U.S. Department of the Interior

U.S. Geological Survey

Techniques and Methods 2–A12

Standardized Methods for Grand Canyon Fisheries 

Research 2015

Chapter 12 of

Section A, Biological Science

Book 2, Collection of Environmental Data
FRONT COVER

A humpback chub (Gila cypha) in the Colorado River. Photo by Randall Babb, Arizona Game and Fish Department.
Standardized Methods for Grand 

Canyon Fisheries Research 2015

By William R. Persons, David L. Ward, and Luke A. Avery

Techniques and Methods 2–A12

U.S. Department of the Interior

U.S. Geological Survey

Chapter 12 of

Section A, Biological Science

Book 2, Collection of Environmental Data
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia/ 

First Release: 2013

Revised: January 2015 (ver. 1.1)

For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod

Telephone: 1-888-ASK-USGS

For more information on the USGS—the Federal source for science about the Earth,

its natural and living resources, natural hazards, and the environment:

World Wide Web: http://www.usgs.gov 

Telephone: 1-888-ASK-USGS

Any use of trade, firm, or product names is for descriptive purposes only and does not imply 

endorsement by the 

U.S. Government.

Although this report is in the public domain, permission must be secured from the 

individual copyright owners to reproduce any copyrighted material contained within this report.

Suggested citation:

Persons, W.R., Ward, D.L, and Avery, L. A., 2013, Standardized methods for Grand Canyon fisheries research 2015 

(ver. 1.1, January 2015), U.S. Geological Survey, Techniques and Methods, book 2, chapter A12, 19 p. 
iii

Contents

Introduction.....................................................................................................................................................1

General Guidelines for Handling Fish.........................................................................................................1

Guidelines for All Projects............................................................................................................................2

Subsampling ..........................................................................................................................................2

Rare-Nonnative-Fish Preservation ....................................................................................................2

Passive Integrated Transponder (PIT) Tagging ..............................................................................2

Protocols for Lees Ferry................................................................................................................................2

Native Fish..............................................................................................................................................2

Nonnative Fish.......................................................................................................................................2

Protocols for the Mainstem Colorado River..............................................................................................3

VIE Tags ..................................................................................................................................................3

Native Fish..............................................................................................................................................3

Nonnative Fish.......................................................................................................................................4

Protocols for the Little Colorado River.......................................................................................................4

VIE Tags ..................................................................................................................................................4

Native Fish..............................................................................................................................................5

Special Conditions for Tagging Bluehead Suckers................................................................5

Nonnative Fish.......................................................................................................................................5

Protocols Common to All Projects ..............................................................................................................5

Length Measurement...........................................................................................................................5

Weight Measurement ..........................................................................................................................6

PIT-Tagging Protocol............................................................................................................................6

Tips for Fish that May Have Multiple PIT Tags........................................................................6

Best Practices for Keeping PIT Tags and Needles Sterile ...................................................6

PIT-Tagging Humpback Chub.....................................................................................................6

PIT-Tagging Suckers ..................................................................................................................7

PIT-Tagging Trout.........................................................................................................................7

PIT-Tagging Catfish and Carp (Dorsal Musculature).............................................................7

Verifying PIT Tags .......................................................................................................................7

Floy-Tagging Protocol ..........................................................................................................................7

Fin-Clipping Protocol............................................................................................................................7

VIE Tags ..................................................................................................................................................8

VIE-Tag Colors, Locations, and Coding ....................................................................................9

Angling Protocol.............................................................................................................................................9

Guidelines for Recording Data ....................................................................................................................9

Standard Data Label for Preserving Specimens .............................................................................9

Preserving Humpback Chub ......................................................................................................................10

Bite Mark Documentation ..........................................................................................................................10

Parasite/Disease Documentation .............................................................................................................11

Document Revisions....................................................................................................................................15

Fall 2002 ...............................................................................................................................................15

Spring 2003...........................................................................................................................................15

September 2003...................................................................................................................................15
iv

Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

mile (mi) 1.609 kilometer (km)

November 2003....................................................................................................................................15

August 2004..........................................................................................................................................15

March 2005 .........................................................................................................................................15

December 2005....................................................................................................................................15

January 2009........................................................................................................................................16

March 2011...........................................................................................................................................16

March 2012...........................................................................................................................................16

January 2015........................................................................................................................................16

Acknowledgments.......................................................................................................................................16

References Cited..........................................................................................................................................17

Appendix A: Field Datasheet Codes .........................................................................................................18

Figures

 1. Illustration showing an example of fork-length and total-length measurements .....................3

 2. Photograph showing a PIT-tag insertion point in a Humpback chub..........................................3

 3. Photograph showing a PIT-tag insertion point in a sucker. ..........................................................4

 4. Photograph showing a PIT-tag insertion point in a rainbow trout. ..............................................4

 5. Photograph showing a PIT-tag insertion point in a channel catfish............................................5

 6. Photograph showing a PIT-tag insertion point in a common carp...............................................5

 7. Example of horizontal lines over letters when recording PIT-tag numbers on a datasheet ...7

 8. Diagram showing Floy-tag insertion point at base of dorsal fin between pterygiophores......7

 9. Drawing showing fins and their corresponding codes on left side humpback chub ...............8

10. Photographs showing the proper adipose-fin clip on trout and catfish .....................................8

11. Line drawing showing possible location codes for visible implant elastomer tag ...................8

12. Picture of Carolina rig used for standardized angling sampling ..................................................9

13. Example of properly completed sample data label ........................................................................9

14. Flow chart showing native fish handling and tagging guidelines at Lees Ferry......................10

15. Flow chart showing nonnative fish handling and tagging guidelines at Lees Ferry...............11

16. Flow chart showing native fish handling and tagging guidelines 

in mainstem Colorado River downstream of Lees Ferry ......................................................12

17. Flow chart showing nonnative fish handling and tagging guidelines 

in mainstem Colorado River downstream of Lees Ferry ......................................................13

18. Flow chart showing native fish handling 

and tagging guidelines in the Little Colorado River ..............................................................13

19. Flow chart showing nonnative fish handling and tagging guidelines 

in the Little Colorado River........................................................................................................14

20. Flow chart showing decision tree for PIT tagging fish which may have multiple tags..........14
Standardized Methods for Grand Canyon Fisheries 

Research 2015

By William R. Persons, David L. Ward, and Luke A. Avery

Introduction

This document presents protocols and guidelines 

to persons sampling fishes in the Grand Canyon, to help 

ensure consistency in fish handling, fish tagging, and data 

collection among different projects and organizations. Most 

such research and monitoring projects are conducted under 

the general umbrella of the Glen Canyon Dam Adaptive 

Management Program and include studies by the U.S. 

Geological Survey (USGS), U.S. Fish and Wildlife Service 

(FWS), National Park Service (NPS), the Arizona Game and 

Fish Department (AGFD), various universities, and private 

contractors. This document is intended to provide guidance to 

fieldworkers regarding protocols that may vary from year to 

year depending on specific projects and objectives. We also 

provide herein documentation of standard methods used in the 

Grand Canyon that can be cited in scientific publications, as 

well as a summary of changes in protocols since the document 

was first created in 2002. 

General Guidelines for Handling Fish

Respectful and careful treatment of fish is critical to 

the long-term success of monitoring and research programs. 

Traumatized fish can exhibit abnormal physiologic, 

behavioral, and ecologic responses that challenge study 

purposes (Nickum, 1988). Rough or improper handling of 

fish is a source of stress that can lead to disease or death. 

