so they all remain clustered after the offset is applied, or apply an offset to only one of
the points in the cluster (e.g., the transect origin) and store the result in the public
coordinates for each point in that cluster.
6) These “public” coordinates are then the only ones to be shared outside NPS – including
all published maps, reports, publications, presentations, and distribution copies of the
data set – in the absence of a confidentiality agreement.
The following components can be used to create individual offsets rounded to the nearest 100
meters in MS Excel:
1) Angle = rand() * 359
2) Distance = ((Max_offset – Min_offset) * rand() + Min_offset)
3) Public_UTME = Round(UTME_final + (Distance * cos(Radians(Angle – 90))), -2)
348

4) Public_UTMN = Round(UTMN_final + (Distance * sin(Radians(Angle + 90))), -2)
Sharing Sensitive Information
Refer to SOP #34: “Product Posting and Distribution” for a more complete description of how to
post and distribute products, and to keep a log of data requests.
No sensitive information (e.g., information about the specific nature or location of protected
resources) may be posted to the IRMA Portal 18 or another publicly-accessible website, or
otherwise shared or distributed outside NPS without a confidentiality agreement between NPS
and the agency, organization, or person(s) with whom the sensitive information is to be shared.
Only products that are intended for public/general-use may be posted to public websites and
clearinghouses – these may not contain sensitive information.
Responding to Data Requests
If requests for distribution of products containing sensitive information are initiated by the NPS,
by a federal agency, or by a partner organization (e.g., a research scientist at a university), the
unedited product (e.g., the full data set that includes sensitive information) may only be shared
after a confidentiality agreement is established between NPS and the agency, organization, or
person(s) with whom the sensitive information is to be shared. All data requests will be tracked
according to procedures in SOP #34: “Product Posting and Distribution.”
Once a confidentiality agreement is in place, products containing sensitive information may be
shared following these guidelines:
1) Always clearly indicate in accompanying correspondence that the products contain
sensitive information, and specify which products contain sensitive information.
2) Indicate in all correspondence that products containing sensitive information should be
stored and maintained separately from non-sensitive information, and protected from
accidental release or redistribution.
3) Indicate that NPS retains all distribution rights; copies of the data should not be
redistributed by anyone but NPS.
4) Include the following standard disclaimer in a text file with all digital media upon
distribution: “The following files contain protected information. This information was
provided by the National Park Service under a confidentiality agreement. It is not to be
published, handled, redistributed or used in a manner inconsistent with that agreement.”
The text file should also specify the file(s) containing sensitive information.
5) If the products are being sent on physical media (e.g., CD or DVD), the media should be
marked in such a way that clearly indicates that media contains sensitive information
provided by the National Park Service.

18

http://irma.nps.gov/App/Portal/Home

349

Confidentiality Agreements
Confidentiality agreements may be created between NPS and another organization or individual
to ensure that protected information is not inadvertently released. When contracts or other
agreements with a non-federal partner do not include a specific provision to prevent the release
of protected information, the written document must include the following standard
Confidentiality Agreement:
Confidentiality Agreement - I agree to keep confidential any protected information
that I may develop or otherwise acquire as part of my work with the National Park
Service. I understand that with regard to protected information, I am an agent of the
National Park Service and must not release that information. I also understand that by
law I may not share protected information with anyone through any means except as
specifically authorized by the National Park Service. I understand that protected
information concerns the nature and specific location of endangered, threatened, rare,
commercially valuable, mineral, paleontological, or cultural patrimony resources such
as threatened or endangered species, rare features, archeological sites, museum
collections, caves, fossil sites, gemstones, and sacred ceremonial sites. Lastly, I
understand that protected information must not be inadvertently disclosed through
any means including websites, maps, scientific articles, presentations, and speeches.
Freedom of Information (FOIA) Requests
All official FOIA requests will be handled according to NPS policy. The Project Lead will work
with the Data Manager and the park FOIA representative(s) of the park(s) for which the request
applies.
References
National Park Service. 2006. Management Policies. Retrieved February 6, 2007, from:
http://www.nps.gov/policy/mp/policies.htm.

350

Standard Operating Procedure (SOP) #34:
Product Posting and Distribution
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure document provides details on the process of posting and
otherwise distributing finalized data, reports and other project deliverables. For a complete list of
project deliverables, refer to SOP #30: “Product Delivery Specifications.”
Product posting and distribution
Once digital products have been delivered and processed, the Data Manager will post the
products to the IRMA Portal 19. The IRMA Portal is the NPS clearinghouse for natural resource
products that are available to the public. The following sets of products are available in the
IRMA Portal:
1) Full metadata records and datasets will be posted to the References service within the
IRMA Portal and made available to the public.
2) A record for reports and other publications will be created in the Reference service. The
digital report file in PDF format will then be uploaded and linked to the reference record.
3) Species observations will be extracted from the database and entered into the Biology
service which is the NPS database and application for maintaining park-specific species
lists and observation data.
The IRMA Portal serves as the primary mechanism for sharing reports, data, and other project
deliverables with other agencies, organizations, and the general public.

