Glen Canyon Dam Adaptive Management Program

Protocols Evaluation Panel

Final Report for the

Fisheries Program Review

December 27, 2016

Panel: Andrew Casper, Donald Jackson, Keith Gido, James Peterson (Chair), and Frank Rahel 
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Executive summary

The Grand Canyon Monitoring and Research Center (GCMRC) fisheries program convened an 

independent protocol review panel on August 2, 2016. The panel was asked to evaluate the 

quality and breadth of the monitoring and research conducted by the fisheries program in the 

Colorado River and its major tributaries. 

The panel was very impressed with the quality of the fisheries-related research being conducted 

in the system and the high-quality peer reviewed publications resulting from these efforts. 

Project scientists and staff are to be commended for their hard work. The panel also believes that 

the program has made significant progress toward incorporating the recommendations from 

previous reviews. As a result, the program has compiled a wealth of data that can be used to 

quantitatively evaluate and refine existing research and monitoring efforts. 

The fisheries program submitted five questions for the panel to consider. During the course of 

the review, the panel also identified management and institutional issues that potentially 

influence the effectiveness of the fisheries program going into the future. Answers to the 

questions and issues are summarized below.

The quality of the catch effort data from the rainbow trout, humpback chub, and system wide 

long-term monitoring is likely reduced due to the inability to account for incomplete capture. 

Monitoring data can be improved by increasing fish Passive Integrated Transponder (PIT) -

tagging efforts and employing new or existing population estimators, such as Cormack Jolly 

Seber and mark-resight, to estimate vital rates and abundance.

Rainbow Trout fishery research has identified more questions than answers regarding the 

ecological mechanisms responsible for population declines. Given the complexity of the system, 

trout research efforts should consider, and if possible, incorporate all levels of ecosystem into 

their study and develop a conceptual model to place all existing hypothesis into a broader 

context.

The fish behavioral changes due to use of bait, handling, and marking can affect the accuracy of 

capture recapture estimators used to estimate humpback chub abundance in the Little Colorado 

River and translocation tributaries and should be evaluated. In addition, monitoring in the Little

Colorado River and at translocation reaches should place a greater emphasis on evaluating the 

factors affecting vital rates using new or existing population estimators rather than focusing on 

abundance.

It was difficult for the panel to assess the success of the Humpback Chub translocation efforts 

because the objectives were unclear. The panel recommends that the program reconsider and 

clarify the goals of the translocation experiments. The reevaluation should also incorporate a new

quantitative analysis of the effects of translocations on the donor population using the 

demographic parameters estimated by the program. 
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Given the wealth of data collected by the program, greater effort should be expended evaluating 

alternative sampling and monitoring designs and assessing tradeoffs with respect to program 

objectives. An evaluation of alternative designs also could be used to identify designs that 

minimize handling of fish and meet program objectives. In addition, the program should expand 

its efforts using PIT tag arrays or similar technologies to improve data quality while minimize 

handling of fish.

Expansions of exotic fish species populations have the potential to reverse recent gains in 

humpback chub populations. The panel recommends that the program consider developing a 

separate invasive species detection program that includes quantitative triggers and remedial 

actions.

The program should continue to engage angler groups by developing tools to enhance 

communication and understanding of the results of rainbow trout monitoring and research. The 

results of evaluations of alternative sample designs, tradeoffs, and the potential effects on fishes 

should be clearly communicated to Native Americans stakeholders. The program also should 

expand citizen science outreach efforts to include fish monitoring, if feasible. 

Adaptive management as currently practiced by the program is hindered by the lack of control of 

management of key management drivers. The program should consider developing an adaptive 

management framework that is sufficiently flexible to accommodate opportunistic learning.

The panel suggests that the program develop of a more formal integration of monitoring and 

research within Lake Powell and the Colorado River below the Glen Canyon Dam. At a 

minimum, modeling of the potential impacts of quagga mussel on water clarity, nutrient 

conditions, and thermal structure should be considered.
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1. INTRODUCTION

The Colorado River is a key resource supporting the diverse ecology, economy, and cultural 

heritage of the Southwest. As such, the success of the Glen Canyon Dam Adaptive Management 

Program (GCDAMP) in managing and integrating the portfolio of different uses is critical to the 

sustained conservation of the river and its inhabitants. As identified by the U.S. Fish and Wildlife 

Service biological opinion (BioOp), a primary focus of the adaptive management program 

(AMP) is to manage the effects of dam operations on the physical and biological resources of the 

Colorado River downstream of the dam. The primary biological issue is the status, trends, and 

conservation of the endangered humpback chub (Gila cypha; hereafter, HBC) population 

centered in the Grand Canyon in general and at the confluence of the Little Colorado River in 

particular. For the past decade, the major issue believed to be limiting this population has been 

recruitment failure reportedly due to some combination of predation of HBC young-of-year 

(YOY) by rainbow trout (Oncorhynchus mykiss; RBT) introduced to the cold tailwater of the 

Glen Canyon Dam above Lee's Ferry and other factors. However, the introduced RBT have 

become an important resource themselves, leading to an additional stakeholder-driven goal of 

managing the system to support both species in a spatially separated manner.

Robust and sound science is the foundation of the adaptive management process, which 

progresses from the identification and prioritization of issues and knowledge needs, to the 

selection of monitoring approaches and response variables, and includes the design of

experiments and construction of models that allow decision makers to arrive at the most effective 

management strategies. The US Geological Survey, Grand Canyon Monitoring and Research 

Center (GCMRC) is the leading provider of scientific information used by the GCDAMP to 

inform the adaptive management of dam operations and the status of ecologically and 

economically important ecosystems to various program collaborators.