Delayed mortality as a result of improper handling may not 

be immediately apparent to researchers but can occur hours 

to days later (Stickney, 1983), causing misleading study 

results and poor public opinion and potentially resulting in 

the loss of permits and cancellation of projects. Researchers 

should be sensitive to public perception and prepared to 

explain sampling activities. All field personnel should be 

familiar with and strictly adhere to research permit guidelines 

and limitations. Sampling procedures should leave sites 

as undisturbed as possible, and capture techniques should 

minimize injury to fish. 

Although specific fish-handling procedures may vary 

from one project to another, all sampling should incorporate 

the following general guidelines:

•	 Be respectful of all fish, regardless of size and species.

•	 Minimize the time that fish are out of the water.

•	 Change water frequently when fish must be held for 

more than a few minutes or if you see fish surfacing for 

air. Remember that handling stress increases as water 

temperature increases. Utilize aerators if available.

•	 Do not put more than 8 to 10 large fish in your workup 

bucket at one time; leave the rest in a net in the river to 

minimize stress.

•	 Be aware that watch straps, lapel badges, and jewelry can 

damage fish.

•	 Do not hold fish tightly around the throat, and avoid 

touching the gills.

•	 Rinse all sunscreen or lotions from hands prior to 

handling fish.

•	 Always wet hands and equipment such as nets and fish 

boards before use. Dry hands and equipment cause 

damage to fish skin by removing coatings that protect 

fish from disease. Equipment such as length boards and 

scales become hot in the sun and can damage fish if not 

wetted before use.

•	 Shake hoop nets when removing them from the water. 

Check carefully for small fish that may have become 

lodged between net folds. Fish mistakenly left in nets are a 

large and avoidable source of researcher-caused mortality.

•	 Document accidentally killed native species on 

datasheets and preserve the specimen with an 

accompanying standard label.

Specific procedures for handling fish vary by location 

and project. General descriptions follow for fish handling 

procedures for Lees Ferry, the mainstem Colorado River, and 

the Little Colorado River.
2 Standardized Methods for Grand Canyon Fisheries Research 2012

Guidelines for All Projects

Subsampling

For abundant small-bodied fishes, for example, speckled 

dace (Rhinichthys osculus), take a subsample (30–50 

individuals of each species), record total length (TL) to the 

nearest millimeter and sexual characteristics, examine all fish > 

40 millimeters (mm) for visible implant elastomer (VIE) tags, 

and then count the remaining, nonsubsampled fish. Attempt 

to randomize your selection process, or else you will bias 

your length data because of your bucket sampling method. Be 

especially careful to avoid selecting for larger specimens.

Current subsampling procedure for rainbow trout is to 

measure the fork length (FL) of the first 50 fish <150 mm FL 

and check the rest for passive integrated transponder (PIT) tags.

Rare-Nonnative-Fish Preservation

If you are trained to do so, take otoliths from rare 

nonnative fish (for example, smallmouth bass [Micropterus 

dolomieu], walleye [Sander vitreus], green sunfish [Lepomis 

cyanellus]) or preserve the head of the fish for later otolith 

removal in the lab. If a rare fish is sampled, record TL to 

the nearest millimeter, weight to the nearest gram (when 

possible), location, date, gear, and disposition (DP=dead 

preserved); add a note in the comments on the datasheet and 

label the sample. If the fish is small, cut open its stomach 

cavity and preserve the fish with ethanol in a labeled 

jar. If the fish is too big to preserve, preserve its head in 

ethanol and check stomach contents (in the field). Record 

stomach contents on the basis of visual observation of large, 

identifiable items; also record in the comments field on the 

datasheet whether stomach contents and head were sampled. 

Back in the laboratory, represerve the specimen with fresh 

ethanol and send to David Ward, USGS Grand Canyon 

Monitoring and Research Center, 2255 N. Gemini Drive, 

Flagstaff, AZ 86001, telephone (928) 556-7280. 

Passive Integrated Transponder (PIT) Tagging 

Become familiar with PIT-tag-reader operation and be 

sure readers are configured to scan and store tags. All native 

fish >300 mm TL should be scanned for the presence of a 

PIT tag using a 134.2-kiloHertz (kHz) reader (either a Biomark FS2001, commonly called a cheeseblock, or a Biomark 

601, commonly called a shoe horn) and a 400-kHz reader 

(old Destron-Fearing blue reader) or a Biomark Pocket 

EX reader. Native fish with only a 400-kHz tag should 

also receive a 134.2-kHz tag, and both numbers should be 

recorded (134.2-kHz tags in PITTAG_1 field and 400-kHz 

tags in PITTAG_2 field). See “PIT-Tagging Protocol” section 

for tips on scanning fish. 

Protocols for Lees Ferry

The following protocols apply primarily to long-term monitoring in the Lees Ferry tailwater reach. The area has been sampled 

by several projects, primarily the Lees Ferry long-term monitoring 

project (Makinster and others, 2011) and the Rainbow Trout Early 

Life Stages study (Korman and Campana, 2009; Korman and 

Melis, 2011), and more recently the Natal Origins project (Project 

BIO 2.E18, Glen Canyon Dam Adaptive Management Program 

Biennial Budget and Work Plan—Fiscal Years 2011–2012). 

Native Fish

Guidelines for handling and tagging native fish at Lees 

Ferry are summarized below and on page 10. Measure TL and 

FL of native fish to the nearest millimeter and examine each 

fish for external parasites, diseases (see “Parasite/Disease 

Documentation” section), and sexual characteristics. Humpback chub (Gila cypha) >80 mm TL should be scanned for the 

presence of a PIT tag, and any humpback chub >80 mm TL 

without a 134.2-kHz tag should be tagged with one. All other 

native fish >149 mm TL should be scanned for the presence of 

a PIT tag, and fish without a 134.2-kHz tag should receive one. 

Nonnative Fish

Guidelines for handling and tagging nonnative fish 

at Lees Ferry are summarized in figure 15. Measure FL of 

rainbow trout (Oncorhynchus mykiss) and TL of all other fish 

to the nearest millimeter. Weigh each fish to the nearest gram 

and examine all:

•	 salmonids for the presence of an adipose- or pelvic-fin 

clip

•	 catfish (that is, channel catfish, Ictalurus punctatus, and 

black bullhead, Ameiurus melas) for the presence of an 

adipose-fin clip 

•	 common carp (Cyprinus carpio) for the presence of a 

dorsal-spine or operculum clip 

Standard protocol is to weigh all fish >150 mm TL, except 

in inclement weather. All salmonids, catfish, and carp with a fin 

clip, and all rainbow trout 80 to 250 mm FL, should be checked 

for the presence of a PIT tag or Floy tag. If large numbers of small 

rainbow trout are collected, batches of fish can be scanned by moving a tag-reader wand in the bucket holding fish. The Natal Origins 

project, which was started in 2011, is PIT-tagging tens of thousands 

of juvenile rainbow trout. All brown trout (Salmo trutta) >149 mm 

TL and all catfish >99 mm TL without a PIT tag should be tagged 

and receive an adipose-fin clip. Carp >99 mm TL without a PIT tag 

should be tagged and receive a dorsal spine clip. In previous years, 

all rainbow trout >199 mm TL caught at random sites received a 

yellow AGFD code Floy tag; this practice is being discontinued in 

2012. All fish except rare nonnatives should be released alive.
Protocols for the Mainstem Colorado River 3

Protocols for the Mainstem Colorado 

River

The following protocols apply to the mainstem Colorado 

River and its tributaries (except the Little Colorado River) 

downstream from Lees Ferry (also see pages 11–12). In 2012, 

projects in the area include AGFD mainstem monitoring 

(Makinster and others, 2010), the Natal Origins project, the 

FWS mainstem humpback chub aggregation-sampling trip, and 

any other trips that may be launched to sample fish. Nonnativespecies-removal efforts may be conducted in the Paria-toBadger Rapid reach of Marble Canyon, for which alternative 

nonnative-fish-handling procedures will apply (Bureau of 

Reclamation, 2011). Additional projects in tributaries which are 

subject to their own protocols include the NPS humpback-chub 

translocations in Havasu and Shinumo Creeks and the fish weir 

in Bright Angel Creek. PIT-tag information from these projects 

will be shared between Grand Canyon National Park and the 

Grand Canyon Monitoring and Research Center.

