1 

Report of the 2009 Protocol Evaluation Panel for Fish

Monitoring Programs of the Grand Canyon Monitoring and

Research Center

Mike Bradford (Chair) 

Mark Bevelhimer 

Michael Hansen 

Gordon Mueller 

Doug Osmundson 

Jim Rice 

Dana Winkelman 

September 30, 2009 

Report to the Grand Canyon Monitoring and Research Center, 

Flagstaff, AZ 
2 

Executive Summary

In May, 2009 a panel of seven scientists was convened to review fisheries 

monitoring programs in the Glen and Grand Canyon reaches of the Colorado River 

as part of the Grand Canyon Monitoring and Research Center’s (GCMRC) Protocol 

Evaluation Program (PEP).  The review is the second for these programs.  Earlier 

reviews were conducted in 2000 and 2001. 

The Panel was impressed by the quality of work being conducted on the Colorado 

River and its tributaries: that quality is reflected in the number of scientific reports, 

theses and refereed journal publications that have resulted from the program. Since 

the first PEP reviews, much has been learned about monitoring and strengths and 

limitations of each program component.  

The over‐arching recommendation of the Panel is that since a number of years of 

data collection have taken place it is time to review the information collected to date 

to evaluate the current program and inform future changes.  A list of management 

objectives has been developed for the river and its resources and a list of 

corresponding information needs are also in place. The Panel believes that more 

explicit linkages between data collected from field programs and information needs 

and objectives should be developed. After this evaluation is completed, the Center 

will be in a position to reallocate resources to those that are in need of further 

development. 
3 

Introduction

The Grand Canyon Monitoring and Research Center (GCMRC) is responsible for a 

program of monitoring and research of natural resources in the Glen and Grand 

Canyons of the Colorado River, and for the evaluation of the effects of operation of 

len Canyon dam on those resources. One component of its activities is a regular 

s.

G

program of independent peer review of the research and monitoring program

This report documents findings of the 2009 Protocol Evaluation Panel (PEP) 

charged to review fish monitoring programs in the Glen and Grand Canyon regions. 

This PEP is the second to evaluate these programs: the Lee’s Ferry monitoring 

program was reviewed in 2000 (Culver et al. 2000) and fish and aquatic science 

programs in the Grand Canyon were reviewed in 2001 (Anders et al. 2001). 

Members of the 2009 panel and their affiliations are listed in Appendix 1.  

The 2009 PEP review was conducted in three stages. The first stage consisted of 

presentations and discussion of the background context and each component of the 

fisheries program at the GCMRC facilities (May 8) and at Marble Canyon (May 9). 

The second stage consisted of site visits in Glen Canyon (May 10) and the Lee’s Ferry 

to Little Colorado River (LCR) region of the Grand Canyon (May 11‐May 14). During 

site visits, discussions and informal presentations were made with program PIs and 

sampling activities were observed in the Colorado River and the LCR. The panel 

returned to Flagstaff on May 15.  During the third stage, the Panel reconvened in 

Flagstaff during May 16‐17 to consider its findings and to develop a draft set of 

recommendations and conclusions. These preliminary findings were presented to 

the Adaptive Management Program Technical Working Group (TWG) on June 22, 

2009 in Phoenix and are finalized in this report.  

The PEP was guided by an overview document that provided an outline of each 

component of the program and a series of questions that were generated by the 

TW (A t, the PEP organized its findings into five 

mai el

G  ppendix 2).  Based on that documen

n  ements: 

1. Overview and institutional matters; 

2. Monitoring of rainbow trout and other fishes in the Glen Canyon reach 

(“Lee’s Ferry” trout program); 

3. Monitoring of humpback chub in the Little Colorado River; 

4. Monitoring of native fish in the Colorado River between Lee’s Ferry and Lake 

Mead; and 

5. Monitoring of non‐native or invasive species in the Colorado River. 

The format of the review is similar for each program element.  The panel’s general 

indings are presented first, followed by recommendations and responses to 

uestions from the TWG.  

f

q

1. Institutional
4 

Since the last PEP panels, considerable progress has been made in the development 

of monitoring and assessment programs for fisheries resources in the Glen and 

Grand Canyons. A large body of data and reports has been amassed. As is commonly 

the case in these situations, the annual cycle of contracting, sampling and reporting 

can overwhelm the responsible agency to leave little or no time for integration and 

analysi

would b

s over time or among program components. The Panel felt that each program

•

enefit from a careful review to address key questions: 

•

What are the objectives and information needs that relate to each program? 

What data will be used to address progress to the management objective and  

• How precisely must parameters be estimated, and what is the minimum level 

of effort needed to satisfy that level of precision? 

The Panel felt that addressing these questions would allow development of 

assessment frameworks for each sampling program. 

Like earlier review (Anders et al. 2001), the Panel expressed concern about the 

Adaptive Management component of the program. A successful Adaptive 

Management program requires a carefully designed, sustained experimental regime 

with treatments that significantly perturb the system to elicit a detectable response. 

The Panel was unclear as to whether those conditions were in place.  

Re ommendations

1. In most cases, monitoring programs are beyond the experimental stage and 

considerable experience and data have been acquired. GCMRC should now be 

able to develop a standardized framework for archiving data and reporting of 

monitoring results for key program elements.  This structure would allow data 

and results from individual contract reports to be synthesized and organized to 

report on CMINs and management objectives.  Maximum success of this 

approach depends on full participation by all cooperators and researchers 

working in the system.  Currently, some impediments (both real and perceived) 

prevent timely and complete data sharing among some cooperators.  These 

impediments should be identified and alleviated.  For example, the USGS critical 

review process overly jeopardizes partnerships and cooperative relationships 

with other Department of Interior agencies and slows the response time of 

GCMRC.  In some cases, formal agreements such as Memoranda of 

c

Understanding may be useful mechanisms to circumvent interagency policy 

conflicts (e.g., among sister agencies under the DOI). 

2. Any effort to recover an endangered species must by necessity take a long‐term 

view.  Numerous lines of evidence suggest that the Colorado River System will 

undergo substantial change over the next 50 years and beyond, both natural and 

anthropogenic, that will affect key characteristics of the system, particularly 

water availability and temperature.  Development of management strategies for 

system conditions that occur or can be created currently, but that will no longer 

exist or be feasible several decades from now, will provide little or no long‐term 

benefit.  We recommend that the AMWG and GCMRC convene a group of experts 

to advise them on likely future trends in conditions that will affect the Colorado 
5 

River system (e.g., changes in temperature and precipitation, water withdrawals 

and diversions, reservoir levels, etc.) and use that information to identify 

probable bounds on management options for the future.  Even if (perhaps 

especially if) those options are different than what seems optimal today, 

agencies should begin testing management scenarios now that are suited to 

conditions in the long‐term to be prepared when those changes occur, rather 

than managing to avoid risks now that are going to become highly likely in the 

future.   

3. Successful adaptive management requires that the magnitude and duration of 

management manipulations be sufficient to generate an effect size in the 

variable(s) of interest that can be detected by ongoing monitoring efforts and 

differentiated from natural variation.  Despite the size and complexity of the 

Grand Canyon system and the extraordinary logistical challenges to sampling, 

the rigor of the fish population monitoring program in the Grand Canyon is 

unprecedented.  Coupled with this monitoring effort, the initial 16‐year plan to 

manipulate predation pressure, temperature and flow in 4‐year blocks seemed 

likely to meet these criteria for success.  Even though drought‐induced 

temperature increases occurred simultaneously with the predator removal 

treatment, modifications to the long‐term plan could still impose treatments of 

sufficient magnitude and duration to be informative in parsing the effects of 

these key variables on the system. All partners should act in consultation and 

cooperation with each other to maintain an effective adaptive management 

strategy.  Otherwise, even the most accurate and precise monitoring program 

will have little chance of confidently identifying the ultimate, or even proximate, 

mechanism(s) driving observed change.  We recommend that AMWG members 

participate in a Bayesian Belief Network exercise, or similar effort, to solidify 

their goals and reach consensus on how best to achieve them, in a way that takes 

into account their disparate individual needs, concerns and responsibilities.  

2. Lee’s Ferry (Glen Canyon) Monitoring Program

Management objectives for the Lee’s Ferry reach are to maintain a recreational 

fishery in the reach while limiting impacts of rainbow trout on native fish that might 

arise from downstream dispersal. Progress towards these management objectives 

are evaluated by a creel survey, and an extensive monitoring program for adult and 

juvenile rainbow trout in the Lee’s Ferry reach.  

The current monitoring program for rainbow trout in the Glen Canyon started in 

1991 using 15 fixed sites that were sampled with boat electrofishing 2–4 times per 

year. The 2000 PEP recommended that sites be reduced in size, increased in 

number, and selected randomly. Following on those recommendations, a combined 

program of nine historical fixed sites and 27 randomly selected sites are currently 

eing sampled.  More recently, electrofishing for estimating abundance of age‐0 fish 

as been used as a tool to evaluate effects of dam operations on recruitment. 

b

h
6 

The Panel was very impressed with the quality of information generated by the 

Lee’s Ferry program. The creel survey is unusual, with only one access point for the 

fishery, so a high sampling rate is attainable. The electrofishing surveys cover >30% 

of available habitat, a high sampling rate compared to most fisheries. The average 

annual CPUE is very precise because of the high sampling intensity. Strong 

covariation in CPUE between random and fixed sites suggests that some reduction 

of sampling intensity may be warranted. Investigators are to be credited for running 

both sampling regimes for 9+ years to establish this relation.  

The Panel felt that management objectives should be clarified to assist in refining 

the program. If management goals were oriented to maintaining desirable aspects of 

the recreational fishery, low mortality resulting from a largely catch‐and‐release 

fishery suggests that detailed population sampling may not be necessary, because 

trends are revealed by angler catch rate and perhaps a less intensive relative 

abundance survey.  

The historical and current annual program is not designed to address the population 

target, which is expressed in terms of absolute abundance in current management 

goals and corresponding CMIN. The Panel did not agree that an effort to estimate the 

absolute abundance would be helpful to managers of the sports fishery.  

Another apparent objective of the program that does not appear in the management 

objectives is to determine the impact of dam operations on recruitment dynamics of 

the trout population. The Panel thought the current information was somewhat 

underutilized because age structures were apparently collected but the results were 

not reported in the most recent Annual Report. A recruitment indicator could likely 

be developed from available information by separating juvenile and adult data for 

CPUE calculations. Timing of electrofishing surveys could likely be adjusted to 

maximize utility of juvenile catch information contained within the ongoing boat 

electrofishing program.  

The Panel was impressed with recent studies on recruitment of age‐0 trout in the 

reach. We were not sure if this information was needed for management of the trout 

fishery, but certainly provides more detailed insight into flow‐recruitment studies. 

As with other components of the program, clarification of management goals would 

ssist in determining whether continuing this program on an annual basis is needed 

or management objectives.    

a

f

Recommendations

1. Recast management objectives as angling catch rate, rather than absolute 

abundance, to frame the management program more directly in relation to the 

current catch‐and‐release angling fishery.  If the fishery develops into a trophy 

fishery (e.g. through flow regulation), management objectives could be changed 

to better reflect a harvest‐based fishery (e.g. catch or harvest of trophy‐sized 

trout). 
7 

2. Retain the creel survey to monitor annual fishery performance and angler 

satisfaction in relation to revised management objectives.  Under the current 

catch‐and‐release fishery, angling catch rate is the best metric for monitoring 

fishery performance.  If the nature of the fishery changes, alternative angler‐

based metrics may be required.  