Periodically, the GCMRC convenes independent review panels to assess various aspects 

of the program including scientific soundness, data quality, and whether the program is 

adequately addressing research and monitoring needs of the GCDAMP. In 2016, the fisheries 

program initiated a review of their existing monitoring and research program by a protocol 

evaluation panel (PEP) that included 5 scientists with expertise in aquatic and landscape ecology, 

population estimation and dynamics, ecological modeling, fishery biology, and adaptive 

management. The review began on August 2, 2016 with a half day of formal presentations on 
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topics that ranged from an historic overview of the Colorado River ecosystem to tribal 

perspectives on the river and the program, followed by a one-day field visit to Glen Canyon Dam 

reach above Lee's Ferry (Appendix A). During the field visit, the PEP interacted with GCMRC

personnel, investigators from cooperating agencies including the Arizona Game and Fish 

Department and US Fish and Wildlife Service, independent scientists conducting monitoring and 

research in the area, and a number of stakeholders (primarily fishing guides). Attendees were 

transported to noteworthy locations along the river and provided with information on the issues 

associated with each location that included: the detection and removal of a concentration of an 

invasive sunfish; changes to the benthic macroinvertebrate community and the ‘bug flow’

hypothesis; changes in the benthic macrophyte community; and water quality, reservoir 

operations, and potential nutrient limitations. The PEP also was provided with a list of questions 

about the program by the stakeholders present (Appendix B). At camp, formal presentations 

were made by program and affiliated staff and agency cooperators on topics that included: the 

compilation and use of traditional ecological knowledge; the results of recent research on trout

reproduction and movement; and ongoing and emerging invasive species issues. The remainder 

of the trip was filled with informal discussions among attendees focusing on the natural history 

of the reach, historic and emerging management issues, and the state of the science. The trip also 

served to provide PEP panelists with a realistic perspective of the challenges associated with 

conducting research, monitoring, and management activities in the area. After returning to 

Flagstaff, the remaining 1.5 days were devoted to formal presentations and discussion topics that 

included fish and benthic invertebrate dynamics, stakeholder perspectives of the program, and 

current monitoring efforts by the program and cooperating agencies. During the discussions, the 

Colorado River Energy Distributors Association also provided the PEP with a set of questions 

regarding current and potential GCDAMP activities (Appendix C). The PEP then met to discuss 

the review and next steps in the process.

Prior to and following the August meeting, the PEP was provided with background 

material, such as reports and peer-reviewed literature, and access to fisheries program staff who 

provided additional information on current and historic program activities. These were reviewed 

by the PEP and used in their assessment of the program. The fisheries program also posed a 

series of five questions to the fisheries program PEP. To fully address these questions and those 

questions posed by the stakeholders, required the consideration of multiple program objectives 
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that include ecological, economic, and sociological values. Attempting to evaluate tradeoffs

among all objectives for current program activities or potential changes in the future are beyond 

the scope of this evaluation. Rather, the practicable role of the fisheries program PEP was to 

evaluate the state of knowledge (i.e., the science), highlight successful efforts, and finally to 

make suggestions concerning results. Sections 2 - 6 of this report uses this approach to addresses

the five topics requested by the fisheries program. During the course of the evaluation, the PEP 

also identified management and institutional issues that many influence the effectiveness of 

program activities. Sections 7-9 address these additional issues.
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2. RAINBOW TROUT MONITORING AND MANAGEMENT

A Rainbow Trout (RBT) fishery was established on the Colorado River in the reach above Lees 

Ferry shortly after the completion of Glen Canyon Dam in 1964. Since then, the 25 km reach has 

garnered a national and international reputation as a blue ribbon recreational RBT fishery that is 

crucial to the local economy. The RBT fishery has been experiencing significant declines in 

recent years that could have a major economic impact if not reversed. Fishery scientists and 

managers have identified multiple factors that are potentially responsible for the decline in the 

RBT fishery. The non-native RBT also are believed to be one of the factors negatively affecting 

the endangered HBC in areas downstream of Lees Ferry at the confluence of the Little Colorado 

River (LCR). To minimize the potential harm of RBT on HBC, managers have developed 

abundance-based criteria that trigger management actions intended to reduce non-native trout 

(both Rainbow Trout and Brown Trout) abundance on reaches above and immediately below the 

LCR confluence. To effectively and efficiently manage the RBT fishery and minimize effects on 

endangered HBC, managers need information on the current status of and the factors affecting 

RBT in the reach above Lees Ferry coupled with estimates of the distribution and abundance of 

RBT in Marble Canyon, the area below Lees Ferry and in the vicinity of the LCR. Towards these

ends, the GCMRC fishery program and cooperating agencies have conducted two loosely 

integrated RBT research and monitoring efforts in Glen and Marble Canyons.

The Arizona Game and Fish Department (AZGFD) has been conducting standardized 

electrofishing surveys during the spring, summer, and fall since 1991. This effort provides 

estimates of RBT catch per unit effort (CPUE) from a relatively large number of randomly 

selected sites in Glen and Marble Canyons. Program managers indicated that these monitoring 

data are primarily useful for evaluating long term trends in RBT populations and for evaluating

coarse response to management actions (i.e., multiple years after implementation). The 

monitoring also provides information on fish body condition, growth, the age structure of the 

population (potentially) and whether CPUE-based management triggers have been reached. 

Because of the sample frequency and large spatial extent, these monitoring efforts also provide 

information on the occurrence and prevalence of other (i.e., non-trout) non-native fish species.

Creel and angler satisfaction surveys also are conducted in conjunction with standardized 

electrofishing efforts. These surveys have been conducted since 1964 and provide information on 
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the human dimensions of the fishery including angler catch and satisfaction, harvest rates, and 

economic benefits.

The other RBT sampling effort in Glen and Marble Canyons is associated with research 

into the factors affecting RBT population dynamics and dispersal and involves two types of 

sampling including 10 day trips twice a year throughout length of the Glen Canyon reach and 

quarterly sampling at one fixed site in Glen Canyon and 4 sites downstream of Lees Ferry. This

Rainbow Trout Early Life Stage Study (RTELSS) sampling effort provides estimates of RBT 

population size and age structure that are adjusted for incomplete capture, population 

demographic rates (i.e., survival, reproduction, emigration), and fish growth and condition. 