Visible Implant Elastomer (VIE) Tags

Fish <150 mm TL (suckers <200 mm) should be checked 

carefully for VIE tags. Record recapture information, color 

and location of any VIE tags in the appropriate datasheet 

fields. See subsection below entitled “VIE Tag Colors, 

Locations, and Coding.”

Native Fish

Measure TL and FL of native fish to the nearest 

millimeter (fig. 1) and examine each fish for external parasites, 

diseases (see “Parasite/Disease Documentation” section), and 

sexual characteristics. Examine bluehead suckers >149mm 

TL for a left-pelvic clip (LP2) and record whether one is 

present. Humpback chub >80 mm TL should be scanned for 

the presence of a PIT tag, and any humpback chub >80 mm 

TL without a PIT tag should receive one (fig. 2). All other 

native fish >149 mm TL should be scanned for the presence 

Figure 1. Illustration 

showing an example of 

fork-length and total-length 

measurements (adapted 

from Anderson and 

Neumann, 1996).

Figure 2. Photograph 

showing a PIT-tag 

insertion point in a 

humpback chub.

Insertion location
4 Standardized Methods for Grand Canyon Fisheries Research 2012

of a PIT tag, and those without a 134.2-kHz tag should receive 

one. Native fish with only a 400-kHz tag should receive a new 

134.2-kHz tag, and both numbers should be recorded (fig. 3).

Nonnative Fish

All salmonids, catfish, and carp with a fin clip, and all 

rainbow trout between 100 and 250 mm, should be scanned 

for the presence of a PIT tag. Measure FL of rainbow trout and 

TL of all other fish to the nearest millimeter and weigh each 

fish to the nearest gram when conditions allow. PIT-tagged 

rainbow trout caught during non-Natal Origins trips should be 

relatively uncommon; however, if such rainbow trout lack an 

adipose-fin clip, they should receive one.

Examine all:

•	salmonids for the presence of an adipose- or pelvic-fin 

clip

•	catfish for the presence of an adipose-fin clip 

•	common carp for the presence of a dorsal-spine or 

operculum clip.

All salmonids, catfish, and carp with a fin clip, and all 

rainbow trout 80–250 mm FL, should be scanned for the presence of a PIT or Floy tag. Brown trout >149 mm TL and all 

catfish >99 mm TL without a PIT tag should be tagged and 

receive an adipose-fin clip. Common carp >99 mm TL without 

a PIT tag should be tagged and receive a dorsal spine clip (see 

fig. 4). In previous years, all rainbow trout >199 mm TL were 

Floy-tagged. For mark-recapture experiments during 2012, 

rainbow trout >100 mm FL should be PIT-tagged and receive 

an adipose-fin clip.

During nonnative-fish-removal efforts, data on nonnatives 

will be collected as detailed above. Rainbow trout without a 

PIT tag will be removed alive from the river and transported to 

an appropriate stocking location to be identified by the AGFD. 

Rainbow trout that do have a PIT tag, and all common carp, 

will be returned alive to the river, and their return location 

will be recorded; all other nonnatives will be euthanized and 

preserved in accordance with the appropriate procedure.

Protocols for the Little Colorado River

The following protocols (see figs. 18, 19) apply to the 

Little Colorado River, including FWS population-estimation 

sampling in spring and fall, FWS translocation monitoring, 

AGFD lower-1,200-m monitoring, and any other sampling 

that may be conducted in the Little Colorado River from Blue 

Springs to the confluence with the Colorado River (Gloss 

and Coggins, 2005; Coggins and others, 2006; Bureau of 

Reclamation and U.S. Geological Survey Grand Canyon 

Monitoring and Research Center, 2010).

VIE Tags

Fish <150 mm TL (suckers <200 mm TL) should 

be scanned carefully for VIE tags. Record the recapture 

information, color, and body location of any VIE tags in the 

appropriate datasheet fields (see appendix entitled “VIE-Tag 

Color and Location Codes”).

Figure 3. Photograph showing a PIT-tag insertion point in a 

sucker.

Figure 4. Photograph showing a PIT-tag 

insertion point in a rainbow trout.
Protocols Common to All Projects 5

Native Fish

Measure TL of all native fish and FL of all large-bodied 

native fish to the nearest millimeter; FL for speckled dace need 

not be measured. Fish do not need to be weighed. Examine 

each fish carefully for fin clips, external parasites and sexual 

characteristics. All humpback chub >80 mm TL and flannelmouth suckers and bluehead suckers >149 mm TL should be 

scanned for the presence of a PIT tag. Any humpback chub 

over 80 mm TL without a 134.2-kHz tag should receive one, 

and any flannelmouth and bluehead sucker >149 mm TL without a PIT tag should receive one. (See next subsection.) 

Special Conditions for Tagging Bluehead Suckers

In some years, the FWS will catch large numbers of 

bluehead suckers during Little Colorado River hoopnetting 

trips. Cooperators have agreed that under such circumstances, 

it would be acceptable to PIT-tag a maximum of 900 and 400 

bluehead suckers during spring and fall trips, respectively. Any 

more fish would be measured but would not receive a new PIT 

tag. Additionally, once these numbers have been met, a representative subsample of 50 fish may be measured and the rest 

counted if the biologist deems this step appropriate.

Nonnative Fish

 Measure FL of rainbow trout and TL of all other 

species to the nearest millimeter. All small-bodied nonnatives 

should be scanned for the presence of VIE tags. Examine finclipped salmonids, catfish, carp, and all rainbow trout >80 

mm FL and <250 mm FL and scan for the presence of a PIT 

or Floy tag. If not previously tagged, brown trout >149mm 

TL and all catfish >99 mm TL should receive a PIT tag and 

receive an adipose-fin clip. Carp >99 mm TL should receive 

a PIT tag and a dorsal-spine clip (see fig. 6).

Protocols Common to All Projects

Length Measurement

•	 TL – measure length from the anteriormost part of the 

fish to the tip of the longest caudal-fin ray, with the lobes 

of the caudal fin pressed together (fig. 1). 

•	 FL – measure length from the most anteriormost part of 

the fish to the tip of the median caudal-fin ray.

Figure 5. Photograph showing a PIT-tag 

insertion point in a channel catfish.

Figure 6. Photograph showing a PITtag insertion point in a common carp.
6 Standardized Methods for Grand Canyon Fisheries Research 2012

Weight Measurement

Record weight to the nearest gram; weigh fish only if 

it is not windy or raining and your equipment is functioning 

properly. Poor data are worse than no data, so do not collect a 

weight if you are not confident of its accuracy.

PIT-Tagging Protocol

All PIT-tag implants must be Biomark HPT12, 

12.5-mm, 134.2-kHz, ISO FDXB tags provided by the Grand 

Canyon Monitoring and Research Center. Do not use old 

400-kHz tags! 