3. Evaluate the effect of reducing electrofishing effort from 3–4 trips per year to 1–

2 trips per year and eliminating fixed sites from the survey design to provide an 

index of trout population density based on random sites only.  Effort to sample 

fixed sites can be redirected to surveillance for non‐native fishes at likely 

locations (e.g., the ‘carp pond’ or location of previous smallmouth bass catches) 

and increasing the number of random sites within a trip. A power analysis 

suggests that reducing sampling effort by one half would only minimally impact 

precision. Metrics from this part of the survey provide a frame of reference for 

trout in downstream reaches and a means by which to evaluate the degree to 

which trout migrate downstream.  Growth rate can be estimated from ongoing 

age estimation, rather than tag‐recapture data. More use of age information is 

recommended to develop year‐class strength indicators. 

4. Monitoring age‐0 trout habitat use and movement is not routinely needed 

because the electrofishing survey provides a direct index of pre‐recruit trout 

density.  Similarly, redd counts are not needed because the electrofishing survey 

provides a direct index of adult trout density. This program’s strength is in 

evaluating the impacts of flow manipulations on early life history, and it should 

be part of the evaluation of future flow tests. 

Responses to TWG Questions

1.1. Are

need to

the current monitoring methods providing the information that managers 

 manage the fishery, or should different metrics be pursued? 

• Harvest on the population is virtually nil, management requirements for the 

fishery are not great. 

• Management objectives for the rainbow trout fishery should be recast in 

terms of angling fishery attributes, such as catch rate (number per angler 

hour) or fish size. 

• Monitoring methods provide precise estimates of relative abundance from 

fishery dependent (creel survey) and fishery independent (electrofishing 

survey) surveys. 

• Electrofishing surveys provide additional estimates of size structure 

(indexed as PSD), body condition (indexed as relative condition), and growth 

(estimates not provided) and presumably age structure. 

• Trends in relative abundance indexed through creel and electrofishing 

surveys are consistent, which suggests that trends in population density are 

indexed accurately. 

1.2. Is the current sampling design sufficiently robust enough both spatially and 

temporally to monitor a change in status and trends in the distribution, condition, 

and abundance of rainbow trout? 
8 

• The current sampling design provides annual estimates of fishery attributes 

throughout the Lee’s Ferry reach of the river, but is probably more intensive 

than necessary. 

• The power analysis suggests that reducing electrofishing effort from 3–4 

trips per year to 1–2 trips per year would still provide an adequate index of 

trout population density and recruitment, with only small impact on 

precision. 

• Comparison of fixed and random sites indicates that both designs provide 

similar indices of population density and suggests that both are not needed 

to accurately index trends in population density. 

• Therefore, the random sampling design should be retained and the fixed 

sampling design can be eliminated (saved effort can be reallocated to other 

parts of the monitoring program). 

1.3. Are standard measures of relative abundance, e.g., catch rate, suitable 

surrogates for calculating absolute annual abundance? What are the relative risks of 

using CPUE instead of determining annual abundance? Does the PEP panel 

recomm

manage

end that absolute annual abundance is needed for managers to make 

ment decisions? 

• Catch rate is a suitable surrogate for indexing abundance if catchability is 

proportional to population density, so the relationship between catch rate 

and population density must be examined for non‐linearity.  

• Risk of using catch rate instead of absolute abundance is related to non‐

constant catchability (i.e., hyper‐stability or hyper‐depletion), where catch 

rate declines more or less rapidly than population density as density 

declines. 

• Absolute annual abundance is not needed for managing the fishery if 

management objectives are recast in terms of angling catch rate and if 

catchability is proportional to abundance. This assumption cannot be 

explicitly tested because annual estimates of abundance are not available. 

Some elements can also be examined by comparing angler and electrofishing 

CPUE and considering whether gear saturation occurs at high densities, or if 

searching behaviour by anglers occurs at low trout densities. The latter is 

likely in a recreational fishery. 

1.4. Sho vival, 

growth

uld a greater emphasis be placed on young‐of‐year rainbow trout sur

 and recruitment in this monitoring program? 

• Monitoring age‐0 survival, growth, and recruitment is needed only if 

management objectives require such knowledge. The Panel suggests that 

 to a 

.  

management objectives should be reformulated in metrics appropriate

recreational fishery, which generally do not include juvenile life stages

• Recruitment can be indexed through the ongoing fishery independent 

sampling program, so added survey effort focused on juveniles is not 

necessary to meet this objective. Better use of age information could result in 

the development of a recruitment indicator from the ongoing electrofishing 

survey. 
9 

• Juvenile recruitment dynamics may need to be understood if management 

objectives for the population include addressing impacts of flow 

manipulation on early life history, including attempts to manage the 

population using flow. 

1.5. Is t  trout population monitoring suitable for 

addres

he frequency of Lees Ferry rainbow

•

sing the CMINs? 

See response to question #2 above. 

• Surveying the reach 3–4 times each year is not likely needed to adequately

monitor status and trends of the trout population in the reach.

• Less intensive survey effort will likely be sufficient if the objective for the 

survey is changed from estimation of absolute abundance to indexing relative 

abundance. This is especially the case if harvest on the population is 

negligible and if angler and electrofishing catch rates are sufficient for 

evaluating long‐term trends. 

• Simulation studies can be used to determine the required amount of 

sampling.  The stated goal of a Coefficient of Variation (CV) of 10% is far 

more precise than most assessments, whereas 20% is often considered as 

more than adequate. 

• If fixed sites are eliminated from the sampling program, some effort can be 

reallocated to surveillance for non‐native fishes (e.g., sampling the ‘carp 

pond’, location of previous smallmouth bass catches) and the remainder used 

to increase the number of randomly chosen sites sampled per trip.  

1.6. What is the best way to monitor downstream movement and fate of rainbow 

trout? W

depend

hat is the best way to determine if downstream movement is density 

ent, or dependent on some other factor? 

• Downstream movement can be monitored by tagging trout in the Lee’s Ferry 

reach and then modeling recapture rates of tagged fish in downstream 

reaches. 

• To enable modeling of movement, numbers of fish tagged must be large 

enough to ensure enough recaptures are observed in downstream reaches. 

Current sampling effort is not likely sufficient to tag adequate numbers of 

fish for modeling density dependent movement from Lee’s Ferry to other 

reaches of the river. Therefore, a power analysis should be undertaken to 

determine the number of fish that would need to be tagged annually to 

estimate movement into downstream reaches. 

• Alternatively, downstream movement can be inferred by comparing catch 

rates of trout species between the Lee’s Ferry reach and downstream reaches 

sampled during mainstem Colorado River monitoring (see below). 

• Existing information may be adequate to evaluate density‐dependent 

movement by 2010 if the apparently large 2008 cohort survives. Age‐specific 

catch rates in Lee’s Ferry and in the 0–60 mile reach can be compared to 

determine if abundance in Lee’s Ferry is non‐linearly or proportionally 

related to abundance further downstream. 
10 

• In addition, tagging, rather removing, fish in the control reach of the 

mechanical removl project may provide information that can be used to 

identify rates of immigration into the removal reach from upstream or 

downstream. 

3. Native Fish Monitoring  

This section primarily focuses on monitoring of the humpback chub (HBC) 

population in the LCR and LCR reach of the Colorado River. The HBC is the fish 

species of greatest management concern in the Grand Canyon and has been a 

subject of intensive investigation for over 20 years. At the time of the 2001 PEP 

review, the Center was in the process of establishing a formalized monitoring 

program for HBC, and was beginning to develop a capture‐recapture model for the 

population using information from PIT tags.  

Currently, the Center runs a variety of programs to assess the status of the HBC 

population. The abundance of fish in the LCR is estimated using closed population 

mark‐recapture models in spring and fall, and an index program that continues a 

long‐standing database each spring in the lower reach of the LCR. In the mainstem, 

HBC are sampled with a somewhat ad‐hoc hoop net program and are captured 

incidentally in electrofishing and other surveys.  Captured fish are PIT tagged and 

their recaptures form the basis for the “age‐structured mark‐recapture” (ASMR) 

model that estimates current population size. The model also generates estimates of 

past population abundance and recruitment. 

In reviewing reports from the various programs, the Panel concluded the HBC 

program would benefit from development of an assessment framework, similar to 

what is used for commercial fish stock assessment, as a means to combine and 

integrate data sources. We noted that no formal process exists to put results in a 

consistent format for comparison, and in some cases, output from reports were too 

different to allow comparison. Development of an assessment framework would 

identify information needs to evaluate status of the population on an annual basis, 

and each investigator would be required to provide that information on the cycle 

(annual, biannual, etc.) deemed required.  

Recent analysis of the ASMR model indicates that the size‐based procedure for 

estimating year‐class strength may not provide precise and unbiased estimates of 

recruitment. If that component of the model’s outputs prove not to be as adequate 

as empirical measures of recruitment, then the need for regular updates of the 

model can be reduced because the total adult population will change slowly given 

the species longevity and correspondingly low natural mortality. Consequently, the 

Panel believes the ASMR model results do not need to be updated annually and that 

 3–5 year cycle would be adequate. Large changes in recruitment or to the adult 

opulation can be assessed in “real‐time” through field programs. 

a

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assessment frameworks are peer reviewed, but annual updates are not rev

unless they deviate significantly from the approved process. 

2. In the context of the assessment framework, evaluate spring and fall hoop 

netting programs to assess the necessity of conducting both surveys.  The 

objective of the fall survey is to provide an index of sub‐adult abundance, but 

spring hoop netting also provides a relative index of sub‐adult abundance 

because length frequency data from spring mimics length frequency data from 

Following from the assessment framework, the Panel believed more work could be 

done to assess the minimum level of sampling, handling and tagging required to 

provide information needed for assessment. The Panel heard that minimizing the 

degree of intrusion into the GCE was an important stakeholder value, and impacts of 

handling and tagging on individuals are uncertain. Given the low apparent natural 

mortality of HBC, results of recent ASMR sensitivity analyses suggest that small 

increases in mortality could significantly alter population trends over the long term. 

An increasing body of evidence indicates that the expulsion rate of PIT tags can be 

significant, and recent study has documented long‐term impacts of PIT tags on 

survival of Pacific salmon (Knudsen et al. 2009). While these studies may not be 

directly relevant to HBC, they confirm a general finding that tag loss and tag and 

handling‐related mortality is generally greater than expected. 

The Panel supported further development of a passive PIT‐tag array in the LCR. This 

technology has the potential to replace some intrusive sampling, and can be used to 

test assumptions of the mark‐recapture program, as well as provide an alternative 

estimate.  The Panel was concerned that some of the assumptions of the mark‐

recapture methodology were violated if fish have fidelity to certain sites and 

trapping occurs at fixed sites for both samples. A fully randomized trapping design 

for the second sample (irrespective of the number of fish actually sampled) may be 

worth considering. A detailed analysis of recapture probabilities is needed to 

determine the severity of bias (if any) in the program.  