These estimates can then be used to elucidate the relation between environmental and ecological 

factors (e.g., flows, nutrients, macroinvertebrate density) and RBT demography. The program 

managers and affiliated scientists indicated that these data are useful for evaluating the effects of 

management actions on RBT populations and dispersal at relative fine resolution, such as weeks 

and months. In addition, the abundance estimates are also used to determine whether RBT 

abundance triggers have been reached.

Each of these two efforts has strengths and limitations. To maintain a quality fishery it is 

necessary to understand the factors affecting vital rates, currently these estimates are only 

provided through the intensive research sampling efforts. Similarly, adaptive management (AM) 

requires the timely integration of monitoring data so that information about system dynamics 

(i.e., hypotheses) can be evaluated and updated quickly enough to improve management. The 

relatively long time period needed to detect changes (trends) in CPUE with the monitoring data

also suggest that its use for adaptively managing the RBT fishery is currently limited. 

Minimizing the effects of the RBT and other exotic species (e.g., green sunfish) on HBC also 

requires information over a greater spatial and temporal extent. The AZGFD monitoring is 

providing a robust view of status and trends of exotic species across the entire area, whereas the 

more intensive research monitoring efforts of the RTELSS have a smaller spatial extent. 

However, the RTELSS efforts indicate that the AZGFD monitoring data also are systematically 

biased due to heterogeneity in capture probability that varies with conditions during sampling 

and fish population size. Based on discussions with angler stakeholders, it also appears that the 

RBT population estimates and trends produced by the AZGFD and RTELSS efforts are either 

misunderstood or not believed by the stakeholders. 
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The degradation of the RBT fishery in the Lees Ferry tailwaters would have a major 

economic impact and potentially influence how the US Bureau of Reclamation (USBR) would 

manage Glen Canyon Dam. While RBT are not native to the Colorado River system, fisheries 

ecology may be able to help provide a management recipe for maintaining this economically 

important resource. The program has identified several factors that are potentially responsible for 

the declines including changes to the hydrologic regime; reduced benthic macroinvertebrate 

productivity due to dam operations; and reduced system productivity due to decreased nutrient 

inputs. However, none of these hypotheses has been fully tested. The recent work on the role of 

benthic invertebrate community composition and production on the RBT population dynamics is 

potentially a step in the right direction. The resulting proposal to run an experimental ‘bug flow’ 

to evaluate whether the current hydropeaking pattern used by Glen Canyon Dam is the ultimate 

cause of the decline in fish production fits well in the AM framework 

The PEP believes that the current RBT monitoring and research activities are high quality

and critical to the objectives of the program. After reviewing the publications, presentations, and 

in conversations with program staff and cooperators, the PEP identified a few changes that could 

improve current efforts and potentially fruitful avenues to focus future research efforts. 

 The program should continue to monitor trends in RBT relative abundance, growth and 

condition. The PEP believes (1) that it is essential to maintain the integrity of the longterm monitoring data collected by AZGFD but also (2) that the program needs to build 

on this long-term monitoring effort to estimate the annual response of RBT to conditions. 

Therefore, the program should consider and evaluate the feasibility of the following 

modifications to provide additional insights and improve data quality. 

 RBT collected during the seasonal monitoring efforts by AZGFD should continue 

to be tagged with PIT tags or similar tags. This would allow for estimation of 

demographic parameters using open-population estimators, such as age 

structured, multi-strata, Cormack-Jolly-Seber (Williams et al. 2002). These

methods do not require any additional sampling effort, other than marking, and 

can be employed using the existing sample design.

 Tradeoffs, such as the number of fish that need to be tagged vs. the additional

time required for tagging and precision of estimates, could be evaluated using 
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simulation. PEP is confident that the program staff have the skills for such an 

evaluation.

 Estimates of recapture probabilities and availability calculated from open 

population models may be useful for adjusting the catch data to provide RBT

abundance estimates and unbiased or minimally biased age-structure estimates.

 The program should continue to develop protocols for incorporating antenna 

arrays suitable for detecting PIT tags into their monitoring and research activities. 

This would potentially decrease the amount of fish handling without comprising 

the estimation of demographic parameters, such as survival and movement. In 

addition, the antenna array detection data may be useful for getting better 

estimates of RBT population size using mark-resight (or similar) estimators 

(McClintock et al. 2008). 

 The PEP recommends that feasibility of the modifications suggested above and 

throughout this document should be evaluated (e.g., through simulation) prior to 

their adoption using estimates of demographic rates and capture probabilities 

generated by the program. 

 The program should continue its important research into the factors affecting RBT 

population dynamics. These efforts are somewhat hindered by the complexity of the 

system being studied and the minimal ability of the fisheries program to control system 

drivers (e.g., flows). The PEP believes that there are a few topics that should be 

improved.

 Given the complexity of the system, RBT research efforts should consider, and if 

possible, incorporate all levels of ecosystem into their study (e.g., nutrients, 

benthic macroinvertebrates, temperature, Lake Powell management and 

dynamics).

 Emigration of RBT to downstream reaches may be related to the abundance and 

relative condition of the population and should be considered for evaluation.

 The program should consider using a RBT specific conceptual model to place all 

existing hypotheses into a broader context and to help identify other drivers (e.g., 

river-reservoir nutrient dynamics, seasonal high/low flows, density-dependent or 
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other intrinsic population controls) that are potentially as important to RBT 

population sustainability. The conceptual model also will facilitate 

communication within and outside the program. 

3. HUMPBACK CHUB MONITORING AND MANAGEMENT

Monitoring activities focused on Humpback Chub (HBC) provide valuable information on the 

size of the population in the LCR confluence area and elsewhere in the canyon. This information 

is of high priority because if low abundance is observed, this will elicit management actions to 

help restore the population. Monitoring also incidentally serves to alert the scientific community 

of the occurrence and abundance of nonnative species that might overlap spatiotemporally with 

HBC populations. Finally, documenting the occurrence of HBC aggregations is valuable in 

understanding the feasibility of habitats other than the LCR confluence to support populations of 

HBC. 