19

http://irma.nps.gov/App/Portal/Home

351

Holding period for project data
To protect professional authorship priority and to provide sufficient time to complete quality
assurance measures, there is a two year holding period before posting or otherwise distributing
inalized data. This means that certified data sets are first posted to publicly-accessible websites
(i.e., the IRMA Portal) approximately 24 months after they are collected (e.g., data collected in
June 2006 becomes generally available through the IRMA Portal in June 2008). In certain
circumstances and at the discretion of the project lead and park biologists, data may be shared
before a full two years have elapsed.
Note: This hold only applies to raw data; all metadata, reports or other products are to be posted
to the IRMA Portal in a timely manner as they are received and processed.
Responding to Data Requests
Occasionally, a park or project staff member may be contacted directly regarding a specific data
request from a federal agency, an organization, scientist, or from a member of the general public.
The following points should be considered when responding to data requests:
1) NPS is the originator and steward of the data, and the NPS Inventory and Monitoring
Program should be acknowledged in any professional publication using the data.
2) NPS retains distribution rights: copies of the data should not be redistributed by anyone
but NPS.
3) The data that project staff members and cooperators collect using public funds are public
records and as such cannot be considered personal or professional intellectual property.
4) No sensitive information (e.g., information about the specific nature or location of
protected resources) may be posted to the IRMA Portal or another publicly-accessible
website, or otherwise shared or distributed outside NPS without a confidentiality
agreement between NPS and the agency, organization, or person(s) with whom the
sensitive information is to be shared. Refer to the section in this document about sensitive
information and also to SOP #33: “Sensitive Information Procedures.”
5) For quality assurance, only the certified, finalized versions of data sets should be shared
with others.

352

The Project Lead will handle all data requests as follows:
1) Discuss the request with other park biologists as necessary to make those with a need to
know aware of the request and, if necessary, to work together on a response.
2) Notify the Data Manager of the request if s/he is needed to facilitate fulfilling the request
in some manner.
3) Respond to the request in an official email or memo.
4) In the response, refer the requestor to the IRMA Portal, so they may download the
necessary data and/or metadata. If the request can not be fulfilled in that manner – either
because the data products have not been posted yet, or because the requested data include
sensitive information – work with the Data Manager to discuss options for fulfilling the
request directly (e.g., burning data to CD or DVD). Ordinarily, only certified data sets
should be shared outside NPS.
5) If the request is for a document, it is recommended that documents be converted to PDF
format prior to distributing it.
6) If the request is for data that may reveal the location of protected resources, refer to the
section in this document about sensitive information and also to SOP #33: “Sensitive
Information Procedures.”
7) After responding, provide the following information to the Data Manager, who will
maintain a log of all requests in the PACN Project Tracking database:
a. Name and affiliation of requestor
b. Request date
c. Nature of request
d. Responder
e. Response date
f. Nature of response
g. List of specific data sets and products sent (if any)
All official FOIA requests will be handled according to NPS policy. The Project Lead will work
with the Data Manager and the FOIA representative(s) of the park(s) for which the request
applies.
Special procedures for sensitive information
Products that have been identified upon delivery by the Project Lead as containing sensitive
information will either be revised into a form that does not disclose the locations of sensitive
resources, or withheld from posting and distribution. When requests for distribution of the
unedited version of products are initiated by the NPS, by an agency, or by a partner organization
(e.g., a research scientist at a university), the unedited product (e.g., the full data set that includes
protected information) may only be shared after a confidentiality agreement is established

353

between NPS and the other organization. Refer to SOP #33: “Sensitive Information Procedures”
for more information.

354

Standard Operating Procedure (SOP) #35:
Revising the protocol
Version 1.00
Change History
New
Revision Author
Version Date
#

Changes Made

Reason
Change

for Previous
Version #

Only changes in this specific SOP will be logged here. Version numbers increase incrementally
by hundredths (e.g., version 1.01, version 1.02) for minor changes. Major revisions should be
designated with the next whole number (e.g., version 2.0, 3.0, 4.0). Record the previous version
number, date of revision, author of the revision, identify paragraphs and pages where changes are
made, who approved the revision, and the reason for making the changes along with the new
version number.
Purpose
This Standard Operating Procedure explains how to make and document changes to the Stream
Macrofauna (fish, shrimp, and snails) Vital Sign Monitoring Protocol narrative and associated
Standard Operating Procedures (SOPs) for the Pacific Island Network. Anyone editing the
Protocol Narrative or any one of the SOPs needs to follow this outlined procedure in order to
eliminate confusion in how data is collected, managed, analyzed, or reported. All personnel
should be familiar with this SOP in order to identify and use the most current methodologies.
The following procedures must be followed when making changes to ensure that previous data
collection and processing procedures are clearly understood and accounted for when using and
interpreting historical data sets. Similarly, clearly articulating new methods is key to credible
interpretation of data acquired since the implementation of changes. Personnel making changes
must be familiar with this SOP to ensure that proper reviews are conducted, and that
documentation standards are followed.
Procedures:
1) Modifications. Modifications must be reviewed for clarity and technical soundness. Small
changes or additions to existing methods will be reviewed in-house by PACN Inventory
and Monitoring staff. An outside review will be encouraged by the networks for wholescale changes in methods. Major changes will be reviewed by regional and national staff
of the National Park Service and experts outside of the park service with familiarity in
stream monitoring and data analysis.