The LCR sampling program has generated a large amount of data over the past 10 

years and we were not aware of attempts to analyze the results beyond the annual 

contract reports. For example, results of sampling programs in the lower 1200 m by 

ADFG and  by the FWS in the same reach should be compared. Further, a 

tandardized recruitment series would be useful, for comparison between the ASMR 

odel and various sampling programs. 

s

m

Recommendations

1. Sufficient information and experience with the LCR HBC population presently 

exists to develop an assessment framework. This framework would identify 

information needs and analysis required for managers to assess population 

status relative to management objectives. The framework would then provide 

guidance to various programs on the types of information needed from annual 

reports, and would house all key information in one annual report. Typically, 

iewed 
12 

the previous fall.  Inclusion of the fixed PIT tag array may alleviate the need for 

fall monitoring. Assessment of the hoop netting program should consider how 

reducing sampling effort affects the number of newly tagged fish, particularly in 

smaller size classes.   

3. Similarly, we suggest that spring hoop net data from the mark‐recapture 

program be compared to the fixed site 1200 meter hoop net data.  The 1200 

meter data is a valuable long‐term series, but may be redundant to the ongoing 

spring program. These two programs should be evaluated by comparing catches 

in the 1200 meter program to data from lower sections of the FWS program. 

Another option would be to continue the AZGF program, but reduce the FWS 

sampling in the same reach to avoid oversampling fish.  

4. Expand the fixed PIT tag antenna array to span the entire channel and consider 

deploying antennas at two locations.  Spanning the entire channel assists in 

estimating capture probability and having two antennas allows determination of 

direction of movement.   The PIT tag array may allow detection of movement 

pathways and habitats used for migration or movement.   The array may also 

inform mark‐recapture estimates of the spawning population by better 

describing the timing of the spawning migration. Our experience elsewhere 

suggests that arrays may need to be continuously serviced and removed before

summer monsoons.  

5. Reduce the frequency of ASMR updates from annual to every 3–5 years, unless 

trends in field data warrant a formal reassessment.  Under the aforementioned 

assessment framework, recruitment can be monitored with empirical catch per 

unit effort of fish less than 150 mm TL.  The LCR adult abundance can be tracked 

annually using the mark‐recapture estimate.  

6. ASMR estimates of recruitment do not match hoop net catch rates because of age 

estimation error in the ASMR.  Body parts from the HBC being collected in the 

nearshore ecology program or as part of disease sampling should be used (e.g. 

anal fin rays, scales, and otoliths) for age verification.  Hopefully, verification 

would allow future non‐lethal sampling for age estimation.  Age estimates from 

fish tagged at small size (young “known” age) and recaptured over a wide range 

of years at liberty should be compared for age validation. Sensitivity of the ASMR 

recruitment index may be increased by using age information in combination 

with tagging of smaller fish. 

7. Management objectives for Chute Falls and other translocations should be 

specified in measurable terms to guide monitoring and reporting.  The panel 

could not comment on current monitoring activities with available information.  

Responses to TWG Questions: Native Fish Monitoring Program

2.1. Are the current monitoring methods and analytical approach employed by 

GCMRC, AZGFD, USFWS, and other cooperators sufficient to address the CMINs? If 

not, how should the field and analytical methods be improved to better address the 

CMINs?
13 

• Current monitoring methods (hoop netting) and analytical approaches 

(ASMR ult 

fraction

modeling) are state of the art for the species, especially for the ad

 of the population in the LCR. 

o Hoop nets are effective for monitoring humpback chub with low 

incidental mortality. 

o The ASMR model is the best available modeling strategy for available 

data. 

• However, patterns of recruitment indexed through hoop netting and 

estimated t

age‐est

hrough ASMR modeling are not consistent, evidently because of 

imation error in the ASMR model. 

o Hoop net catches of fish shorter than 150 mm show strong alternating 

year classes with dominant year classes in 2002, 2004, 2006 and

2008. 

th. 

o Model‐based estimates of age‐2 recruitment show an increasing 

recruitment trend, but no biannual fluctuation in year‐class streng

• Age‐est

some fi

imation error in the ASMR model could be assessed by sacrificing 

sh for direct estimation of age and growth. 

o Samples (e.g. anal fin rays, scales, and otoliths) should be collected 

from a sample of fish over the range of observed lengths for age

verification. 

o Age estimates from fish tagged at small size (young “known” age) and 

recaptured over a wide range of years at liberty should be compared 

for age validation. 

• Current monitoring and analytical approaches are not likely sufficient for the 

mainstem of the Colorado River (see Mainstem Colorado River

Monitoring).  We suggest that trammel nets are not appropriate for 

sampling in the LCR, but could be valuable for use in eddy fences in the 

mainstem where water temperatures are cooler.  

2.2. The current biological opinion requires an annual update of the ASMR model of 

the adu  to 

achieve

lt humpback chub population. What is the most efficient way to monitor

 this annual update? 

• Current empirical monitoring programs provide relatively rapid annual 

updating of stock status, so should provide an early indication of stock status 

and trends (the periodicity of reports suggests that annual updates are 

obtainable at present levels of effort). 

• Standardized reporting of field programs should be implemented so that 

results can be compared and time series for all programs are readily 

available. 

• The species is so long lived that annual abundance estimates of the adult 

population are not needed or warranted.     

• Annual updates of field sampling data are easier and cheaper than ASMR 

model updates, so should be considered as a replacement for annual updates 
14 

implications of adding, removing or modifying programs on program 

capability can then easily be evaluated.  

• Both hoop netting surveys may provide similar indices of stock status and 

trends, but comparison of the two surveys has not been attempted and 

differing formats of data provided in reports by each agency hinder direct 

comparison. Therefore, the 2 hoop netting surveys should be compared to 

determine if sampling effort can be reduced or consolidated to provide more 

concise assessment of stock status and trends. 

of the ASMR model. For instance, recruitment can be monitored with 

empirical catch per unit effort of fish shorter than 150 mm TL.   

• The intensity of sampling effort required for annual updating of the ASMR 

model would require increased support for the ASMR model, perhaps by 

hiring a position to maintain the model. 

• Even though BO calls for ASMR to be updated annually, the panel

recommends a 3–5 year reporting cycle instead. 

2.3. Does the panel agree that parasite monitoring be conducted every 5–6 years as 

recomm  How 

should 

ended? If not, what alternative monitoring schedule is recommended?

parasite monitoring data be used? 

• The rationale for parasite monitoring on any temporal scale relative to 

management objectives is not clear and use of results from a parasite 

monitoring program is difficult to assess.  Therefore, a time scale for 

sampling is difficult to recommend.    

• If lethal monitoring is conducted, other tissues should be saved for analysis, 

especially otoliths, fin rays and other structures for age estimation and 

possibly soft tissues for genetic analysis.   

• If water temperatures rise, more intensive surveys may be needed, but these 

may be non‐lethal sampling methods. External parasites should be 

monitored opportunistically, in conjunction with other monitoring.   

2.4. Can the panel recommend a range of stock assessment options at differing levels 

of effort and expense so that managers can evaluate the relative range of 

information to be gained from a range of expenditures? In other words, what are the 

most pr

precise

ecise, most expensive stock assessment methods, and what are the less 

, less expensive methods? 

• Current levels of field sampling include large‐hoop netting by AZFG in the 

lower 1,200 meters of the LCR since 1987 (20–30 days each spring) and four 

small‐hoop netting trips by USFWS in the lower 14 km of the LCR since 2000 

(2 spring and 2 fall sampling events). These field programs are supported by 

extensive analytical work on the tag database. 

• Evaluation of HBC programs would benefit from development of an

assessment framework that lays out how the information being collected in 

the various monitoring programs is used for assessment of population status. 

The framework can be used for annual or semi‐annual updates. Further, 
15 

CMINS for mainstem fish populations are to “determine and track abundance (or 

recruitment) and distribution....” for native and non‐native predatory fishes. From a 

practical perspective, tracking relative abundance is more likely to be used as a 

• The ASMR model requires data from field sampling programs and is an small 

incremental cost to field programs. The ASMR analysts should consider their 

minimum tagging requirements as a lower benchmark of effort for programs 

tagging HBC. 

2.5. Does the panel have any concern over the amount of handling (monitoring) of 

humpback chub that is currently conducted? Is too much monitoring being 

conduc is 

concern

ted now? If so, what handling should be curtailed or eliminated to reduce th

? 

• Monitoring of humpback chub subjects 65–80% of all fish in the population 

to handling at current rates of PIT tagging and sampling, although the 

frequency at which individual fish may be handled, especially during 

spawning season, was not clear. 

• Despite this level of handling, the population has been increasing since 2000, 

lation. 

. 

which suggests that handling stress is not causing a decline in the popu

However, population recovery may have been slowed by handling mortality

• Handling protocols have been developed for the Colorado River Basin, 

especially for bonytail chub.  Therefore, written protocols for the Colorado 

River humpback chub monitoring may be desirable.  A HBC PIT tagging 

protocol has been established. 

• Overall, the panel feels that PIT tagging mortality for adult fish is probably 

low and is pleased that crews tagging in the field in AZ are trained in tagging 

protocols.  

• Tagging mortality should be assessed, especially for small fish.  This could be 

accomplished in live cages during annual PIT tagging. . Fish held in the LCR 

should probably not be held longer than 24 hours, and perhaps less than 12 

hours.  

• Recent studies with Pacific salmon have found that tag expulsion rates of 

18% occur when small fish are tagged and are at liberty for several years. PIT 

tagging was also found to cause a 10% increase in long‐term mortality.  This 

highlights the potential risks of PIT tagging small HBC.  

• A programmatic goal should be established to reduce handling of any 

endangered species. The Panel views the PIT tag antenna array as a 

potentially useful tool to meet this goal. The intensity of sampling and 

agging in the LCR should be evaluated to determine minimum requirements 

o meet assessment and surveillance needs.  

t

t

4. Mainstem Colorado River Monitoring Program
16 

sampling may be required, perhaps coupled with less frequent adult sampling.  

Monitoring invasions and trends of potentially harmful non‐native species was 

identified as an information need. Detecting invasions and tracking relatively scarce 

species is challenging in a large environment. In other systems, available 

information on habitat requirements and vectors for potential invaders are used to 

identify sampling locations most likely to harbor invaders (Campbell et al. 2007; Lee 

et al. 2008) and speaks to the relative merits of randomized versus informed 

sampling. In 2001, the PEP identified a need for risk analysis of potential invaders to 

establish their relative risk to native fish, and the current Panel understands that 

management tool because estimating absolute abundance is daunting in such a large 

environment.  

The anchor of the mainstem sampling program is a boat electrofishing survey that 

has been conducted annually for the past 10 years. While originally directed at trout 

species, this program is also suited to indexing carp and sucker relative abundance. 

The program has established a rigorous objective of CV = 10% for annual CPUE 

estimates for the whole system and in some years nearly 1300 individual samples 

(i.e. electrofishing runs) have been taken. The panel questioned whether this level of 

precision was needed for management that seems to rely on tracking trends rather 

than estimates of absolute abundance. The informative power analyses conducted 

by AZGF suggest that a large reduction in effort would have only small impact on CV 

and perhaps a target CV of 15% for rainbow trout would still yield adequate 

information for all species sampled by the gear.  

Over the years, various hoop and trammel net surveys have been conducted to 

sample fish not vulnerable to electrofishing surveys, and in particular HBC. Much 

has been learned about sampling and recent results were nicely summarized by 

Ackerman (2008), which suggests that a tighter link between management 

objectives and sampling protocols is needed. Currently, a clearly defined assessment 

procedure is needed for developing annual monitoring data into a format or time 

series for identifying status relative to management objectives. For example, a mark‐

recapture estimate for HBC in the LCR reach of the mainstem was attempted in 

2005, but the purpose of the estimate in the overall assessment of HBC status was 

not clear. By modifying the sampling protocol for this one‐time estimate, results 

from the 2005 survey for HBC were rendered incomparable to other years of 

sampling. As noted by the 2001 PEP, maintaining a continuous, comparable series of 

data is paramount in a successful monitoring program. 