Research priorities of the program have focused on determining vital population 

dynamics through an age-structured multi-strata population model for HBC at the LCR 

confluence, using capture-recapture studies to identify and model dispersal of HBC between the 

LCR and mainstem Colorado River as well as elsewhere, and mesocosm experiments testing the 

effects of temperature and turbidity on predation of HBC by trout.

The PEP considers the current monitoring and research activities to be high quality (as 

evidenced by peer-reviewed publications) and of considerable importance to the overarching 

goals of the GCDAMP. During the PEP review, a number of presentations were given and ideas 

presented that were noted as particularly valuable areas for monitoring and research.

 Quantifying impact of trout predation on natural populations of HBC. - It was well 

demonstrated through diet analysis and mesocosm experiments that trout can prey on 

HBC, but it is much more difficult to evaluate the importance of trout predation on HBC 

at a population level in the canyon. Can the data collected (e.g., trout predation and 

abundance) be incorporated into the multi-strata models to evaluate the potential for trout 

predation to result in a critical decline in HBC population? Data are already available to 

at least develop some scenarios that could be used to evaluate the effect of trout. The 

ability of rainbow trout to negatively affect HBC populations is difficult to demonstrate.
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 Continuing efforts to find and document other reproducing populations of HBC in the 

canyons is of considerable importance and is encouraged.

 Efficiency of HBC monitoring and research might be improved by enhanced 

coordination among agencies and sampling efforts, as well as by power analyses to 

optimize sampling effort.

 Some potential suggestions for monitoring trends in HBC abundance, growth and 

condition are to use open-population estimators or preferably, the robust design, using 

PIT tagging of fish (during each survey) to get abundance, survival and movement. 

 For baited hoop netting, researchers should investigate whether baiting affects fish 

behavior, particularly if using Chapman - Lincoln - Peterson mark-recapture estimates

that require assumptions of constant capture probability (e.g., see Peterson et al. 2015). 

 There was discussion among the PEP if enough resources were available to continue 

current intensive monitoring efforts at the LCR confluence as well as expand to another 

site? If so, is it necessary to sample on a seasonal or annual basis? Could sampling of 

population dynamics occur in alternating years to allow intensive sampling at multiple 

sites? How much information is gained with seasonal sampling? Could a simulation 

based on a resampling approach be used to evaluate the importance of sampling 

intensity?

HBC translocation research

Efforts since 2003 have involved translocating HBC from the core population in the LCR to sites 

upstream in the LCR (Chute Falls), Havasu Creek and Shinumo Creek. Additionally, fish have 

been moved to the U.S. Fish and Wildlife Service Native Aquatic Resources and Recovery 

Center (ARRC) to maintain a “genetic” refuge population. The data on the success of these 

translocations are equivocal, but data on growth rate and evidence of reproduction in Havasu 

Creek suggest the possibility of establishing populations of HBC. That said, a large number of 

fish emigrate from the tributaries and uncontrollable events (i.e., wildfire) have caused the 

elimination of others. 

PEP recommended prioritization for HBC translocation efforts.

 The main objectives of the translocations are to supplement or establish new populations. 

Based on the translocations to date, it is still not clear if this is a feasible management 
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activity. It would be useful to reconsider the goals of the translocation experiments to 

guide future efforts. It appears the translocations can have a number of potential roles 

that might include: 1) establishing a new reproducing population; 2) providing nursery 

habitat to raise juvenile HBC to a large enough size to escape predation, 3) provide a 

refuge population; and 4) increase the genetic diversity of supplemented populations.

 Could high emigration rates be mitigated by using alternative stocking methods (different 

sizes of stocked fish or acclimation periods)?

 Continued monitoring for evidence of reproduction by translocated individuals and 

quantifying emigration, through remote PIT antenna are valuable projects that will help 

evaluate the success of the program.

 A relatively large number of HBC have been translocated with no apparent harm to the 

core population. The effects of translocating individuals were evaluated using a 

population viability model before the recent development of the integrated population 

model. The PEP suggests that the program use the new integrated population model to 

evaluate potential harmful effects on donor populations. This model also could be used to 

assist decision making under adaptive management.

 The genetic considerations of translocations or refuge populations at AARC do not seem 

to be very well developed. Has the genetic diversity of HBC populations been 

thoroughly assessed and are there strategies to maintain genetic diversity within and 

among populations in the canyon? If it turns out that sub-populations of HBC are 

genetically distinct, you could maximize genetic diversity by intermixing the populations. 

However, mixing populations may not be a good idea if local adaptation is somehow 

beneficial.

Additional reproducing HBC populations

One important outcome of the spatially extensive fisheries monitoring programs has been the 

identification of a discrete population of HBC far downstream of the Lower Colorado River 

(LCR) population, as evidenced by the consistent capture of a small number of YOY and 

juvenile HBC in this downstream reach. The significant spatial gap in the occurrence of earlier 

ages implies that there may be a second population of HBC, however conclusive evidence is 

lacking at this point. Because of the implications for the conservation status of this species, the 
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PEP encourages the fisheries program to consider a project that could provide a more definitive 

answer of whether this might be a second population.

4. EVALUATING TRADEOFFS IN MONITORING EFFORTS

Power Analysis Review of Monitoring and Research Studies

The program conducts various monitoring and research projects to address important issues. 

Examples include both emerging issues (e.g., quagga mussels, non-native warm-water fishes) 

and those recognized to be increasing in their importance (e.g. establishment of one or more 

additional populations of humpback chub), which require additional resources. Given budgetary 

constraints, it is important to identify areas within existing projects where resources may be 

reallocated without compromising ongoing and essential monitoring and research. Existing 

studies and monitoring often include sampling at many locations and sometimes multiple times 

per year. Having had many of these field studies underway for multiple years, the program is in 

an enviable position of having extensive datasets that provide information necessary to determine 

the degree of sampling adequacy (e.g., power analysis).