All catfish and carp >99 mm TL, humpback chub 

>80mm TL, brown trout >149 mm TL, and all other native 

species >149 mm TL (except for bluehead suckers under 

certain circumstances) without a 134.2-kHz tag should 

receive one even if they already have an old 400-kHz PIT 

or a Floy tag. Rainbow trout are also being PIT tagged on 

the Natal Origins project (see Project BIO 2.E.18 Bureau 

of Reclamation and U.S. Geological Survey Grand Canyon 

Monitoring and Research Center, 2010). When recording PIT 

tags, be sure to mention whether the fish is a recapture (Y) or 

was not a recapture and was given a new tag (N). Use a test 

tag to verify that readers are working before each use. 

Ensure that PIT-tag readers are configured with the 

correct date and time stamp. Reader configuration needs to be 

done in the office using a personal computer before leaving 

for the field. Download the data from readers after each trip 

and transmit reader files to the Grand Canyon Monitoring and 

Research Center. 

Tips for Fish that May Have Multiple PIT Tags

In the event that you catch a native fish >300 mm TL 

and cannot detect a PIT tag with an FS-2001 “cheeseblock” 

reader, and you do not have a working 400-kHz reader, do

insert a new tag. If you suspect that a fish already has a new 

PIT tag (large fish or evidence of a PIT tag scar) but you 

are unable to detect the tag, the fish may have multiple tags 

that are nullifying each other. Multiple-tagged fish are not 

uncommon. Scan the fish by moving the reader wand in 

several different orientations. Place a test tag next to the fish 

and try rescanning the fish. If the reader fails to detect the test 

tag, the fish probably already has one or more PIT tags that 

are nullifying each other. Do not insert a new PIT tag into a 

fish that is believed to already have multiple tags, and note 

this observation on the datasheet (see fig. 20). 

PIT-tag insertion points vary by species, as will be 

discussed further in the following subsections. Become 

familiar with PIT-tag-reader operation and ensure that readers 

are configured to scan and store tags. 

Best Practices for Keeping PIT Tags and 

Needles Sterile

If you are using bulk PIT tags, soak tags in ethanol 

or isopropyl alcohol before use to check for broken tags 

(inside of tags will often change from copper color to red 

if broken). Return broken tags with lot IDs to Dave Foster, 

USGS Grand Canyon Monitoring and Research Center, 

2255 N. Gemini Drive, Flagstaff, AZ 86001, 928-556-

7107, as soon as the trip is off river. Some tags will scan 

even if the glass is broken, but they will fail over time.

If you are using bulk PIT tags, verify that the needle 

is sharp and clean. Biomark guidelines recommend that 

needles be changed every 10 fish. If you are using single 

needles for many fish, disinfect the needle and tag in 60 to 

80 volume-percent ethanol or isopropyl alcohol. Needles 

should be cleaned between each use to remove adhering 

slime and scales that can be a path of infection between 

fish (Columbia Basin Fish and Wildlife Authority—PIT 

Tag Steering Committee, 1999) Columbia Basin Fish and 

Wildlife Authority, 1999).

Starting in 2011, the Grand Canyon Monitoring and 

Research Center will provide Biomark preloaded sterile 

needles and MK-25 implant guns. Keep used needles 

in a safe container (for example, Nalgene bottle) and 

return used needles to the Grand Canyon Monitoring and 

Research Center for recycling.

PIT-Tagging Humpback Chub

1. Hold the fish with its abdomen up and its tail pointing 

toward you.

2. Insert the needle just posterior to the pelvic fin (fig. 2).

3. The insertion point should be on the abdomen of the 

fish to the right of the midventral line, with the tag 

placed posterior to the left pelvic girdle. The forward 

position of the pelvic fins on humpback chub allows the 

tag to be inserted higher on the abdomen than on other 

species. 

4. The depth of needle penetration should be only enough 

to place the tag within the body cavity. Preliminary data 

from laboratory studies suggest that inserting the needle 

too far and perforating the intestine is the main cause 

of PIT-tag mortality (adapted from Biomark guidelines; 

visit http://www.biomark.com for the latest guidelines 

and training videos).

5. Do not PIT-tag small humpback chub that appear 

bloated because of the danger of perforating the 

intestine with the PIT-tag needle.
Protocols Common to All Projects 7

PIT-Tagging Suckers 

Use the same procedures for suckers as for humpback 

chub, or insert the PIT tag toward the tail of the fish under 

the left pelvic girdle (fig. 3). The needle should be directed 

posterior so that the tag is injected away from the heart and 

other vital organs. 

PIT-Tagging Trout

Use the same procedures for trout as for humpback chub. 

Insert the PIT tag on the abdomen of the fish to the left of the 

midventral line, under the pelvic girdle (fig. 4). 

PIT-Tagging Catfish and Carp (Dorsal 

Musculature)

1. Hold the fish with its abdomen down and the tail pointing 

toward you.

2. Insert the needle just posterior to the dorsal fin, to the 

left of the middorsal line (fig. 5). Scales may need to be 

removed from carp at the insertion point of the tag (fig. 6).

3. The depth of insertion should be only enough to place the 

PIT tag inside the dorsal musculature. 

Verifying PIT Tags 

Unacceptable errors can be made when transcribing and 

entering PIT tags into computer databases. The following 

procedures help to minimize errors that may occur when 

transcribing and entering PIT tags:

•	 Verify that the PIT-tag reader is turned on and in “scan/

store” mode.

•	 Scan the fish for tags.

•	 Read and record the entire 10- to 14-digit code using 

words instead of letters to avoid confusion between letters 

and numbers that sound alike. For example, tag code 

12A3F45E6B should be read as “one, two, alpha, three, 

foxtrot, four, five, echo, six, bravo.”

•	 Always cross zeros when recording PIT tags to distinguish 

a zero from a “D” on a datasheet. When recording PIT 

tags, draw a horizontal line above any letters in the tag 

number (fig. 7) to distinguish letters from numbers that 

can easily be confused (for example, B and 8, D and 0, S 

and 5).

•	 The data recorder will repeat the tag code back to verify 

that it has been recorded correctly.

•	 Be sure to record whether the fish is a recapture (Y) 

or not (N).

Floy-Tagging Protocol

Rainbow trout are the only fish in the mainstem Colorado 

River that should receive a Floy tag for mark-recapture 

experiments. Floy tags, also known as T-Bar anchor tags, should 

be inserted just below the dorsal fin (fig. 8). Scales should be 

removed first at the insertion point of the tag. Insert the tag at an 

acute angle to the body so that the tag lies next to the body when 

the fish swims. Insert the needle far enough to pass the midline 

but not to puncture the opposite side. Be sure to place the 

anchor behind the pterygiophores to prevent excessive tag loss 

(Waldman and others, 1990). Twist applicator 90° to dislodge the 

tag from the applicator before removing the needle from the fish.

Fin-Clipping Protocol

•	 Fins should be clipped at the base and completely removed 

from all fish that receive a fin clip. Fin clip codes should 

reference the side of the fish and the fin location (fig. 9; see 

appendix A, “datasheet codes”).

•	 The adipose fin should be clipped at the base and completely 

removed from all rainbow trout in the Lees Ferry reach that 

receive a Floy tag (fig. 10). Again, Floy tags should be used 

only for short-term mark-recapture experiments. Use yellow 

“AGFD” Floy tags in the Lees Ferry reach, and gray “USGS” 

Floy tags downstream from Lees Ferry. 