The sparseness of aggregations of HBC in the mainstem represents a significant 

challenge for monitoring. The Panel suggests that GCMRC carefully consider its 

objectives and information needs when developing a sampling protocol for these 

fish. If the objective is to track relative abundance of these fish, which are largely 

older aged individuals, periodic sampling (every 2–3 years) focused on selected 

locations using trammel nets may be adequate. Conversely, if the focus is on 

reproduction and recruitment within aggregations, annual larval or juvenile 
17

periodicity that would be most effective.  

4. Designing a monitoring program for non‐LCR HBC remains challenging, but 

should be based on refined management objectives and CMINs that clarify 

information needs. For example, if the focus is on status of a few aggregations 

such an analysis is underway, along with an analysis of environmental 

equirements, points of introduction and habitat use. This work should provide 

nformation to rank species (and habitats or locations) for sampling.  

r

i

Re ommendations

1. Monitoring trends in relatively abundant species throughout the mainstem, and 

also detecting the occurrence of rare species, would be best served by a two‐

pronged approach.  The current stratified random electrofishing survey should 

be continued to provide information on trends and distribution of relatively 

abundant native and non‐native species.  However, effort could likely be reduced 

with little loss of information.  This extensive approach needs to be 

complemented by a second strategy intended to detect rare species, such as 

more intensive sampling using a variety of passive and active gears at a smaller 

number of fixed surveillance locations where potentially detrimental non‐native 

species are most likely to be found.  This sampling component can also include 

locations where more detailed information on native species is warranted (e.g., 

known HBC aggregations).  Together, these two sampling strategies address a 

range of monitoring goals, each to varying degrees (Table 1), and in combination 

c

address many of the questions posed by the TWG. 

2. Evaluate impacts of reducing river‐wide electrofishing from 2 trips to 1 trip per 

year. The primary goal of the stratified random electrofishing survey is to track 

general changes in distribution and relative abundance of trout populations and 

other species captured by this gear. A single trip currently yields 350–450 

samples along 360 km of river, which is a relatively high rate of sampling.  An 

annual CV (for trout at least) of 10% is probably more precise than is really 

needed, especially for longer‐lived species that are unlikely to change in 

abundance significantly year to year. Existing data could be used to evaluate loss 

of precision in relation to reduction in sampling intensity.  

3. Add a targeted sampling program at likely locations for non‐native species 

colonization (e.g. above Lake Mead, below Lake Powell, and stream mouths, 

springs, below large rapids). This program would deploy a suite of sampling 

gears, such as trammel nets, hoop nets, minnow traps, angling, set‐lining, 

seining, and back‐pack electrofishing (these sites could also be sampled by boat 

electrofishing during the stratified random electrofishing survey trip).  The 

primary objective is to detect colonization by non‐native species and changes in 

their distribution in the mainstem that would not be detected in the stratified 

random electrofishing  survey.  The proposed risk assessment for invasive 

species could be used to determine the locations, habitats, gear types, and 
18 

mainstem aggregation monitoring program. 

3.2. Given that various levels of monitoring effort are required to assess various 

levels of fish population changes, and unlimited funding is not available, can the 

outside of the LCR region, a focused sampling regime to assess abundance and 

recruitment may be appropriate. This program could be tied (or alternated) with 

targeted mainstem sampling. Given the extensive experience with trammel and 

hoop net sampling from earlier surveys, determining if the information 

generated by a proposed sampling regime will satisfy the information needs 

should be possible. 

5. Alternative means of sampling should continue to be pursued to identify the 

most efficient means to detect new species and changes to the distribution and 

abundance of existing species. 

Responses to Questions: Mainstem Colorado River Monitorin

3.1. Giv

monito

g

en the distribution of humpback chub in Grand Canyon, how should 

ring efforts for this species be distributed? 

• The current tag‐ASMR program adequately assesses abundance of the LCR 

and LCR inflow aggregations of HBC, which is the largest component of the 

population and thereby drives overall trends.  

• Curren C 

through

t monitoring programs enable indexing status and trends of HB

out the Grand Canyon by: 

o Electrofishing at 11 sampling reaches during 2000–Present to 

monitor native and non‐native species distribution and population 

density. 

o Trammel netting for adult native species and hoop netting for juvenile 

native species in 11 sampling reaches was conducted during 2002–

2006 b ling 

mortali

ut was discontinued because of concerns about post‐hand

ty on humpback chub (particularly in trammel nets).   

 However, recent laboratory studies suggest that trammel 

netting induces little mortality on a related species at 

temperatures occurring in the mainstem Colorado River. 

 Therefore, trammel netting can be safely added back into 

sampling design without risking significant incidental 

mortality of native species. 

• Sampling design is based on random selection within reaches, which is useful 

for identifying a major change in distribution or development of a new 

aggregation, but is not likely to be efficient at monitoring known sites where 

humpback chub are likely to occur. 

• If a program goal is to monitor specific aggregations of HBC in the mainstem, 

then a fixed sampling design will be needed for these areas and translocation 

sites. 

• Sufficient data likely exist to determine the relation between sampling 

intensity and precision to evaluate what can be accomplished with a 
19 

panel r

resourc

ecommend one or more processes for determining how to allocate limited 

es to native and nonnative fish monitoring? 

• Monitoring programs in the LCR and mainstem are mature enough that some 

thought should be given to how the information from the programs will be 

used for reporting or decision‐making. An assessment or reporting 

framework for each component of the program should be developed to 

clearly show how results of monitoring activities contribute to evaluation of 

nt of 

. 

status and trends. This type of process would then permit an assessme

the implications of modification to delivery of status and trend information

• The current sampling design includes only one active capture method 

(electrofishing surveys), so should be enhanced by adding passive capture 

methods, such as trammel and hoop nets, that are known to be effective for 

sampling native species with little post‐handling mortality at temperatures 

that are likely to occur in the mainstem Colorado River. 

• The current sampling design is stratified to encompass 11 reaches within the 

Colorado River between Lake Powell and Lake Mead, so provides an 

excelle e 

and non

nt design for assessing status and trends of relatively abundant nativ

‐native species throughout the river. 

o However, the design should be modified by adding known points of 

likely invasion of non‐native species based on a risk analysis of 

species colonization (e.g. tributaries). 

o Similarly, the design should be modified by adding known points of 

likely populations for native species (e.g. translocation areas and 

tributaries). 

o These sampling sites for non‐native species invasions and native 

species recovery should be the focus of targeted surveillance sampling 

(see below). 

3.3. Considering the trade‐offs between monitoring cost and sampling precision, are 

there any suggested spatial sampling designs (systematic, random, stratified) that 

optimize the sampling distribution (e.g., use a multi‐level approach that integrates a 

priori t t 

are pre

he sampling efforts among existing research and monitoring programs tha

sently conducted independently)? 

• As stated in response to question #2, available data from trammel netting 

and ele

samplin

ctrofishing surveys can be examined when designing a hybrid 

g program. 

o Systematic sampling at fixed index locations should focus on detecting 

invasions by non‐native species and recovery of native species at 

known aggregations and translocation sites. 

o Random sampling at stratified‐random locations should focus on 

status and trends of both non‐native and native species throughout 

the Colorado River. 

• Staff within the GCMRC has the expertise to design a hybrid sampling 

program that optimizes across objectives (see 4.1‐2). 
20 

• Models that employ simulated sampling to test different sampling schemes 

could be useful for determining how to best allocate sampling effort (e.g., 

whether to sample a few sites many times or many sites a few times).   

3.4. How should the monitoring program allocate sampling effort in the monitoring 

design 

season

that temporally accounts for sampling constraints (e.g., NPS non‐motor 

) or seasonal differences (e.g., developmental and dispersal histories)? 

• Current mainstem sampling protocol for electrofishing likely over‐samples at 

2 trips per year, so can likely be reduced to an annual trip. A target CV of 20% 

rather than 10% is an appropriate level of precision for annual CPUE 

estimates.  

• Surveillance monitoring of status and trends can likely be set at a single point 

within the year, so periodic or seasonal sampling within years is not likely 

needed.  This sampling can be scheduled during the motor season to facilitate

logistics. 

• Allocation of sampling effort within years is estimable by analysis of existing 

data from surveys that are conducted multiple times each year. 

• Effort saved by reducing the electrofishing survey protocol can be 

reallocated for monitoring colonization by non‐native species and recovery 

of native species at fixed sites (see above). 

• Monitoring at fixed sites in the mainstem should be scheduled during the 

motor season because rapid movement among sites will be necessary. 

3.5. Should routine monitoring methods be altered to allow detection of nonnative 

fish inv ?  If not, what sampling program should be 

institut

asions and expansions?  If so, how

•

ed to allow detection of new invasions or significant expansions? 

See responses to questions #1–4. 

• A mixed sampling design of stratified‐random and fixed‐index sampling 

locations is needed for monitoring both status and trends of established 

populations and detecting fish invasions and small populations of recovering 

native species. 

• Local knowledge should be employed to identify “hotspots” such as creek 

mouths, or below large rapids for surveillance of new species or changes in 

distribution of existing species. 

3.6. Given that the primary focus of many GCDAMP management actions is to 

improve spawning and rearing conditions for native fish in the Colorado River, what 

metrics

abunda

should be evaluated for assessing these actions (survival, growth, 

nce, distribution) and what are promising sampling designs? 

• Spawning and initial rearing success are measured most directly through 

sampling of native species at an early life age or stage, such as yolk‐sac 

larvae, as is presently done elsewhere in the basin for razorback sucker and 

bonytail chub. 

• Early life‐stage sampling is part of the nearshore ecology project, which will 

help to frame future monitoring needs and methods for the mainstem. 
21 

• See responses to questions #1–4. 

3.10. When allocating sampling effort, should river segments or habitat features be 

used to stratify the sampling distribution?  And if so, should the number of sample 

• Detecting recruitment of native species requires a sampling method, such as 

electrofishing or hoop netting, to which pre‐recruit age classes of native 

species are vulnerable to capture. 

• Detecting recruitment of native species also requires sampling where 

populations are being established, such as through translocations. 

• Successful spawning and production of early life stages can be indexed by 

age‐0 catch rate in an appropriate sampling gear in an appropriate location 

(e.g. seining in backwaters). 

• Alternatively, the ultimate success of management actions can be measured 

by monitoring adult abundance at locations for population recovery (see 

above). 

3.7. Ho ub mainstem aggregations best be 

conduc

w can monitoring of the humpback ch

•

ted to determine if humpback chub are spawning in these locations? 

See response to questions #1 and #6. 

• Sampling for larval or juvenile life stages of HBC directly indexes successful 

spawning and rearing of mainstem populations. However, determination of 

recruitment success is probably more important than spawning alone. 

• Alternatively, telemetry can be used to determine if adult fish aggregate for 

spawning (assuming the species aggregate for spawning, which is not known 

at present). 

• For some species, a predictable cycle of hormones precedes reproduction, so 

small blood samples can be used to evaluate maturation of these

aggregations. 