 The PEP recommends taking advantage of datasets from both long-term and short-term 

studies to conduct power analyses or sampling simulations to determine whether a 

reduction in the frequency of sampling (e.g., two rather than three sampling periods per 

year, alternating years rather than annual sampling) or reductions in the number of 

individual fish handled (e.g., tagging) would provide the information necessary to 

achieve objectives for monitoring and research while freeing up valuable resources (both 

financial and human capital) that can be deployed to address these emerging and 

upcoming issues. By contrast, such an examination may highlight monitoring or research 

studies that have inherently high variation and limited ability to detect variation or 

change in attributes of interest (e.g. trends in population abundance). In such cases, the 

monitoring needs to be carefully assessed to determine whether increased resources 

should be applied to the field study, the study design should be modified, or that aspect of 

monitoring be discontinued. The 2009 PEP report discussed issues related to power 

analysis with regards to a limited number of aspects of the overall program. The PEP 

suggests a thorough examination of the various sampling programs in this manner to 
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maximize efficacy and overall scope of work that can be undertaken within the program. 

Capitalize on the wealth of data now available in order to better assess allocation and 

redeployment of effort where appropriate.

An additional benefit of identifying appropriate reductions in the sampling and handling of 

fish, or providing increased justification for the need for particular levels of sampling (whether 

decreases, increases or status quo), is that it will help address one of the concerns raised by 

Native Americans, as discussed below (Section 6). Furthermore, the clear demonstration of the 

need for particular levels of sampling to achieve required outcomes (e.g., legal obligations under 

the ESA or priorities determined by the Department of the Interior) and such an evaluation of 

existing programs may strengthen the case if requests for further resources (i.e., budgetary 

increases) are needed.

5. MONITORING BROAD-SCALE FISH COMMUNITY STATUS AND TRENDS

Broad-scale monitoring of fish community trends in the Grand Canyon is primarily 

accomplished through the System Wide Electrofishing Project, a collaboration among the 

Arizona Game and Fish Department and the U.S. Geological Survey. During the PEP meeting at 

the GCMRC in August 2016, there was considerable discussion about the relative merits of 

continuing the current System Wide Electrofishing Project with its emphasis on CPUE data, or 

switching to a more intensive but less expansive sampling effort that would generate population 

estimates. A major concern with CPUE data is that the assumption of equal catchability of a 

species among sites and years is often violated when sampling the Colorado River in the Grand 

Canyon. The primary factors that affect catchability when electrofishing in the Colorado River 

are high water turbidity that makes it difficult to see immobilized fish, high river discharge that 

reduces the areas that can be effectively/safely sampled, and inexperienced crew members that 

reduce netting success (Rogowski et al. 2016). In addition, presentations by program staff 

indicated that the effects of stream habitat characteristics affect catchability. These factors are 

difficult to control, hence CPUE data will continue to be noisy. 

The PEP supports the conclusions of two previous external review panels that spatially 

expansive, long-term sampling with standardized techniques is a valuable tool for tracking 

changes in fish assemblages throughout the mainstem Colorado River in the Grand Canyon 

(Anders et al. 2001, Bradford et al. 2009). Such monitoring can detect relatively large changes 
15

in fish abundance and can document range expansions of nonnative species that inhabit 

mainstem habitats. Switching to a mark/recapture sampling effort would make it easier to detect 

changes in abundances of individual species. The trade-off would be sampling at fewer sites 

since a minimum of two nights would have to be spent at each site to provide for a marking 

event and at least one recapture event.

A compromise would be to implant fish collected during the system-wide electrofishing 

effort with PIT tags. This would allow for estimation of abundance and demographic parameters 

using open population estimators, such as age structured, Cormack-Jolly-Seber models (Williams 

et al. 2002). These methods do not require any additional sampling effort, other than marking, 

and can be employed using the existing sample design. PIT-tagged fish could be recaptured 

during subsequent system-wide electrofishing efforts and by the use of portable PIT-tag antenna 

units recently developed by Marsh and Associates, LLC. This design would also allow for the 

abundance estimation using a mark-resight estimator (McClintock et al. 2008). The PEP 

encourages continuing and expanding the use of portable PIT-tag antenna units during the 

system-wide electrofishing efforts. In addition, the GCDAMP could consider deployment of 

portable PIT-tag antenna units by rafting guides as part of a citizen science/outreach effort. 

Current system-wide electrofishing by AZGFD is considered effective at capturing 

nonnative species know to be present, such as rainbow trout, brown trout and common carp, and 

will likely be effective at sampling some potentially invasive species such, as walleye and

smallmouth bass. But channel catfish, bullheads, striped bass and small-bodied fishes are not 

effectively sampled by this method (Hilwig and Andersen 2011). Also, the AZGFD sampling 

uses a stratified random design to allocate sampling locations each year – thus sites important as 

entry points for invasive species may not be sampled yearly. For example, the area around the 

confluence of Bright Angel Creek was not sampled in 2014, despite the importance of this 

tributary as a source of brown trout to the Colorado River (Rogowski et al. 2015). For these 

reasons, the PEP recommends that a separate invasive species detection program be considered. 

This separate program would use a variety of sampling gears deployed at fixed sites where 

nonnative fish are known to exist or where introduction is most likely to occur. Such an invasive 

species monitoring program could build upon the strategies proposed by Hilwig and Andersen 

(2011).
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Areas targeted for invasive species monitoring should be sampled using the “slow” 

electrofishing techniques described for nearshore habitats by Korman et al. (2015) and other gear 

such as seining, minnow traps and hoop nets (Hilwig and Andersen 2011). Detecting young of 

year of recently introduced nonnative species should be a goal of this monitoring because it 

would signal the potential for further spread and population increases of invasive species that 

could harm native fishes.

Four areas should be intensively monitored for occurrences/increases in nonnative fish 

populations.