•	 As part of short-term mark-recapture experiments, rainbow 

trout downstream of Lees Ferry that receive a “USGS” gray 

Floy tag should also receive a left pelvic-fin (LP2) clip. 

Clip pelvic and pectoral fins at the base, removing the entire 

pelvic or pectoral fin. 

•	 All brown trout >149 mm TL and catfish >99 mm TL should 

receive a PIT tag and an adipose-fin clip.

•	 Common carp receiving a PIT tag should also receive a dorsalspine clip.

Figure 7. Example 

of horizontal lines 

over letters when 

recording PIT-tag 

numbers on a 

datasheet.

Figure 8. Diagram 

showing Floy-tag 

insertion point 

at base of dorsal 

fin between 

pterygiophores.
8 Standardized Methods for Grand Canyon Fisheries Research 2012

VIE Tags

Several colors of VIE tags have been placed in 

humpback chubs and other fish as a part of the Near 

Shore Ecology project. Marks were placed around all fins, 

operculum, and snout (fig. 11). All fish >40 mm and <149 

mm TL (suckers <200 mm TL) should be scanned for the 

Figure 11. Line drawing showing possible location 

codes for visible implant elastomer tag: AN, anal fin; 

CD, caudal fin; DR, dorsal fin; FD, forward dorsal fin; 

RD, rear dorsal fin; HD, head, LP, lip; P1, right pelvic 

fin; P2, left pelvic fin. .

Figure 9. Drawing showing fins and 

their corresponding codes on left side 

of humpback chub (from http://www.

coloradoriverrecovery.org/generalinformation/the-fish/humpback-chub.

html).

Figure 10. Photographs showing the proper 

adipose-fin clip on trout (left) and catfish (right).

presence of VIE tags. Fish captured in the Little Colorado 

River and in the mainstem near the Little Colorado River 

confluence and downstream to Unkar Creek Rapid should 

be carefully examined because all fish captured by the Near 

Shore Ecology project were tagged in this reach of the river. 

Colors should be compared to color standards provided by 

the Grand Canyon Monitoring and Research Center. 
Guidelines for Recording Data 9

VIE-Tag Colors, Locations, and Coding

Codes for VIE tag colors and locations should be 

reported color first, then side, and then location. For example, 

an orange VIE tag located by the left pelvic fin would be 

recorded as “OLP2.” Codes for VIE-tag color and location are 

listed in appendix A (“Field Datasheet Codes”).

Angling Protocol

Standardized angling in the Grand Canyon consists of 

three anglers fishing for 20 minutes, for a total of 60 anglerminutes per site. Spinning rods are outfitted with 10-poundtest monofilament line, a 1⁄2-ounce (14 gram) egg sinker, a 

barrel swivel, and a no. 6 Eagle Claw baitholder hook baited 

with half a worm. The setup is fished by using a Carolina 

rig where the egg sinker is slipped on to the main line then 

a barrel swivel is attached. A leader of 8 to 10 inches (in) 

of 10-pound-test monofilament line with a no. 6 Eagle Claw 

hook attached on one end is then attached to the other end of 

the barrel swivel (fig. 12).

Guidelines for Recording Data

•	 If you do not record data in the field, you will 

unlikely be able to reconstruct them in the office. 

It is better to record too much information on a 

datasheet than to return to camp or the office and 

try to reconstruct it. Take your time and record 

clean data. It is better to have correct data than a 

lot of data with irresolvable problems.

•	 Proper recording of data is the most important 

aspect of field research. You may feel pressured 

to process fish quickly, especially when catches 

are high. Remember that you can process fish 

only as fast as the recorder can accurately record 

legible data. If you proceed too quickly, the data 

get sloppy. If your handwriting is illegible, the data 

are basically lost. Communicate with your data 

recorder and ask whether you are going too fast. 

Data recorders must stop the fish processor if they 

are going too fast. 

Trip ID LC20120622

Biologist Engelbert Humperdinck

Sample site Camp and net in LCR (Site at LF and mainstem, NSE use Site-HSU)

River LCR

Date June 25, 2012

Time 1630

Mile RM in mainstem, RKM upstream from the mouth in Tributaries

Gear HB (Hoopnet baited)

Species STB

Length 85 mm

Weight 35 g

Sample id (what preserved) Try to keep Sample_IDs unique during a trip.

Preservative Formalin, Ethanol, etc.

Figure 13. Example of properly completed sample data label.

Figure 12. Picture of Carolina rig used for standardized angling sampling.

•	 Do not forget to record “Y” or “N” in the recapture field. 

Do not assume that the data recorder is observing whether 

you are injecting a tag or not. Each mistake can be costly 

during analysis. Slow down in the field and ensure that 

the recapture field is filled in. Examine datasheets daily to 

verify that data recording problems are not occurring. 

•	 Where possible, record Global Positioning System (GPS) 

waypoints on the datasheet and the serial number from the 

GPS unit being used. If you cannot obtain a waypoint, note 

it on the datasheet.

•	 A blank data field indicates that the fish was not checked. 

Be sure to fill in all columns of the datasheet and note 

whether such things as parasites or ripeness were checked: 

blank = you didn’t check; “undetermined” = you checked 

but couldn’t make a distinction.

Standard Data Label for Preserving Specimens

Fill out all sample information on write-in-the-rain paper 

with a pencil only. Label all preserved specimens so that they 

can be clearly linked to the datasheet (fig. 13).
10 Standardized Methods for Grand Canyon Fisheries Research 2012

Preserving Humpback Chub 

All dead humpback chub must be saved and preserved in 

ethanol. Humpback chub too large to preserve whole should 

have their heads and gut contents preserved in ethanol. At 

the very least, otoliths should be extracted before bacterial 

decomposition compromises potential microchemical analyses. 

Bite Mark Documentation

Record any bite marks observed on all native fish 

in the comments section of the datasheet. If possible, 

photograph and describe suspected bite marks. If you 

have photographed the fish, title the photograph with the 

species and date (for example, “HBC06122012”) so that 

multiple photographs can be distinguished from each other 

upon return to the office. Note the photograph title in the 

comments section of the datasheet. 

Figure 14. Flow chart showing native fish handling and tagging guidelines at Lees Ferry.

Native fish in Lees Ferry

• Measure TL (mm) and weight (g)

• Measure FL (mm) for all non-SPD

• Examine for external parasites/

 diseases and sexual characteristics

• Record color(s) and location(s) of 

• VIE tag(s) if present

Humpback chub >80 mm TL

or other native >149 mm TL

Humpback chub ≤80 mm TL

or other native ≤149 mm TL

Scan for 134.2 kHz Pit tab

134.2 kHz tag present No 134.2 kHz tag present

Record tag number and

recapture (recap-Y) Insert 134.2 kHz tag

Scan for old 400 kHz tag with appropriate scanner

400 kHz tag present Na400 kHz tag present

Record tag number Release

Subsample 

speckled dace, if 

significantly more 

than 30 individuals 

in the sample
Parasite/Disease Documentation 11

Figure 15. Flow chart showing nonnative fish handling and tagging guidelines at Lees Ferry.