3.8. Sho lish separate monitoring for natives and 

nonnat

uld GCMRC and cooperators estab

•

ives, or can the CMINs be addressed if these efforts are conducted together?

See responses to questions #1–4. 

• Established populations of native and non‐native species can be monitored 

for status and trends by the current stratified‐random electrofishing 

sampling design (and perhaps enhanced by judicious use of trammel and

hoop nets; see 3.2). 

• Colonization of non‐native species and recovery of native species can be 

monitored for detection by the proposed surveillance sampling design 

(mixed gears; see below). 

• In late summer or autumn, many species are active, so are vulnerable to 

capture in passive gears that are proposed for use in the targeted sampling 

design. 

3.9. Are there multiple sampling methods and gear types (nets, traps, electrofishing, 

hydro‐a mbination (temporally/spatially) that 

would b ves? 

coustics) that could be used in co

est inform the monitoring objecti
22 

units b

among 

e selected based on the proportion of available strata or evenly distributed 

strata? 

• The current strategy for stratifying sampling effort (which is based on river 

segments) is appropriate for monitoring status and trends of relatively 

abundant species, but is not likely appropriate for detecting invasions by 

non‐native species or recovery of rare native species. 

• For surveillance of non‐native species colonization, other information about 

where these species might occur should be used to inform the selection of 

sites (e.g., through a risk analysis). 

• In addition, analysis of existing capture data may be useful to devise habitat

associations, from which samples could be drawn. 

• Adaptive sampling for non‐native fish in target areas may also be useful for 

detecting new non‐native species or small populations of native species. 

Non­Native Fish Downstream Monitoring Program

4.1. Is the current sampling design sufficiently robust enough both spatially and 

tempor

compos

ally to monitor a change in status and trends in the distribution, 

ition, and abundance of nonnative fish species? 

• The current design is adequate for monitoring status and trends of 

established populations of native and nonnative fish species, but not for rare 

species.  Further, the prescribed level of precision (CV < 10%) is likely more 

restrictive than needed for detecting realistic changes in relative abundance, 

especially if surveys are conducted annually. 

• The current design should be modified to include surveillance monitoring at 

likely locations for non‐native species colonization and recovery of native 

species (see above). 

• Analysis of the relation between the number of species captured and 

sampling effort may be helpful in allocating overall effort and choosing 

among gear types. 

4.2. Would using alternate sampling methods or gear types in addition to 

electro

abunda

fishing provide greater insight on fish distribution, composition, and 

nce? 

• Yes. Many species known to be present in the watershed are vulnerable to 

electrofishing, so will likely be detected (e.g. Centrarchids and Percids).  

However, some species known to be present in the watershed are less 

vulnerable to electrofishing, so would not be as easily detected (e.g. 

Ictalurids). 

• The mainstem electrofishing survey should continue with surveillance forays 

at prime locations for non‐native species colonization (e.g. carp pond at Lee’s 

Ferry; upstream and downstream reservoirs, and tributary streams). 

• A second survey using a mix of passive and active capture methods other 

than boat electrofishing (e.g., trammel nets, hoop nets, hooks, and backpack, 

barge or prepositioned electrofishing) should focus on prime locations for 

non‐native species colonization.  The likelihood of detecting rare species 

increases with repeated samples using multiple gears.  
23 

4.3. Should electrofishing effort be quantified by time and/or distance? 

• Electrofishing effort can be quantified by either time or distance and is 

commonly standardized to both metrics of sampling effort. 

• Existing survey data can be explored to understand how time and distance 

relate to one another as measures of sampling effort, but both should be 

recorded and used as appropriate. 

4.4. Sho er 

type of

uld sampling areas be stratified by geomorphic reaches? Or should anoth

 strata be used in the sampling design? 

• Stratified‐random sampling design for mainstem electrofishing survey is 

correct for monitoring of existing, widespread, populations (i.e., stratification 

by geomorphic reaches is appropriate). 

• However, sampling for monitoring colonization by non‐native species should 

not be randomized, but rather, should be focused in areas where non‐native 

species are likely to be introduced (tributary streams) or in habitats where

they are more likely to be found.  

• Likely sources for non‐native species introductions are already known, so 

should be added to the mainstem monitoring program (see above).

4.5. Wo

approp

uld other types of abundance indices (e.g., occupancy rate) be more 

riate for monitoring than conventional catch rate indices? 

• Occupancy rate is the fraction of sites visited in a year at which a particular 

species is captured (detected) in a year. 

• This typically requires much more sampling than is presently invested in 

monitoring, so does not represent a reasonable alternative to catch rate from 

current sampling, although models that allow for multiple years of sampling 

should be investigated. 

• Detection probability is the likelihood that a particular species will be 

captured (detected) during a visit to a particular site.  Baseline values can be 

calculated during multiple pass removal or mark‐recapture studies. 

• If past and future sampling can be used to derive relationships between 

detection probability and the density of various target species, then 

confidence values can be derived for the likelihood that a species is indeed 

absent from a location after repeated samples of non‐detection. 

4.6. Is the sampling coverage sufficiently representative of this system? 

• Sampling effort is allocated throughout the river between Lake Powell and 

Lake Mead, so seems to be representative of the entire river system for 

widely distributed species, but probably not for rarer species.  Small 

populations will not likely be detected by the current stratified‐random 

design, so should be monitored using targeted sampling at likely points of 

colonization. 

• Existing data can be explored to determine if reduced sampling intensity in 

the stratified‐random survey would produce similar estimates of species 

status and trends (accuracy and precision). 
24 

4.7. Can

distribu

 native and non‐native fish be concurrently monitored to detect changes in 

tion, composition, and abundance? 

• Yes.  See responses to earlier questions related to mainstem and non‐native 

monitoring. 

4.8. Wh ve 

non‐na

at is the best monitoring design to detect newly invading, rare, or evasi

tives? 

• See responses to earlier questions related to mainstem and non‐native 

monitoring. 
25 

Table 1. Degree to which various sampling efforts inform program monitoring 

goals 

System‐wide

trends in

established

species (RBT,

BRT, Carp,

HBC, FMS,

BHS, others)

Detection of

rare/new

species

(non‐natives

and natives)

HBC juvenile

abundance

and size at

aggregations

HBC adult

abundance

and size at

aggregations

(and

movement)

Size,

abundance

and

movement of

natives at the

LCR

confluence

Mainstem‐wide

stratified‐random

EF sampling

High Low Low or n/a?? Low or n/a??  

(except for

possible

movement)

n/a

Mainstem fixed‐site

EF sampling (HBC

aggregations)

Low Med. High High n/a

Mainstem fixed‐site

EF sampling

(potential non‐

native sentinel

locations/hotspots)

Low High n/a n/a (except for

possible

movement)

n/a (except

for possible

movement)

Mainstem‐wide

multi‐gear fixed‐site

sampling (HBC

aggregations)

Low Med. High High n/a (except

for possible

movement)

Mainstem‐wide

multi‐gear fixed‐site

sampling (potential

non‐native sentinel

hotspots)

Low High n/a n/a (except for

possible

movement)

n/a (except

for possible

movement)

LCR confluence

reach predator‐

removal EF

n/a   (low?) Med. n/a n/a (except for

possible

movement)

n/a (except

for possible

movement)

LCR confluence

reach ho po netting

Low Low n/a n/a (except for

possible

movement)

High

•
26 

References Cited:

Anders, P., M. Bradford, P. Higgins, K.H. Nislow, C. Rabeni, and C. Tate. 2001. Report 

of the Aquatic Protocol Evaluation Program Panel. Report to GCMRC, October 13, 

2001. 

Campbell, M.L., B. Gould, and C.L. Hewitt. 2007. Survey evaluations to assess marine 

bioinvasions. Mar. Poll. Bull. 55:360‐378. 

Culver, D.A., B. Kerans, M. Liermann, and G. Wilde. Final report of the Lee’s Ferry 

Rainbow Trout Monitoring Peer Review Panel. Report to GCMRC September 10, 

2000. 

Knudsen, C.M. and 5 coauthors. 2009. Effects of passive integrated transponder tags 

on smolt‐to‐adult recruit survival, growth and behaviour of hatchery spring chinook 

salmon. N. Am. J. Fish. Manage. 29:658‐669. 

ee, H. and 8 coauthors. 2008. Integrated monitoring and information systems for 

anaging aquatic invasive species in a changing climate. Cons. Biol. 22:575‐584. 

L

m
27 

Appendix 1, Panel Affiliations

Dr. Mike Bradford (chair) 

ada and 

ental Management 

Fisheries and Oceans Can

School of Resource and Environm

imon Fraser University 

. CANADA 

S

Burnaby, BC, V5A 1S6

ens Point 

Dr. Michael J. Hansen 

University of Wisconsin – Stev

College of Natural Resources 

00 Reserve Street 

sin 54481‐3897 

8

Stevens Point, Wiscon

n 

Dr. Mark Bevelhimer 

ivisio

ry 

Environmental Sciences D

Oak Ridge National Laborato

.O. Box 2008, Bldg 1504 

ak Ridge, TN  37831‐6351 

P

O

Dr. Gordon Mueller (retired) 

Research Fisheries Biologist 

U.S. Geological Survey 

Fort Collins Science Center 

Current address:  Box 79, Bennington, Nebraska, 68007. 

t 

Dr. Douglas B. Osmundson 

ec

e 

Colorado River Fishery Proj

U. S. Fish and Wildlife Servic

64 Horizon Drive, Bldg. B,

O  81506 

7

Grand Junction, C

Dr. James A. Rice 

Department of Biology 

orth Carolina State University 

7695‐7617 

N

Box 7617, Raleigh NC 2

esearch Unit 

Dr Dana L. Winkelman 

 and Wildlife R

us Delivery 

Colorado Cooperative Fish

201 Wagar Bldg ‐ 1484 Camp

Colorado State University 

Fort Collins, CO 80523‐1484 
28 

Appendix 2, PEP Briefing Document

LEES FERRY TROUT MONITORING PROGRAM 

Background

In 1991, a trout monitoring program for the sport fishery in the 25 km long Lees 

Ferry reach was established and sampled quarterly at 15 fixed sites (550‐1200 m) 

distributed downstream from Glen Canyon Dam to Lees Ferry.  In 1996, 

modifications were made that reduced the frequency and number of fixed sampling 

sites (9 fixed sites).  Each of the sites had been continuously sampled for over a 10‐

year period and was valued for seasonal and inter‐annual comparisons.  In 2000, a 

Lees Ferry Protocol Evaluation Panel (PEP) was convened to evaluate the current 

monitoring program.  Panel recommendations included increasing the number of 

sites, reducing the size of sites, randomizing the selection of sampling sites, 

subdividing sites by habitat type (i.e., consistent with habitat designation used in 

Grand Canyon), greater emphasis on young of year, and implementing an alternate 

sampling method to account for under‐sampling due to gear type biases with the 

conventional electrofishing method.  In 2001, a solicitation and supplement was 

released that specified the sampling protocols to use for monitoring the Glen 

Canyon Lees Ferry Trout Fishery.  The current monitoring program (2001‐2009) 

uses a stratified random and fixed sampling design for site selection.  Sampling 

frequency has varied between three and four times a year.  A total of 36 sample sites 

are sampled each sample period; 9 fixed sites (historical) and 27 randomly selected 

sites.  Annually, randomly selected sites are stratified without replacement based on 

habitat proportions (cobble bar, 9.2%; cliff, 15.4%; alluvial terrace/sand bar, 34.4%; 

and talus, 37.7%.  In total, approximately 32% of the total shoreline in the Lees 

erry/Glen Canyon section will be annually sampled by combining both fixed and 

andom sampling sites. 