1) Glen Canyon from Glen Canyon Dam to Lees Ferry, including the large, warm backwater 

area known as the 12-mile slough. Potentially invasive fish species that could colonize the 

Grand Canyon from Lake Powell include gizzard shad, white sucker, walleye, green 

sunfish, northern pike and smallmouth bass. Smallmouth bass would be of particular 

concern as this species is highly piscivorous and has harmed native fish assemblages in 

other parts of the Colorado River drainage (Johnson et al. 2008; Hilwig and Andersen 

2011).

2. The Little Colorado River and its confluence with the Colorado River. This area is 

critical habitat for the humpback chub. The lower, perennial portion of the Little Colorado 

River already harbors several nonnative species such as channel catfish and common carp 

that could have negative effects on humpback chub. In addition, this section of the LCCR

is occasionally colonized by other nonnative species that are flushed downstream during 

high flow events in upper portions of the LCCR watershed (Stone et al. 2007). 

3) Bright Angel Creek and its confluence with the Colorado River. Bright Angel Creek is 

considered to be a hotspot for brown trout recruitment in the Grand Canyon. Brown trout 

are more piscivorous than rainbow trout but their overall effect on the humpback chub 

population is lower because brown trout are believed to be less abundant than rainbow 

trout in the CRe. Any change in river conditions that would allow brown trout to increase 

would therefore be highly detrimental to humpback chub throughout the CRe.

4) The Colorado River where it flows into Lake Mead. The Lake Mead fish community is 

dominated by warmwater, nonnative species including piscivorous species such as striped 

bass and channel catfish that could be detrimental to native fish populations in the 

Colorado River. Because these nonnatives could easily move upstream with warming 
17

climate, the Colorado River inflow to Lake Mead is considered to be area where 

introduction of new species is likely to occur (Hilwig and Andersen 2011). 

In addition to above four areas, the PEP recommends that other invasion hotspots also be 

monitored such as warm spring inflows and near mouths of tributary streams known to contain 

populations of nonnative fish species. These recommendations mirror those of Hilwig and 

Andersen (2011).

PEP recommendations regarding monitoring of broad scale fish community status and trends:

 Continue the system-wide electrofishing project in place since 2000 and PIT-tag fish 

before release.

 Use information on recaptures of PIT-tagged fish (obtained by electrofishing and from 

portable PIT-tag antenna units) to estimate population abundances and demographic 

parameters from open population estimators, such as age-structured, multi-strata, 

Cormack-Jolly-Seber models (Williams et al. 2002).

 Develop a separate invasive species detection program using a variety of sampling gears 

at fixed sites where nonnative fish are known to exist or where introduction is most likely 

to occur.

 Identify nonnative fish population or distribution (occupancy) indices or rules sets that 

would trigger nonnative fish control options to be deployed.

 Develop ways to routinely solicit information from fishing guides and anglers regarding 

the composition of the recreational fishery. Such information could serve as an earlywarning system for changes in the distribution and population size of nonnative sportfish 

that are potential threats to HBC, especially brown trout.

6. MINIMIZING EFFECTS OF PROGRAM ACTIVITIES ON FISH WELFARE

We commend the fisheries program for their awareness and consideration of the diverse and 

often conflicting cultural and economic needs of the many stakeholders in the AMP process. In 

particular, efforts to substitute quantitative methods that reduce the mortality and handling of fish 

in the Colorado River (e.g., embracing hydroacoustic monitoring methods or automated [Vemco-
18

type] telemetry, e.g., Scheerer et al 2015) into data collection for capture-recapture population 

models will likely increase the useful data as well as decrease objectionable actions.

These issues and differences in approaches are not restricted to this location and do 

include some fundamental differences in philosophies and approaches – there can also be 

differences within both the western scientific and Native American perspectives. The PEP was 

encouraged by the willingness of all parties to discuss issues and work towards solutions. Such 

willingness and engagement does not occur in all situations and it appears that there has been 

progress over time to foster these interactions. The PEP has suggestions to help further reduce 

concerns by Native Americans and enhance interactions.

 Use power analyses and simulation associated with the various monitoring and research 

programs to help determine ways to reduce the number of fish that may need to be 

captured and the associated work needed on individual fish (e.g., Peterson et al. 2015). 

This will provide better justification for the numbers of fish that need to be sampled, 

potentially reduce costs or allow reallocation of efforts to other priorities, and 

demonstrate a recognition of the importance of life within the river and willingness to 

modify sampling programs to achieve the required goals while minimizing impacts on the 

fish.

 There may be the potential to acquire some necessary tissues (e.g., otoliths for natal 

origin studies) from humpback chub through means other than sacrificing HBC

individuals. It may be possible to acquire some HBC samples through non-lethal gastric 

lavage of other fishes (e.g., striped bass or trout) that may have eaten chub. At present it 

is unknown how many chub individuals, already dead, may be sampled in this manner 

but this approach may provide an option to minimize the number of humpback chub that 

will need to be euthanized to accomplish the goals of the natal origins study. 

 Engage Native Americans in the monitoring and research programs on the river when 

possible to further strengthen connections between the various stakeholders, help reduce 

barriers to understanding by all parties, and provide valuable employment and training 

opportunities. 
19

7. PROGRAM COMMUNICATION AND OUTREACH

The GCDAMP has a daunting task to address complex scientific questions while being sensitive 

to a diversity of stakeholder interests. Communicating the results of different tasks and projects 

in professional presentations and peer-reviewed publication is certainly necessary for scientific 

legitimacy; however this is not sufficient for a program like the GCDAMP. Establishing a clear 

framework so that peer scientists as well as stakeholders can understand how priorities are set, 

the logical sequence of experiments and projects, and how all of the different data and insights, 

past, present, and future, fit together is crucial. The use of conceptual models has been essential 

for facilitating communication and transparency for other similarly complex programs including 

the Everglades Restoration, the Sacramento-San Joaquin Delta Restoration Project, and the 

USACEs Missouri River Restoration to name a few. While an integrated conceptual model 

promotes better planning and decision making in the science process, the process of developing 

such a model alone is often extremely valuable for educating all the stakeholders and 

constituencies on progress, failures and what is learned from both. Because of its critical role in 

building transparency and trust, as well as facilitating the communication of results to the 

regional stakeholders, the Federal leadership and the cooperating agencies, and Congress, the 

PEP recommends that the program and its stakeholders make the development of an integrated

conceptual model a top priority for the fisheries program. The focus of such an effort should be 

on outlining both the established and hypothetical interactions among drivers, stressors, and 

response variables of the Grand Canyon socio-ecological system.