Nonnative fish in Lees Ferry reach

Record tag number

and release

Check for fin, 

dorsal spine, or

operculum clips

Preserve

according

Check for PIT or Floy tab to protocol

Tag present No tag present Rainbow trout

Carp >99 mm TL

Release

Brown trout >149 mm TL,

catfish >99 mm TL

Insert 134.2 kHz tag

and clip adipose fin

Insert 134.2 kHz tag 

and clip dorsal spine

Check for VIE

marks and subsample

when appropriate

Between 80 and 250 mm FL

Rare

nonnatives All others Brown trout,

catfish and carp

Rainbow trout; measure 

FL (mm) and weight (g)

All other nonnatives; measure TL (mm) and weight (g)

Examine all for parasites and sexual characteristics

Parasite/Disease Documentation

Record any visible parasites and diseases (see appendix A, 

“Field Datasheet Codes”). If a parasite or disease is unknown 

or in question, take a photograph and write detailed comments 

on the datasheet for further examination later. Include a piece 

of paper in the photograph with enough information to link it 

with the fish datasheet, or record information about the camera 

(model, owner, image numbers) on the datasheet so that the 

photograph can be linked to the fish.

 If you see anchor worms (Lernaea) do not remove them 

from the fish (R. Cole, National Wildlife Health Center, USGS, 

written commun., 2009). Removal can create an open wound and 

lead to infection. Anchor worms may also provide a biological 

marker indicating that the fish was in warm water (for example, 

the Little Colorado River) long enough for the parasite to develop. 

This information might help to establish the recent history of 

the fish. If Asian tapeworm (Bothriocephalus acheilognathi, 

commonly found in humpback chub in the Little Colorado River) 

is suspected and a small fish appears to be bloated, do not PIT-tag.
12 Standardized Methods for Grand Canyon Fisheries Research 2012

Native fish in mainstem Colorado River

Measure TL (mm) and weight (g)

measure FL (mm) for all except

speckled dace.

<150 mm TL (suckers

<200 mm TL);

check for VIE tags(s)

Humpback chub 

>80 mm TL

or other native

 >149 mm TL

Scan for 134.2 kHz Pit tag

No 134.2 kHz tag present 134.2 kHz tag present

400 kHz tag present No 400 kHz tag present

Record tag number Release

Record tag number

and recapture (recap-Y)

Scan for old 400 kHz tag with appropriate scanner

Insert 134.2 kHz tag

Humpback chub

≥80 mm TL

or other native 

≥149 mm TL

Subsample

speckled dace

if significantly

more than

30 individuals

in the sample

Examine all for

external

parasites/diseases

and sexual

characteristics

Figure 16. Flow chart showing native fish handling 

and tagging guidelines in mainstem Colorado River 

downstream of Lees Ferry.
Parasite/Disease Documentation 13

Figure 17. Flow chart showing nonnative 

fish handling and tagging guidelines in 

mainstem Colorado River downstream of 

Lees Ferry.

Figure 18. Flow chart showing native fish handling 

and tagging guidelines in the Little Colorado River.

Nonnative fish in mainstem Colorado River

Rainbow trout;

measure FL (mm)

and weight (g)

Between 80 and

250 mm FL for

PIT tag

Check for PIT or Floy tag

Tag present No Tag present

Record tag number and release

Check for fin, 

dorsal spine, or

operculum clips

Preserve

according

to protocol

Carp >99 mm TL Rainbow trout

Release

Brown trout >149 mm TL,

catfish >99 mm TL

Insert 134.2 kHz tag

and clip ADP fin

Insert 134.2 kHz tag 

and clip dorsal spine

Check for VIE

marks and subsample

when appropriate

Rare

nonnatives All others Brown trout,

catfish and carp

All other nonnatives; measure TL (mm) and weight (g)

Native fish in Little Colorado River

Measure TL (mm), measure FL (mm) for all except speckled dace.

<150 mm TL (suckers <200 mm TL);

check for VIE tags(s)

Humpback chub >80 mm TL

or other native >149 mm TL

Scan for 134.2 kHz PIT tag

134.2 kHz tag present No 134.2 kHz tag present

400 kHz tag present No 400 kHz tag present

Record tag number Release

Record tag number and recapture (recap-Y)

>300mm TL; Scan for old 400 kHz tag with appropriate scanner

Insert 134.2 kHz tag

Humpback chub ≤80 mm TL

or other native ≤149 mm TL

900+ Fall Bluehead sucker;

Subsample if significantly more

than 50 individuals in the sample

Examine all for external parasites/diseases and sexual characteristics
14 Standardized Methods for Grand Canyon Fisheries Research 2012

Figure 20. Flow chart 

showing decision 

tree for PIT tagging 

fish which may have 

multiple tags.

Figure 19. Flow chart showing 

nonnative fish handling and 

tagging guidelines in the Little 

Colorado River.

Nonnative fish in Little Colorado River

Check for ADP,

LP2, or RP2 fin, 

dorsal spine, or

operculum clips

Preserve

according

to protocol

Check for Visible

Elastomer Implants

and subsample

when appropriate

Rare

nonnatives All others Brown trout,

catfish and carp

Rainbow trout; All other nonnatives; measure TL (mm) and weight (g)

measure FL (mm)

and weight (g)

Between 80 and

250 mm FL for

PIT tag

Check for PIT or Floy tag

Tag present No Tag present

Record tag number and release

Carp >99 mm TL Rainbow trout

Release

Brown trout >149 mm TL,

catfish >99 mm TL

Insert 134.2 kHz tag

and clip ADP fin

Insert 134.2 kHz tag 

and clip dorsal spine

Capture

native fish

Scan with

134.2 kHz reader

Record tag Recapture? Fish >300 mm TL or suspected

to already have a tag

Scan with

400 kHz reader Implant tag

Recapture?

Place test tag

next to fish and

scan again.

Tags are nullifying

Release fish DO NOT IMPLANT TAG

Implant tag

NO

NO YES

NO

NO

YES

YES

YES Detect test tag?
Document Revisions 15

Document Revisions

Fall 2002 

• Discontinued baiting hoopnets after laboratory studies 

revealed that PIT-tagging of recently-fed fish led to high 

mortality. 

• Native fish >150 mm TL without a PIT tag received one, and 

dorsal fin was punched as a secondary mark to evaluate tag loss.

• September trip received a left-pelvic-fin clip. Fish 100 to 

149 mm TL caught during the Little Colorado River October 

trip received a left-pelvic-fin clip if they did not already 

have one and a right-pelvic-fin clip if the left pelvic fin was 

previously clipped to get an early estimate of recruitment.

Spring 2003

• Started PIT-tagging previously untagged native fish with 

the new 134.2-kHz tags. 

• Started PIT-tagging all carp ≥150 mm TL.

• Experimented with the use of elastomer dye to mark suckers.

• Chub translocated above Chute Falls were tagged with 

elastomer dye.

September 2003

• Started PIT tagging all chub ≥100 mm TL and all other 

native fish ≥150 mm TL. Fish with 400-kHz PIT tags were 

double-tagged with new 134.2-kHz tags.

• Discontinued taking weights on humpback chub to reduce 

handling.

November 2003

• PIT-tagging size for any species of fish is ≥150 mm TL 

until further notice, but humpback chub >100 mm still need 

to be scanned for the presence of a PIT tag.

• No weighing of fish until further notice. Trout projects 

downstream and in Lees Ferry will experiment with new 

types of scales and attempt to find equipment that will work 

better under field conditions.

• 400-kHz PIT tags will no longer be inserted in any fish 

downstream of Lees Ferry.

• Brown trout caught on downstream trips will now receive a 

134.2-kHz PIT tags at 

• ≥150 mm TL instead of 120 mm TL as previously. Do not 

insert a 134.2-kHz PIT tag into brown trout if they already 

have an old 400-kHz PIT tag.