F

r

Management Objectives and Core Monitoring Information Needs

The following tables contain the management objectives (MO) and associated core 

monitoring information needs (CMIN) for Lees Ferry trout as specified by the 

Program stakeholders.  The goal of the protocol evaluation panel (PEP) is to

provide GCMRC with a critical review and guidance on the conduct of a fish

monitoring program to address the CMINs listed below.

Table 1.  Management Objective Related to Lees Ferry Rainbow Trout 

MO # Objective

4.1 

Maintain or attain rainbow trout abundance, proportional stock density, 

length at age, condition, spawning habitat, natural recruitment and 

prevent or control whirling disease and other parasitic infections.

4.2 

Limit Lees Ferry rainbow trout distribution below the Paria River of the 

Colorado River ecosystem to reduce competition or predation on 

downstream native fish 
29 

Table 2.  Core Monitoring Information Needs Related to Management Objectives 4. 

CMIN Objective

4.1.1 Determine annual population estimates for age II+ rainbow trout in th

Lees Ferry reach

e 

4.1.2 Determine annual proportional stock density of rainbow trout in the

Lees Ferry reach

4.1.3  Determine annual rainbow trout growth rate in the Lees Ferry reach

4.1.4  Determine annual standard condition (Kn) and relative weight of 

rainbow trout in the Lees Ferry reach

4.1.5

Determine if whirling disease is present in the Lees Ferry reach. Determine 

annual incidence and relative infestation of trout nematodes in rainbow 

trout in the Lees Ferry reach

4.1.6 Determine quantity and quality of spawning habitat for rainbow trout in 

the Lees Ferry reach as measured at 5‐year intervals 

4.1.7  Determine annual percentage of naturally recruited rainbow trout 

Lees Ferry reach 

in the 

4.2.1

Determine and track the abundance and distribution of nonnative

predatory fish species in the Colorado River ecosystem and their 

impacts on native fish.

Mon oit ring Questions

1. Are the current monitoring methods providing the information that 

managers need to manage the fishery, or should different metrics be 

pursued? 

2. Is the current sampling design sufficiently robust enough both spatially and 

temporally to monitor a change in status and trends in the distribution, 

condition, and abundance of rainbow trout? 

3. Are standard measures of relative abundance, e.g., catch rate, suitable 

surrogates for calculating absolute annual abundance? What are the relative 

risks of using CPUE instead of determining annual abundance? Does the PEP 

panel recommend that absolute annual abundance is needed for managers to 

make management decisions? 

4. Should a greater emphasis be placed on young‐of‐year rainbow trout 

survival, growth and recruitment in this monitoring program? 

5. Is the frequency of Lees Ferry rainbow trout population monitoring suitable 

for addressing the CMINs? 

6. What is the best way to monitor downstream movement and fate of rainbow 

trout? What is the best way to determine if downstream movement is density 

dependent, or dependent on some other factor? 

Relevant Literature

Culver, D.A., B.L. Kerans, M. Lermann, and G.R. Wilde. 2000. Protocols Evaluation 

Program (Lee’s Ferry Trout PEP): Final report of the Lee’s Ferry rainbow trout 

monitoring peer review panel. 
30 

Korman, J. 2008. Early life history dynamics of rainbow trout in a large regulated river. 

University of British Columbia, Ph.D. Dissertation. 211 p. 

Korman, J., M. Kaplinski, J.E. Hazel III and T.S. Melis. 2005. Effects of the 

experimental fluctuating flows from Glen Canyon Dam in 2003 and 2004 on the early 

life history stages of rainbow trout in the Colorado River. GCMRC Final Report, 183 p. 

Korman, J., M. Yard, and D. Speas. 2006. An evaluation of the utility of snorkel surveys 

for estimating population size and tracking trends in relative abundance of rainbow 

trout in the Lee's Ferry Reach of the Colorado River. GCMRC Final Report, 49 p. 

Korman, J., M. Yard, C. Walters, and L.G. Coggins. 2009. Effects of flow, habitat, fish 

size, and density on capture probabilities of age-0 rainbow trout estimated from 

electrofishing at discrete sites in a large river. Transactions of the American Fisheries 

Society. 138:58-75. 

Maddux, H.R., D.M. Kubly, J.C. deVos, Jr., W.R. Persons, R. Staedicke, and R.L. 

Wright. 1987. Effects of varied flow regimes on aquatic resources of Glen and Grand 

Canyons. Final Report to U.S. Department of Interior, Bureau of Reclamation. Arizona 

Game and Fish Dept, Phoenix, AZ. 291 pp. 

Makinster, A.S., M.A. Hangsleben, R.S. Rogers, and W.R. Persons. 2008. Status of the 

Lees Ferry rainbow trout fishery with additional input regarding potential impacts of 

the 2008 High Flow Experiment. Annual Report, Arizona Game and Fish Department 

Research Branch, Phoenix, AZ. 

McKinney, T. and W. R. Persons. 1999. Rainbow trout and lower trophic levels in the 

Lee’s Ferry tailwater below Glen Canyon Dam, Arizona: A review. Report to the 

Grand Canyon Monitoring and Research Center, Flagstaff, AZ. Arizona Game and Fish 

Dept, Phoenix, AZ. 53 pp. 

McKinney, T., D.W. Speas, R.S. Rogers, and W.R. Persons. 2001. Rainbow trout in a 

regulated river below Glen Canyon Dam, Arizona, following increased minimum flows 

and reduced discharge variability. North American Journal of Fisheries Management, 

21:216-222. 

McKinney, T., R. S. Rogers, and W. R. Persons. 1999. Effects of flow reduction on 

aquatic biota of the Colorado River below Glen Canyon Dam, Arizona. North 

American Journal of Fisheries Management 19:984-991. 

McKinney, T., R. S. Rogers, and W. R. Persons. 1999. Lotic community responses in 

the Lees Ferry Reach, pp. 249-258. In R. H. Webb, J. C. Schmidt, G. R. Marzolf, R A. 

Valdez, Eds., The Controlled Flood in Grand Canyon. American Geophysical Union, 

Washington, D.C. 

McKinney, T., W. R. Persons, and R. S. Rogers. 1999. Ecology of flannelmouth sucker 

in the Lee’s Ferry tailwater, Colorado River, Arizona. Great Basin Naturalist 59:259-

265. 

Montgomery, W.L., and K. Tinning. 1993. Impact of fluctuating water levels on early life 

history of rainbow trout. Report to U.S. Department of Interior, Glen Canyon 

Environmental Studies, Bureau of Reclamation. Northern Arizona University. CA OFCB40-09620. 71 pp. 
31 

Yard, M. and B. Ralston. 2000. Sampling protocol for Glen Canyon Lees Ferry Trout 

Fishery. Grand Canyon Monitoring and Research Center, Flagstaff, AZ. 30 pp. 

Native Fish Monitoring Program

Native fish populations in Grand Canyon are key resources of concern influencing 

decisions on both the operation of Glen Canyon Dam (GCD) and other non-flow actions. 

To inform these decisions, it is imperative that accurate and timely information on the 

status of native fish populations, particularly the endangered humpback chub Gila cypha

(HBC), be available to managers. Status and trends information on other native species 

and nonnative species are also important for managers. The assessments generated from 

monitoring programs are used, in part, to evaluate the effects of experimental actions, 

many of which are carried out under the auspices of the Glen Canyon Dam Adaptive 

Management Program (Program). The USGS Grand Canyon Monitoring and Research 

Center (GCMRC) is the primary science provider to the Program, in cooperation with 

U.S. Fish and Wildlife Service, Arizona Game and Fish Department, and National Park 

Service. This information is therefore crucial to (1) inform the program as to attainment 

of identified goals, (2) provide baseline status and trend information to be used as a 

backdrop to further understand mechanisms controlling native fish population dynamics, 

and (3) evaluate the efficacy of particular management policies in attaining program 

goals. Finally, results from this project are potentially useful in assessing changes to 

Federal Endangered Species Act listing status of HBC in the Colorado River. 

Management Objectives and Core Monitoring Information Needs

The following tables contain the management objectives (MO) and associated core 

monitoring information needs (CMIN) for native fish as specified by the Program 

stakeholders.  The goal of the protocol evaluation panel (PEP) is to provide

GCMRC with a critical review and guidance on the conduct of a fish monitoring

program to address the CMINs listed below.

Table 3. Native Fish Management Objectives 

M.O. # Objective 

2.1 Maintain or attain humpback chub abundance and year-class strength in the Little 

Colorado River and other aggregations at appropriate target levels for viable 

populations and to remove jeopardy 

2.2 Sustain or establish viable humpback chub spawning aggregations outside of the Little 

Colorado River ecosystem below Glen Canyon Dam to remove jeopardy 

2.3 Monitor humpback chub and other native fish condition and disease/parasite numbers 

in Little Colorado River and other aggregations at an appropriate target level for 

viable populations and to remove jeopardy 

2.4 Reduce native fish mortality due to nonnative fish predation/competition as a 

percentage of overall mortality in the Little Colorado River and mainstem to increase 

native fish recruitment 

2.5 Attain razorback sucker abundance and critical habitat condition sufficient to remove 

jeopardy as feasible and advisable in the Colorado River ecosystem below Glen 

Canyon Dam 
32 

2.6 Maintain flannelmouth sucker, bluehead sucker, and speckled dace abundance and 

distribution in the Colorado River ecosystem below Glen Canyon Dam for viable 

populations 

Table 4. Revised Science Planning Group (SPG) Core Monitoring Information Needs. 

SPG ranking where 1) is considered most important. 

REVISED CMINs 

(SPG 2005) 

1) CMIN 2.1.2 Determine and track recruitment (identify life stage), abundance and distribution 

of HBC in the Little Colorado River (LCR).

2) CMIN 2.1.2 Determine and track recruitment (identify life stage), abundance and distribution 

of HBC in the mainstem.

3) CMIN 2.3.1 Determine and track the parasite loads on HBC and other native fish found in the 

LCR and in the Colorado River ecosystem.

4) CMIN 2.4.1 Determine and track the abundance and distribution of nonnative predatory fish 

species in the Colorado River.

5) CMIN 2.6.1 Determine and track the abundance and distribution of flannelmouth sucker, 

bluehead sucker, and speckled dace populations in the Colorado River ecosystem. 

Little Colorado River Monitoring

The humpback chub is the primary focus of native fish monitoring in Grand Canyon.  

The humpback chub population in Grand Canyon is centered near the confluence of the 

Colorado and Little Colorado rivers (LCR) in Grand Canyon. Valdez and Ryel (1995) 

describe the humpback chub distribution as consisting of nine aggregations 

throughout Marble and Grand canyons. However, the aggregation near the 

confluence of the LCR and Colorado River (hereafter referred to as the LCR 

population) is known to successfully reproduce.  In recent years, most monitoring 

efforts have focused on the LCR population since it is the most numerous (~7500 

adults compared to less than 500 in the rest of the aggregations combined) and the 

only documented source aggregation in Grand Canyon.  Owing to logistical concerns 

and sampling efficacy, most effort to monitor this population is concentrated within 

the LCR even though this population resides both in the LCR and the mainstem 

Colorado River near the confluence.