355

2) Records. All changes must be documented, and updated protocol versions must be
recorded in the Revision History Log that accompanies the Protocol Narrative and each
SOP. Changes are recorded only in the Protocol Narrative of the SOP being modified.
Version numbers increase incrementally by hundredths (e.g. version 1.01, version 1.02,
etc.) for minor changes. Major revisions will be designated with the next whole number
(e.g., version 2.0, 3.0, 4.0 …). Record the previous version number, new version number,
date of revision, author of the revision, identify paragraphs and pages where changes are
made, the reason for making the changes, and the person who approved the revision.
3) Narrative and SOP updates may occur independently. A change in one SOP will not
necessarily invoke changes in other SOPs, and a narrative update may not require SOP
modifications. All narrative and SOP version changes must be noted in the Master
Version Table (MVT), which is maintained in this SOP. Any time a narrative or an SOP
version change occurs, a new Version Key number (VK#) must be created and recorded
in the MVT, along with the date of the change and the versions of the narrative and SOPs
in effect. The VK number increments by whole integers (e.g., 1,2,3,4,5). Updates to the
MVT also must be provided to the Data Manager for inclusion in the Master Version
Table database. The Version Key number is essential for project information to be
properly interpreted and analyzed. The protocol narrative, SOPs, and data should not be
distributed independently of this table.
4) New versions. New versions of the Protocol Narrative and SOPs must be posted on the
PACN web page. Previous versions of the Protocol Narrative and SOPs must be archived
in the appropriate library.
Rationale
The stream monitoring protocol narrative and associated SOPs for the Pacific Island Network
represents an effort to document and employ scientifically rigorous methodologies for collecting,
managing, analyzing, and reporting benthic marine community monitoring data and information.
However, all protocols, regardless of initial rigor require editing as new and different
information, techniques, or technologies become available. Required edits should be made in a
timely manner and appropriate reviews undertaken. Careful documentation of changes to the
protocol, and a library of previous protocol versions are essential for maintaining consistency in
data collection and for appropriate treatment of the data during data summary and analysis. The
MS Access database for each monitoring component contains a field that identifies which
version of the protocol was in use when the data were collected.
In this context of revising the protocol, the rationale for dividing this document into a Protocol
Narrative with supporting SOPs is based on the following:
1) The Protocol Narrative is a general overview of the protocol that gives the history and
justification for monitoring and an overview of the sampling methods, but does not
provide all of the methodological details. The Protocol Narrative will only be revised if
major changes are made to the protocol.

356

2) The SOPs, in contrast, are very specific step-by-step instructions for performing a given
task. They are expected to be revised more frequently than the protocol narrative.
3) When an SOP is revised, in most cases, it is not necessary to revise the Protocol Narrative
to reflect the specific changes made to the SOP.
4) All versions of the Protocol Narrative and SOPs will be archived in a Protocol Library.
Procedure
All edits require review for clarity and technical soundness. Small changes or additions to
existing methods should be reviewed in-house by Pacific Island Network staff (e.g., version
changes by hundredths). However, if there is a complete or major change in methods, then an
outside review may be required (e.g., version changes by whole numbers). If there is a major
change in methodology, either to the entire protocol or individual SOPs or narrative components,
the Program Manager of the Pacific West Region Inventory and Monitoring Program should be
consulted to determine the appropriate level of peer review required. Typically, regional and
national staff of the NPS, and outside experts in government, private sector, and academia with
familiarity in stream monitoring in the Pacific Islands will be utilized as reviewers.
Metadata
Any changes to associated database design and organization are documented in the Metadata of
the project database(s).
Notification
The Data Manager should be informed about changes to the Protocol Narrative or SOPs so the
new version number can be incorporated in the Metadata of the project database. Changes in the
Protocol Narrative or SOPs may require the Data Manager to edit the database.
The appropriate PACN staff should be notified of the changes and appropriate level review
process initiated, as determined collaboratively by the network staff and Project Lead.
Once review comments are received, incorporated, and approved, the Project Lead should post
revised versions on the internet and forward copies to all individuals with a previous version of
the affected Protocol Narrative or SOPs. The PACN Data Manager should also be provided with
this
documentation
for
inclusion
in
the
network’s
protocol
library.

357

The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and
other information about those resources; and honors its special responsibilities to American Indians, Alaska Natives, and affiliated
Island Communities.
NPS 988/111725, December 2011

National Park Service
U.S. Department of the Interior

Natural Resource Stewardship and Science
1201 Oakridge Drive, Suite 150
Fort Collins, CO 80525
www.nature.nps.gov

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