• All chub in the Little Colorado River must be examined 

for yellow VIE tags with blue light and amber glasses. VIE 

tags are located in the dorsal musculature near the dorsal 

insertion on the left side of the fish. 

• Mainstem trips are not required to use blue light and amber 

glasses to scan for VIE tags in chub.

• VIE dyes will no longer be used as a secondary mark to 

evaluate tag loss in suckers, but be sure to record whether 

you see pink or green VIE tags in the head of suckers.

• In the event that you catch a humpback chub >350 mm 

TL, cannot get a read with the new PIT-tag reader, and you 

do not have a working old reader, do not insert a new PIT 

tag—just record and release.

August 2004

• All data submitted to the Grand Canyon Monitoring and 

Research Center should include all digits and the period for 

new PIT-tag numbers, for example, “3D9.1BF4A3C2E.”

March 2005 

• It has been 2 years since any fish 100 mm TL have been 

tagged. Fish between 100 and 149 mm TL no longer need 

to be scanned for PIT tags. Any fish previously tagged (in 

2003) at 100 mm TL would now be >150 mm TL.

December 2005

• Take otoliths from all catfishes and centrarchids. Preserve 

in ethanol, include vial label, and record on nonnative 

datasheet (bottle number). 

• Take 20 to 30 catfish samples when possible (spines, 

otolith). If catfish are similar in size, take a subsample of 

spines and otoliths.

• Check all catfish stomachs for the presence or absence of 

fish remains (in the field).

• Bring all warmwater nonnatives (bass and so on) back to 

the office, whole when possible. Preserve in ethanol and 

cut open stomach cavity to allow internal organs to be 

preserved.

• If species is too large to bring back whole, take stomachs 

and otoliths (preserved in ethanol). Take scales from 

posterior side of pectoral fin below or above lateral line (dry 

preservation), as well as a fin clip (also preserved in ethanol).

• Disposition code is “DP” if specimen is preserved.

• Record all information on datasheets (date, disposition, 

location [river mile], bottle numbers, and what was 

removed and (or) preserved).
16 Standardized Methods for Grand Canyon Fisheries Research 2012

January 2009

• PIT-tag humpback chub >99 mm TL rather than 149 mm TL 

unless fish is bloated or appears to have Asian tapeworm.

• Check for VIE tags on all fish <149 mm TL.

• Soak PIT tags in ethanol to check for broken tags in the field.

• Document rare nonnative fish in writing to Kara Hilwig, 

Grand Canyon Monitoring and Research Center, with 

associated sample(s) taken.

• FWS will PIT-tag a maximum of 900 bluehead sucker 

>149 mm TL during the first spring sampling trip and a 

maximum of 400 bluehead sucker during fall sampling 

trips. All other bluehead suckers will receive an LP2 clip.

• In the event that you catch a native fish >300 mm TL and 

cannot get a PIT-tag code with the new scanner, then scan the 

fish with a test PIT tag held next to it. If you detect the test tag, 

then insert a new PIT tag. If you do not detect the test tag, then 

the fish is likely double tagged, and so do not insert another tag.

• Standardized angling effort and gear throughout canyon.

• Record bite marks in comments section on datasheet.

March 2011

• Edited document for clarity and to avoid redundancy.

• Revised figures to clarify tagging procedures.

• Added information on VIE-tag color and location coding.

• Clarified that all rainbow trout should be Floy tagged. The 

Grand Canyon Monitoring and Research Center will provide 

Floy tags and guns to the Near Shore Ecology project.

• Starting in 2011, the Grand Canyon Monitoring and Research 

Center will provide Biomark preloaded sterile needles and 

MK-25 implant guns. Keep used needles in a sharps container 

(such as a Nalgene bottle) and return to the Grand Canyon 

Monitoring and Research Center for recycling.

March 2012

• Changed tagging protocol for bluehead suckers in the Little 

Colorado River. Only a subset of bluehead suckers will be 

PIT tagged by the FWS in the Little Colorado River.

• FL of rainbow trout will be measured to accommodate the 

Natal Origins project.

• All rainbow trout 80 to 250 mm FL will be scanned for PIT 

tags to accommodate the Natal Origins project.

• All rainbow trout with an adipose-fin clip will be scanned 

for a PIT tag.

• Added alternative nonnative-fish-handling procedure for 

mechanical-removal efforts.

• Updated VIE tag location table and figure.

• Changed contact person for preserved nonnative specimens 

to David Ward, USGS Grand Canyon Monitoring and 

Research Center, 2255 N. Gemini Drive, Flagstaff, AZ 

86001, telephone (928) 556-7280.

• Except for mark-recapture experiments, fish will no longer 

be Floy tagged in Lees Ferry or downstream.

• Updated flowchart figures.

• Updated all field codes on datasheets for consistency with 

latest version of Access data-entry template (2012_02_08).

January 2015

Changed length of humpback chub to PIT tag or check for 

PIT tag presence from >= 99 mm TL to 80 mm TL to allow for 

PIT tag insertion into smaller humpback chub. See Ward and 

others (in press) for documentation and justification of this change. 

Acknowledgments

Development of these standardized methods has been 

a group effort taking place over several years. We are 

especially grateful for contributions by Aaron Bunch, Mike 

Anderson, Robin Osterhoudt, Brian Cark, Pilar Woltors, 

and Andy Makinster of the AGFD; D.R. Van Haverbeke, 

Dennis Stone, Pamela Sponholtz, and Mike Pillow of the 

FWS; Brian Healy and Emily Omana of the NPS with Grand 

Canyon National Park; Josh Korman of Ecometric, Inc.; 

Bill Pine of the University of Florida; and Scott Vanderkooi, 

Michael Yard, Kyrie Fry, and Meredith Hartwell of the 

USGS Grand Canyon Monitoring and Research Center. 
References Cited 17

References Cited

Anderson, R.O., and Neumann, R.M., 1996, Length, weight, 

and associated structural indices, in Murphy, B.R., and 

Willis, D.W., eds., Fisheries techniques (2d ed.): Bethesda, 

Md., American Fisheries Society, p. 447–481 [http://www.

fw.vt.edu/murphybr/web/Readings/Anderson%20and%20

Nuemann.pdf, accessed December 22, 2010].

Coggins, L.G., Jr., Pine, W.E., III, Walters, C.J., Van 

Haverbeke, D.R., Ward, D., and Johnstone, H.C., 2006, 

Abundance trends and status of the Little Colorado River 

population of humpback chub: North American Journal 

of Fisheries Management, v. 26, no. 1, doi: 10.1577M05-

075.1, p. 233–245 [http://www.usbr.gov/uc/rm/amp/twg/

mtgs/06may24/Attach_06f.pdf, accessed July 19, 2011].

Columbia Basin Fish and Wildlife Authority—PIT Tag Steering 

Committee, 1999, PIT tag marking procedures manual—

version 2.0: Portland, Ore., 22 p. [http://php.ptagis.org/wiki/

images/e/ed/MPM.pdf, accessed March 21, 2012].

Gloss, S.P., and Coggins, L.G., 2005, Fishes of the Grand 

Canyon, in Gloss, S.P., Lovich, J.E., and Melis, T.S., eds., The 

state of the Colorado River ecosystem in Grand Canyon—A 

report of the Grand Canyon Monitoring and Research Center 

1991–2004: U.S. Geological Survey Circular 1282, p. 33–56 

[http://pubs.usgs.gov/circ/1282/, accessed May 10, 2010].