Abundance and recruitment trends of the LCR population of HBC are assessed via 

catch‐rate and open and closed population abundance estimators.  In particular, we 

rely heavily on age‐structured mark‐recapture models (ASMR) to determine trends 

in HBC abundance and recruitment.  Capture‐recapture data collected in the system 

since 1989 support the annual stock assessment conducted with the Age‐Structured 

Mark‐Recapture (ASMR) model.  Additionally, annual capture‐recapture data are 

used to inform closed population abundance estimators. The primary data used to 

populate these models are collected during spring and fall and described below. 
33 

Annual Spring (March and April) Humpback Chub Data Collection in the Little

Colorado River

In the spring two mark-recapture trips (12-day) are conducted annually in the lower 13.57 

river kilometers (rkm) of the LCR to estimate the abundance of HBC > 150 mm TL. 

This program has been ongoing since 2000 and annually produces assessments of the 

abundance of HBC using closed population models. These efforts rely on multiple event 

mark-recapture analysis of Passive Integrated Transponder (PIT; Biomark, Inc.) tag data 

to produce abundance estimates using closed population models. Additionally, this 

sampling effort provides both data for populating the ASMR model as well as measures 

of relative abundance on the spawning and resident populations of HBC in the LCR 

below Chute Falls. Unbaited hoop nets (50-60 cm in diameter, 100 cm long, a single 10 

cm throat, and covered with 6 mm nylon mesh netting) were the sole fishing gear used in 

this study. During both monitoring trips, each reach was sampled with 20 nets for the first 

~24 h haul, then re-sampled by redeploying nets, often to new locations within the same 

reach. Evaluation of relative trends of other fishes, especially native bluehead suckers 

Catostomus discolbolus and flannelmouth suckers Catostomus latipinnis, is a desirable 

side benefit of this sampling. Some nonnative species, often ictalurids, are also captured 

with these methods. 

Annual Fall (September and October) Humpback Chub Abundance Assessments

in the Lower 15 km of the Little Colorado River  

The fall sampling is aimed primarily at providing an estimate of the abundance of 

subadult HBC rearing in the LCR. These data support the ASMR model to assess HBC 

population numbers. Two trips into the LCR are conducted to collect the data used to 

construct these estimates in the fall (September and October). Findings from the fall trip 

are used as a complimentary comparison to the spring abundance estimates. Sampling is 

predominantly conducted using hoop nets evenly distributed throughout the lower 15 km 

f the LCR. Other types of sampling gear are not used in the LCR because they have 

een shown to be less efficient at capturing HBC >150 mm total length in the LCR. 

o

b

Annual Spring Relative Humpback Chub Abundance Assessment in the Lower

1,200 m of the Little Colorado River  

This program was established by the Arizona Game and Fish Department (AZGFD) in 

1987 and has operated continuously through 2009 with the exception of the years 2000–

01. This program annually produces assessments of the relative abundance (catch rate) of 

all size classes of humpback chub, flannelmouth suckers, bluehead suckers, speckled 

dace Rhinichthys osculus, and a host of nonnative fishes in the lower 1,200 m of the 

LCR. Data are collected during a 30–40-day period in spring (April and May) using hoop 

nets set in standardized locations distributed throughout the reach. In general, this effort 

represents the longest and most consistent relative abundance dataset available to infer 

trends for the population of HBC in the LCR. Results provide an independent comparison 

to the mark-recapture-based assessments. The statistical power of this portion of the 

monitoring program has not yet been assessed, but statistically significant differences in 

relative abundance are apparent in current data. 

Monitoring and Translocation Above Chute Falls
34 

Beginning in 2003, juvenile humpback chub have been “translocated” within the LCR 

from near the confluence of the LCR and Colorado Rivers to a location approximately 16 

km upstream in an attempt to increase juvenile survivorship. As part of the monitoring 

program, two separate trips are conducted in the summer above Chute Falls in the LCR to 

monitor translocated individuals and potential offspring. These trips occur during late 

May when the LCR discharge is at base flow to provide an annual abundance estimate of 

HBC within this region. In addition to the annual population estimates, these data can be 

incorporated into the ASMR model. Moreover, because we have and will continue to 

implant these fish with PIT tags, it is likely that some individuals will eventually be 

recaptured in the lower LCR corridor and/or Colorado River, which would increase our 

knowledge of migration patterns. 

Baited hoop nets are fished in the LCR corridor above Chute Falls (13.6 rkm), which 

is the upstream extent of the current LCR monitoring. Approximately 50 hoop nets 

are fished throughout this upper reach from 13.6 rkm to 18.0 rkm, with the average 

spacing between nets approximately 100‐150 m. The overall reach will be broken 

down into two sub‐reaches and each sub‐reach fished for 3 days. The upper reach 

designation will be from 18.0 to 15.0 rkm (undesignated point below Blue Spring to 

first travertine dam above Chute Falls). Currently 18 rkm is the highest point in 

which HBC have been located above Chute Falls. The lower subreach will extend 

rom 15.0 to 13.6 rkm (first dam above Chute Falls to Lower Atomizer Falls where 

ower LCR monitoring begins). 

f

l

Que io st ns for the PEP

1. Are the current monitoring methods and analytical approach employed by 

GCMRC, AZGFD, USFWS, and other cooperators sufficient to address the 

CMINs? If not, how should the field and analytical methods be improved to 

better address the CMINs? 

2. The current biological opinion requires an annual update of the ASMR model 

of the adult humpback chub population. What is the most efficient way to 

monitor to achieve this annual update? 

3. Does the panel agree that parasite monitoring be conducted every 5‐6 years 

as recommended? If not, what alternative monitoring schedule is

recommended? How should parasite monitoring data be used? 

4. Can the panel recommend a range of stock assessment options at differing 

levels of effort and expense so that managers can evaluate the relative range 

of information to be gained from a range of expenditures? In other words, 

what are the most precise, most expensive stock assessment methods, and 

what are the less precise, less expensive methods? 

5. Does the panel have any concern over the amount of handling (monitoring) 

of humpback chub that is currently conducted? Is too much monitoring being 

conducted now? If so, what handling should curtailed or eliminated to reduce 

this concern? 

Relevant Literature
35 

Choudhury, A., T. L. Hoffnagle, and R. A. Cole. 2004. Parasites of native and nonnative 

fishes of the Little Colorado River, Grand Canyon, Arizona. Journal of Parasitology 

90:1042-1053. 

Clarkson, R. W. and M. R. Childs. 2000. Temperature effects of hypolimnial-release 

dams on early life stages of Colorado River big-river fishes. Copeia 2:402-412. 

Coggins, L. G., Jr., W. E. Pine, III, C. J. Walters, D. R. Van Haverbeke, D. Ward, and H. 

C. Johnstone. 2006a. Abundance trends and status of the Little Colorado River 

population of humpback chub. North American Journal of Fisheries Management 

26:233-245. 

Coggins, L. G., Jr., W. E. Pine, III, C. J. Walters, S. J. D. Martell. 2006b. Age-structured 

mark-recapture analysis: a virtual-population-analysis-based model for analyzing agestructured capture-recapture data. North American Journal of Fisheries Management 

26:201-205. 

Coggins, L.G., Jr. 2008b. Active adaptive management for native fish conservation in the 

Grand Canyon: implementation and evaluation: Gainesville, University of Florida, 

unpublished Ph.D. dissertation, 173p. 

Coggins, L.G., Jr., 2008a, Abundance trends and status of the Little Colorado River 

population of humpback chub; an update considering 1989-2006 data: U.S. Geological 

Survey Open-File Report 2007-1402, 53 p. 

Coggins, L.G., Jr., and Waters, C.J., 2009, Abundance trends and status of the Little 

Colorado River population of humpback chub; an update considering data from 1989-

2008: U.S. Geological Survey Open-File Report 2009-1075, 18 p. 

[http://pubs.usgs.gov/of/2009/1075/]. 

Douglas, M. E., and P. C. Marsh. 1996. Population estimates/population movements of 

Gila cypha, an endangered cyprinid fish in the Grand Canyon region of Arizona. 

Copeia 1996:15–28. 

Gloss, S. P. and L. G. Coggins, Jr. 2005. Fishes of Grand Canyon. Pages 33-56 in S. P. 

Gloss, J. L. Lovich, and T. S. Melis, editors. The state of the Colorado River ecosystem 

in Grand Canyon. U.S. Geological Survey Circular 1282. 

Gorman, O. T., and D. M. Stone. 1999. Ecology of spawning humpback chub (Gila 

cypha) in the Little Colorado River near Grand Canyon, Arizona. Environmental 

Biology of Fishes 55:115–133. 

Hoffnagle, T. L., A. Choudhury, and R. A. Cole. 2006. Parisitism and body condition in 

humpback chub from the Colorado and Little Colorado Rivers, Grand Canyon, 

Arizona. Journal of Aquatic Animal Health 18:184-193. 

Hoffnagle, T. L., A. Choudhury, and R. A. Cole. 2006. Parisitism and body condition in 

humpback chub from the Colorado and Little Colorado Rivers, Grand Canyon, 

Arizona. Journal of Aquatic Animal Health 18:184-193. 

Kitchell, J. F., C. Grimes, S. T. Lindley, D. Otis, and C. Schwarz. 2003. Report to the 

adaptive management work group, Glen Canyon Dam Adaptive Management Program: 

An independent review of ongoing and proposed scientific methods to assess the status 

and trends of the Grand Canyon population of the humpback chub Gila cypha. Final 

report submitted to the Grand Canyon Monitoring and Research Center, Flagstaff, 
36 

Arizona. Available: www.gcmrc.gov/ 

library/reports/biological/Fish_studies/Kitchell2003.pdf. (January 2008). 

Melis, T. S., S. J. D. Martell, L. G. Coggins, Jr., W. E. Pine, III, and M. E. Andersen. 

2006. Adaptive management of the Colorado River ecosystem below Glen Canyon 

Dam, Arizona: using science and modeling to resolve uncertainty in river management. 

In Proceedings of the American Water Resources Association, 2006. 

Persons, W., Clark, B, and D. Ward. In Review. Little Colorado River lower 1200 m 

hoop net monitoring 2008 annual report. Submitted to the Grand Canyon Monitoring 

and Research Center 

Speas, D. W., C. J. Walters, D. L. Ward, and R. S. Rogers. 2004. Effects of intraspecific 

density and environmental variables on electrofishing catchability of brown and 

rainbow trout in the Colorado River. North American Journal of Fisheries 

Management 24:586-596. 

Stone, D. M. and O. T. Gorman. 2006. Ontogenesis of endangered humpback chub (Gila 

cypha) in the Little Colorado River, Arizona. American Midland Naturalist 155:123-

135. 

Stone, D. M., D. R. Van Haverbeke, D. L. Ward, and T. A. Hunt. 2007. Dispersal of 

nonnative fishes and parasites in the intermittent Little Colorado River, Arizona. 

Southwestern Naturalist 52:130-137. 

VanHaverbeke, D., and Stone, D. 2008. Stock assessment and fisheries monitoring 

activities in the Little Colorado River within Grand Canyon during 2007. Submitted to 

the Grand Canyon Monitoring and Research Center 

Mainstem Colorado River Monitoring

Finding the appropriate design for monitoring native fishes in the mainstem 

Colorado River has been one of the most difficult challenges for the Program and 

GCMRC.  The debate has centered around systemic sampling according to an 

appropriate randomized design versus focused sampling on areas of known higher 

abundance of native fishes, primarily humpback chub.  Systemic surveys using hoop 

and trammel nets typically yield low and highly variable catches with low power of 

change detection.  Focused surveys around the areas of known HBC aggregations 

typically yield higher and less variable catches, but provide no information about 

abundance or distribution of fish in the majority of the Colorado River.  As 

mentioned above, in recent years efforts have focused solely on the LCR Inflow 

reach. 