In discussions with angler stakeholders, it was apparent to the PEP that there were some 

areas of disagreement with program staff and affiliated scientists about the state of the fishery 

and the factors affecting it. To address these issues, the PEP recommends that the program 

establish a process for engagement and communication with anglers with an emphasis on two

different areas.

 The development of a population metric or set of metrics for characterizing the RBT 

population that are understood by and acceptable to the angler stakeholders. 

 Continue and expand citizen science outreach efforts such as those used to monitor insect 

emergence throughout the canyon by rafters (Kennedy et al. 2016). New opportunities 

could include having guides on rafting trips employ portable PIT tag readers to collect 

data on fish locations and having fishing guides report catches of species of special 
20

concern (e.g., more frequent occurrence of brown trout in the Lees Ferry area or the 

appearance of smallmouth bass in the fishery).

8. ADAPTIVE MANAGEMENT

There are two primary approaches to adaptive management that have been defined as the 

resilience-experimentalist approach and the decision-theoretic approach (McFadden et al. 2011). 

The major difference between these approaches is the role of experimentation in the learning 

process. The resilience-experimentalist approach relies primarily on experimental manipulation 

of the system to learn about how the system works. This approach employs the scientific method 

with the development of falsifiable hypotheses, the implementation of the experiment 

(management action), and the evaluation of hypotheses with the use of monitoring data. In 

contrast, the decision-theoretic approach facilitates learning through the integration of 

management and monitoring in a decision-theoretic framework. That is, a predictive model or set 

of models are created that represent alternative ideas of how the system works. Learning then is 

accomplished by comparing predicted outcomes to actual outcomes as measured by monitoring 

data. Decisions that increase the rate of learning (experiments) also can be incorporated into the 

decision-theoretic approach. From the beginning of the program, the GCDAMP has employed 

the resilience-experimentalist approach to adaptive management. This approach, however, 

requires that the implementation of the experiment be under the control of the program. During 

discussions with program staff, it was clear that many of the management decisions are heavily 

influenced by other GCDAMP objectives that may not be directly related to and even in conflict 

with fish program objectives. The best example of this was ending the experimental reduction of 

RBT inhabiting the reaches near the confluence of the LCR before the experiment was complete. 

This lack of experimental control and consistency in the application of treatments has hindered 

the adaptive management process for the fishery program. For instance, when queried, program 

staff indicated that learning was primarily opportunistic and there were few if any hypotheses 

that have been falsified or eliminated. To take advantage of these learning opportunities, the PEP 

recommends that the fish program adopt the decision-theoretic approach to adaptively manage 

the RBT fishery and HBC population in the LCR and confluence. The adoption of a decisiontheoretic adaptive management approach would not require a new major research effort and 

could be accomplished by completing the following steps.
21

 Modify the existing integrated RBT population model to incorporate alternative 

hypotheses of the factors affecting survival, growth, emigration, and recruitment. This 

could be facilitated by the development of a conceptual model.

 Modify the existing integrated HBC population model to incorporate alternative 

hypotheses of the factors affecting demographics.

 Formally integrate the two population models to facilitate assessing the potential effects 

of RBT on HBC and the potential effects of system wide factors (nutrients, flow) on both 

species.

The one research area of the fisheries program that appears to be under their greatest 

control is the ongoing experimental management involving translocation of HBC within the LCR

and to other tributaries. After reading the reports and publications and discussion with 

translocation project staff, it was unclear what key uncertainties (unknowns) the project faces, 

which alternative management actions (experiments) are available to the project (i.e., feasible), 

and what the alternative hypotheses of system dynamics might be. To minimize confusion and 

facilitate communication with stakeholders and other outside the program, the PEP recommends 

the following points.

 The fisheries program needs to develop clear set of alternative hypotheses regarding the 

factors responsible for the success or failure of HBC translocations.

 The hypotheses should be linked to specific management actions and descriptions of the 

criteria and methods that will be used to conclude that a hypothesis is falsified or 

supported. For example, what criteria define a successful translocation?

 These should be accompanied by steps that will be taken following the evaluation of 

hypotheses.

9. EMERGING ISSUES

9.1 Enhanced Integration of Reservoir and Lees Ferry Ecosystem Monitoring and 

Research

Conditions within Lake Powell directly affect conditions in the Colorado River below the Glen

Canyon Dam, through alterations in water temperature, turbidity, and nutrient levels. The waters 

of Lake Powell and the Colorado River above Lake Powell also serve as biological reservoirs for 
22

additional exotic fish species (e.g., smallmouth bass, northern pike) that currently have been 

limited potential to colonize downstream due to the hypolimnetic (cold, deepwater) discharge 

from Lake Powell and the cold river water immediately downstream of the dam. There is clear 

recognition that reductions in water levels within Lake Powell presents an ecological risk 

downstream due to the potential for water releases shifting from hypolimnetic to epi- or 

metalimnetic regions of the reservoir. Such releases will be of water warmer and lower in 

nutrient levels than water released currently, which will be detrimental to the trout fishery. 

Warmer temperatures will potentially increase the likelihood of downstream dispersal and 

establishment of nonnative species such as smallmouth bass.

Quagga mussels have established within Lake Powell. Discussions during the PEP visit 

indicated that the program has evaluated the potential threat to the river ecosystem by quagga 

mussel establishment in the river below the dam. Given the rate of flow and sediment surface 

area available, it has been estimated that quagga mussels would effectively filter about 10% of 

the river water and therefore are not considered to pose a significant risk to the river food web.

The PEP believes that this estimate is likely too low and is concerned that quagga mussels in 

Lake Powell could have a greater effect on the trophic dynamics of the downstream river 

ecosystem.