Korman, J., and Campana, S.E., 2009, Effects of hydropeaking 

on nearshore habitat use and growth of age-0 rainbow trout 

in a large regulated river: Transactions of the American 

Fisheries Society, v. 138, no. 1, doi: 10.1577/T08-026.1, 

p. 76–87 [http://www.tandfonline.com/doi/abs/10.1577/T08-

026.1, accessed June 1, 2011].

Korman, J., and Melis, T.S., 2011, The effects of Glen Canyon 

Dam operations on early life stages of rainbow trout in the 

Colorado River: U.S. Geological Survey Fact Sheet 2011–

3002, 4 p. [http://pubs.usgs.gov/fs/2011/3002/fs2011–3002.

pdf, accessed January 19, 2011].

Makinster, A.S., Persons, W.R., and Avery, L.A., 2011, 

Status and trends of the rainbow trout population in the 

Lees Ferry Reach of the Colorado River downstream 

from Glen Canyon Dam, Arizona, 1991–2009: U.S. 

Geological Survey Scientific Investigations Report 

2011–5015, 17 p. [http://pubs.usgs.gov/sir/2011/5015/, 

accessed June 13, 2011].

Makinster, A.S., Persons, W.R., Avery, L.A., and Bunch, A.J., 

2010, Colorado River fish monitoring in Grand Canyon, 

Arizona—2000 to 2009 summary: U.S. Geological Survey 

Open-File Report 2010–1246, 26 p. [http://pubs.usgs.gov/

of/2010/1246/, accessed November 5, 2010].

U.S. Bureau of Reclamation, 2011, Environmental 

assessment—Non-native fish control downstream 

from Glen Canyon Dam: Salt Lake City, Utah, Bureau 

of Reclamation, Upper Colorado Region, 102 p. + 

appendixes [http://www.usbr.gov/uc/envdocs/ea/gc/nnfc/

NNFC-EA.pdf, accessed March 21, 2012].

U.S. Bureau of Reclamation and U.S. Geological Survey 

Grand Canyon Monitoring and Research Center, 2010, 

Glen Canyon Dam Adaptive Management Program 

biennial budget and work plan—fiscal years 2011–12: 

Salt Lake City, Utah, Bureau of Reclamation, Upper 

Colorado Regional Office, 250 p. + appendixes.

Waldman, J.R., Dunning, D.J., and Mattson, M.T., 1990, 

A morphological explanation for size dependent anchor 

tag loss from striped bass: Transactions of the American 

Fisheries Society. v. 119, p. 920–923.

Ward, D.L., Persons, W.R., Young, K.L., Stone, D.M., 

Vanhaverbeke, D.R., and Knight, W.K., in press, A 

laboratory evaluation of tagging-related mortality and 

tag loss in juvenile Humpback Chub: North American 

Journal of Fisheries Management, doi:10.1080/0275594

7.2014.986345.
18 Standardized Methods for Grand Canyon Fisheries Research 2012

VIE TAG COLOR AND LOCATION CODES

Color Code Location Code

Orange O Anal AN

Green G Caudal CD

Red R Dorsal DR

Blue B Front dorsal FD

Pink P Rear dorsal RD

Yellow Y Head HD

Black BK Lip LP

Brown BN Pectoral P1

Purple PU Pelvic P2

TURBIDITY CODES

H High Secchi (< 0.5m)

L Low Secchi (> 0.5m)

Appendix A: Field Datasheet Codes

SUBSTRATE

0 SM Clay-silt-mark (< 0.06 mm)

1 SI Silt-sand (0.07 - 0.10 mm)

2 SA Sand (.11 - 2.0 mm)

3 GR Gravel (2.1 - 15 mm)

4 PB Pebble (16 - 31 mm)

5 RK Rock (32 - 100 mm)

6 CO Cobble (101 - 255 mm)

7 SB Small boulder (256 - 1000 mm)

8 BO Boulder (1 - 3 m)

9 LB Large boulder (>3 m)

10 BE Bedrock

11 OR Organic matter/detritus

COVER TYPE

V Vegetative

B Boulder 

L Ledge or lateral cover

N None

U Undetermined

HYDRAULIC UNIT

BA Backwater

ED Eddy (countercurrent)

RI Riffle

RU Run

RA Rapid

PO Pool (still)

RC Return channel

GL Glide

SC Side channel

RIVER CODES

BAC Bright Angel Creek

BAD Badger Creek

BCC Big Canyon (LCR RKM 11.5)

CHU Chuar Canyon

CLR Clear Creek

COR Colorado River

CRY Crystal Creek 

DIA Diamond Creek (RM 225.7)

DRC Deer Creek

EMF Emery Falls Creek (RM 274.3)

FAL Fall Creek (RM -2.5)

HAV Havasu Creek

HER Hermit Creek

KAN Kanab Creek

LCR Little Colorado River

LOS Lost Creek (RM 248.9)

MAT Matkatamiba Creek

NAN Nankoweap Creek

PAR Paria River

PHA Phantom Creek

PIP Pipe Creek

QUA Quartermaster Creek (Rm 259.8)

ROY Royal Arch Creek (Elves Chasm)

SAL Salt Creek (RM 92.5)

SHI Shinumo Creek 

SHW Shinumo Wash

SPR Spring Canyon Creek (RM 204.1)

STO Stone Creek

TAP Tapeats Creek

TRA Travertine Creek (RM 230.5)
Appendix A: Field Datasheet Codes 19

FINCLIP CODES

ADP Adipose

ANL Anal

CAU Caudal

DOR Dorsal

LCD Lower caudal

LOP Left opercle punch

LP1 Left pectoral

LP2 Left pelvic

ROP Right opercle punch

RP1 Right pectoral

RP2 Right pelvic

UCD Upper caudal

WA Wire tag adipose fin

WH Wire tag in head

WN No wire tag detected (fish was checked)

SEXUAL CONDITION CODES

I Immature, sex organs not developed

M Mature, sex organs well developed, eggs distinguishable

N Not Ripe

R Ripe, Gametes extrudable in response to light pressure

S Spent, testes or ovaries empty or red, genital aperture inflamed

U Undetermined

SEXUAL CHARACTERISTICS CODES

B Both spawning colors and tuberculated

C Exhibiting spawning colors

N None

T Tuberculated

U Undetermined

PARASITE CODES

L Lernaea

B Asian tapeworm

BL Asian tapeworm & Lernaea

U Unidentified

N None

SPECIES CODES

BBH Black bullhead

BGS Bluegill sunfish

BHS Bluehead sucker

BKC Black crappie

BKT Brook trout

BNT Brown trout

CCF Channel catfish

CRP Carp

CUT Cutthroat trout

FHM Fathead minnow

FMS Flannelmouth sucker

FRH Flannelmouth/razorback hybrid

GAM Gambusia

GSF Green sunfish

GSH Golden shiner

GZD Gizzard shad

HBC Humpback chub

LMB Largemouth bass

NOP Northern pike

PKF Plains killifish

RBS Razorback sucker

RBT Rainbow trout

STB Striped bass

SUC Unidentified sucker

TFS Threadfin shad

UID Unidentified fish

UTC Utah chub

WAL Walleye

YBH Yellow bullhead

DISPOSITION CODES

RA Returned alive

DR Dead, released

DP Dead, preserved

DS Dead, stomach contents

SK Dead, skeletonized

Menlo Park Publishing Service Center

Manuscript approved for publication December 3, 2012

Edited by George Havach and Claire Landowski

Layout and design by Jeanne S. DiLeo
Persons and others—Standardized Methods for Grand Canyon Fisheries Research 2015—Techniques and Methods 2–A12