Mainstem native fish monitoring has historically focused on hoop and trammel nets 

as an appropriate gear type for capturing juvenile and adult native fishes.  This was 

predominantly due to the observation that adult humpback chub were more readily 

captured using trammel nets than electrofishing.  However, since about 2002, 

systemic electrofishing sampling trips (see NONNATIVE FISH DOWNSTREAM 

MONITORING PROGRAM below) have indicated a large increase in the catch‐rate of 

flannelmouth and bluehead suckers and we now believe that this may be an 

appropriate gear type for monitoring abundance of these species.  Additionally, the 
37 

slow electrofishing of shorelines (~10 seconds/meter, the “Korman Slow Shocking 

Method”) also appears to be effective at sampling juvenile humpback chub.  

However, trammel netting still appears to be the most effective method for 

capturing adult humpback chub. 

In addition to the issues above related to sampling design and gear for monitoring 

changes in the abundance and distribution of native fishes in the mainstem Colorado 

River, perhaps the most relevant and difficult monitoring problem is to determine 

survival rate of juvenile native fishes in the mainstem Colorado River.  This is 

particularly important as many proposed or implemented experimental 

management actions are aimed at improving rearing conditions for native fishes in 

the mainstem Colorado River.  This is the topic of a current research initiative 

ermed “Nearshoreline Ecology” and PEP input on this topic would be particularly 

elpful. 

t

h

Que io st ns for the PEP

1. Given the distribution of humpback chub in Grand Canyon, how should 

monitoring efforts for this species be distributed? 

2. Given that various levels of monitoring effort are required to assess various 

levels of fish population changes, and unlimited funding is not available, can 

the panel recommend one or more processes for determining how to 

allocate limited resources to native and nonnative fish monitoring? 

3. Considering the trade‐offs between monitoring cost and sampling precision, 

are there any suggested spatial sampling designs (systematic, random, 

stratified) that optimize the sampling distribution (e.g., use a multi‐level 

approach that integrates a priori the sampling efforts among existing 

research and monitoring programs that are presently conducted 

independently)?  

4. How should the monitoring program allocate sampling effort in the 

monitoring design that temporally accounts for sampling constraints (e.g., 

NPS non‐motor season) or seasonal differences (e.g., developmental and 

dispersal histories)?   

5. Should routine monitoring methods be altered to allow detection of 

nonnative fish invasions and expansions?  If so, how?  If not, what sampling 

program should be instituted to allow detection of new invasions or 

significant expansions? 

6. Given that the primary focus of many GCDAMP management actions are to 

improve spawning and rearing conditions for native fish in the Colorado 

River, what metrics should be evaluated for assessing these actions (survival, 

growth, abundance, distribution) and what are promising sampling designs?

7. How can monitoring of the humpback chub mainstem aggregations best be

conducted to determine if humpback chub are spawning in these locations? 

8. Should GCRMC and cooperators establish separate monitoring for natives 

and nonnatives, or can the CMINs be addressed if these efforts are conducted 

together? 
38 

9. Are there multiple sampling methods and gear types (nets, traps, 

electrofishing, hydro‐acoustics) that could be used in combination 

(temporally/spatially) that would best inform the monitoring objectives?  

10. In allocating sampling effort, should river segments or habitat features be 

used to stratify the sampling distribution?  And if so, should the number of 

sample units be selected based on the proportion of available strata or evenly 

distributed among strata? 

Relevant Literature

Andersen et. al. In prep. Evidence of mainstem overwinter survival of humpback chub 

Choudhury, A., T.L. Hoffnagle and R.A. Cole. 2004. Parasites of native and nonnative 

fishes of the Little Colorado River, Grand Canyon, Arizona. The Journal of 

Parasitology 90:1042-1053. 

Clarkson, R.W., and M.L. Childs. 2000. Temperature effects of hypolimnial-release dams 

on early life stages of Colorado River basin big-river fishes. Copeia 2000:402-412. 

Coggins, Jr., L.G., W.E. Pine III, C.J. Walters, and S.J.D. Martell. 2006. Age-structured 

mark–recapture analysis: a virtual-population-analysis-based model for analyzing agestructured capture–recapture data. North American Journal of Fisheries Management 

26:201-205. 

Converse, Y.K., C.P. Hawkins and R.A. Valdez. 1998. Habitat relationships of subadult 

humpback chub in the Colorado River through Grand Canyon: spatial variability and 

implications of flow regulation. Regulated Rivers Research and Management 14:267-

284. 

Douglas, M. E., and P. C. Marsh. 1998. Population and survival estimates of Catostomus 

latipinnis in northern Grand Canyon, with distribution and abundance of hybrids with 

Xyrauchen texanus. Copiea 1998:915-925. 

Douglas, M. R., and M. E. Douglas. 2000. Late-season reproduction by big-river 

Catostomidae in Grand Canyon (Arizona). Copiea 2000:238-244. 

Hunt, T.A., 2008, Effects of trammel nets on capture of Colorado River native fishes, 

Master’s thesis, Northern Arizona University (hard copy on left hand bookshelf in 

MEA’s office, about third shelf down) 

Maddux, H.R., D.M. Kubly, J.C. deVos, Jr., W.R. Persons, R. Staedike and R.L. Wright. 

1987. Effects of varied flow regimes on aquatic resources of Glen and Grand Canyons. 

Final report, U.S. Bureau of Reclamation Contract 4-AG-40-01810. Arizona Game and 

Fish Department, Phoenix. 

Petersen, J.H. and C.P. Paukert. 2005. Development of a bioenergetics model for 

humpback chub and evaluation of water temperature changes in the Grand Canyon, 

Colorado River. Transactions of the American Fisheries Society 134:960-974. 

Robinson, A.T., R.W. Clarkson and R.E. Forrest. 1998. Dispersal of larval fishes in a 

regulated river tributary. Transactions of the American Fisheries Society 127:772-786. 

Stone, D.M. 2005. Effect of baiting on hoop net catch rates of endangered humpback 

chub. North American Journal of Fisheries Management 25:640-645. 
39 

Thieme, M.L., C.C. McIvor, M.J. Brouder, and T.L. Hoffnagle. 2001. Effects of pool 

formation and flash flooding on relative abundance of young-of-year flannelmouth 

suckers in the Paria River, Arizona. Regulated Rivers: Research and Management 

17:145–156. 

Valdez, R.A. and T.L. Hoffnagle. 1999. Movement, habitat use, and diet of adult 

humpback chub. Pages 297-307 in R.H. Webb, J.C. Schmidt, G.R. Marzolf and R.A. 

Valdez, eds. The Controlled Flood in Grand Canyon. Geophysical Monograph 110. 

American Geophysical Union, San Francisco, California. 

Valdez, R.A. and W.J. Masslich. 1999. Evidence of reproduction by humpback chub in a 

warm spring of the Colorado River in Grand Canyon, Arizona. Southwestern Naturalist 

44:384-387. 

Valdez, R.A., and R.J. Ryel. 1995. Life history and ecology of the humpback chub (Gila 

cypha) in the Colorado River, Grand Canyon, Arizona. Final Report Bureau of 

Reclamation, Contract Number 0-CS-40-09110, Salt Lake City, Utah. 

Ward, D.L. 2002. Standardized methods for handling fish in Grand Canyon research. 

Report submitted to the Grand Canyon Monitoring and Research Center. Grand 

Canyon Monitoring and Research Center, Flagstaff, Arizona. 

Weiss, S.J., E.O. Otis, and O.E. Maughan. 1998. Spawning ecology of flannelmouth 

sucker, Catostomus latipinnis, (Catostomidae), in two small tributaries of the lower 

Colorado River. Environmental Biology of Fishes 52:419-433. 

Yard, Baxter, and Coggins, in prep, diet analysis of rainbow and brown trout from the 

LCR reach 
40 

NONNATIVE FISH DOWNSTREAM MONITORING PROGRAM 

Background

The current downstream non‐native fish monitoring program (2 trips/yr) uses a 

stratified random sampling design, such that sampling areas are distributed evenly 

among 12 geomorphic reaches found in the Colorado River that extend from Lees 

Ferry to Lake Mead (360 km).  A sub‐reach is randomly selected and sampled within 

each of the geomorphic reaches in the spring and early summer.  Two electrofishing 

boats per trip each sample nightly 11 shoreline sites sequentially along opposing 

shorelines.  The first site is randomly selected; the remaining sites are then sampled 

in series and separated by time (300 sec).  Average number of samples per trip is 

between 350 and 450.  Electrofishing is the primary gear type used and is quite 

affective in capturing rainbow trout and flannelmouth suckers.  Under the current 

sampling design, the power to detect a change in CPUE of 21% decrease and 26% 

increase over a five–year period using an estimated coefficient of variation (CV ≤ 

.10) is 0.80.  Fishing effort does not relate catch to linear shoreline distance or 

elineate sampling sites by macro habitat features. 

0

d

Que io st ns for the PEP

1. Is the current sampling design sufficiently robust enough both spatially and 

temporally to monitor a change in status and trends in the distribution, 

composition, and abundance of nonnative fish species? 

2. Would using alternate sampling methods or gear types in addition to 

electrofishing provide greater insight on fish distribution, composition, and 

abundance? 

3. Should electrofishing effort be quantified by time and/or distance? 

4. Should sampling areas be stratified by geomorphic reaches? Or should

another type of strata be used in the sampling design? 

5. Would other types of abunace indices (e.g., occupancy rate ) be more

appropriate for monitoring than conventional catch rate indices?  

6. Is the sampling coverage sufficiently representative of this system?  

Relevant Literature  

Rogers, R. 2003. Grand Canyon long-term non-native fish monitoring, 2003 Annual 

Report. Arizona Game and Fish Dept., Phx., AZ. 

http://www.gcmrc.gov/library/reports/ 

biological/Fishstudies/AZGame&Fish/2003/Rogers2006.pdf

McKinney, T., D.W. Speas, R.S. Rogers and W.R. Persons. 1999. Rainbow trout in the 

Lee’s Ferry recreational fishery below Glen Canyon Dam, Arizona, following 

establishment of minimum flow requirements. Final Report. Grand Canyon Monitoring 

and Research Center. 

McKinney, T., D.W. Speas, R. S. Rogers, and W.R. Persons. 2001. Rainbow trout in a 
41 

regulated river below Glen Canyon Dam, Arizona, following increased minimum flows 

and reduced discharge variability. North American Journal of Fisheries Management 

21:216-222. 

Speas, D.W., D.L. Ward, R.S. Rogers, and W.R. Persons. 2002. Salmonid population 

size, relative density and distribution in the Colorado River in Grand Canyon during 

2001 with reference to sampling designs for long term monitoring. Draft Annual 

Report. Arizona Game and Fish Department, Phoenix, AZ. 

Speas, D.W., C.J. Walters, D.L. Ward, and R.S. Rogers. 2004. Effects of intraspecific 

density and environmental variables on electrofishing catchability of salmonids in a 

large river. North American Journal of Fisheries Management. 24:586-596.