Lake Powell is a large, deep body of water and during the PEP visit, it was suggested that 

due to its physical dimensions it is not likely to be impacted by quagga mussels in contrast to

smaller lakes or even Lake Erie (which has a relatively shallow western basin). Since the 

establishment of zebra and quagga mussels in lakes Michigan and Ontario, associated issues 

have developed related to off-shore (pelagic) declines in nutrient levels, large-scale declines in 

important food-web components such as the amphipod Diporeia, and increasing frequency of 

algal blooms in the nearshore areas – all factors in reshaping the food web and fisheries of these 

lakes. In conjunction with the decline in offshore productivity (reduction in total phosphorus and 

chlorophyll a) there has been an increase in water clarity (e.g., spring Secchi depth can be 2-3

time greater in Lake Michigan since dreissenids establishment) and an alteration of thermal 

structure (deepening of the mixing zone and warm epilimnetic zone; Cuhel and Aguilar 2013). 

As Lake Michigan and Lake Ontario both greatly exceed the area, volume and depth of Lake 

Powell, a potential outcome of quagga mussels in Lake Powell may be a similar reduction in 

offshore nutrients and production, increased light penetration and a deeper layer of warm water. 
23

Given current concerns about the reduction in reservoir depth and discharge of warmer waters, 

the potential for quagga mussels to further increase the probability of warmer water discharges 

with concomitant reductions in nutrient levels presents significant but unquantified risk to 

downriver ecological resources (e.g. the likelihood of such an outcome is currently unknown but 

the significance of the effects could be very high). Direct impacts to the trout fishery through the 

increased water temperature and impacted food web via reduced nutrients and indirect effects of 

heightened potential for additional non-native warm-water species to disperse past the dam and 

establish downstream represent significant concerns to the humpback chub, trout and other 

species. At present there is some monitoring of conditions within the reservoir, but little to no 

research underway to determine the potential impact of quagga mussels within Lake Powell and 

the resulting effects downstream.

Water is essential in the arid west and large areas of the region are experiencing 

substantial changes in the water cycle; the Colorado River basin is no exception. Reduced 

inflows from their headwaters have caused reservoirs to be managed differently or behave in 

ways that are outside their original design parameters. In particular, the very low reservoir water 

levels have the potential to change conditions in tailwater systems. However, there is no clear 

understanding of either the sort of changes that can be expected if the current water balance 

trajectories continue or how these changes might influence attributes of either the cold tailwater 

or the warmer Colorado River further downstream. 

 The PEP suggests the development of a more formal integration of monitoring and 

research within Lake Powell and the Colorado River below the Glen Canyon Dam. At a 

minimum, modeling of the potential impacts of quagga mussel on water clarity, nutrient 

conditions, and thermal structure should be considered. Integrating these findings with 

those regarding future water-level scenarios will provide a means to develop some risk 

scenarios for the resources downstream.

 During discussions in the field, project scientists indicated that detection limits under 

ongoing water quality monitoring were based on State Water Quality Standards and may 

be too coarse for ecological investigations. The PEP suggests that the program review 

the sensitivity of existing water quality monitoring and revise if necessary to ensure that 

sensitivity of the measurements are appropriate for program needs.
24

 Finally, we suggest that effort could be placed on modeling future scenarios based on the 

best available data from past conditions in Lake Powell.

9.2 Invasive species

Invasive species can have profound and long lasting ecological effects that are frequently beyond 

our ability to manage. The recent discovery of a concentration of YOY Green Sunfish (Lepomis 

cyanellus) and the GCDAMP response highlights three critical points about the arrival of a major 

invasive species: they are nearly impossible to predict with any accuracy; they are often only 

identified after the fact and by chance; and a large multiagency control efforts can work but are 

incredibly complex to execute and likely distract from other planned management actions (e.g., 

planed flow releases). Prevention is by far the more economically effective approach. With the 

presence of warm water habitats and a pool of potentially detrimental warmwater invasive 

species upstream and downstream of the main HBC population, invasive species outbreaks may 

be the fisheries program’s most immediate risk. 

9.3 Shifts in benthic macrophyte community 

In addition to the more obvious threat posed by the invasive warmwater fish, the panel notes the 

recently observed shift in aquatic vegetation, from a community that was predominately 

Cladophora glomerata in the early 2000s to a community dominated today by bryophyte species

in the tailwaters in the Lees Ferry reach and we encourage investigation of this phenomenon. 

Despite the importance of submerged aquatic vegetation in regulating many aspects of coldwater 

systems, it may also influence important aspects of the Colorado River system linked to adaptive 

management issues including nutrient cycles and habitat for a declining benthic invertebrate 

community. The consequences of such a major shift in a primary producer in an otherwise low 

productivity, arid region river seem to have been given little attention. Although the shift is 

already completed, we encourage the fisheries program to consider capturing what knowledge of 

the prior conditions exists as well as consider exploring and modeling what the trophic, food web 

and habitat impacts-constraints of the current dominant species might be on the tailwaters and 

downstream Colorado River (e.g., nutrient assimilation and stoichiometry dynamics, differences 

in secondary production of benthos).
25

9.4 Mitigating the effects of climate change

The proliferation of nonnative, warmwater fishes in Grand Canyon has been limited by the cold 

water released from Lake Powell. However, warmer air temperatures, reduced inflows and 

perhaps higher water clarity associated with quagga mussels will increase the temperature of 

water being discharged from Glen Canyon Dam into the Colorado River. A glimpse of such 

future conditions occurred in 2005 when a hot summer and drought conditions resulted in 

discharged water temperatures several degrees warmer than in other years. Although warmer 

water may provide a bioenergetic benefit to native species, warmer water would almost certainly 

allow colonization and expansion of nonnative warmwater native species likely to have negative 

effects on humpback chub and other native fish species. Actions involving the discharge of 

water from Lake Powell could mitigate the negative effects of warming temperatures. The PEP 

recommends that the program investigate the possible effects of temperature control device

operation (in Glen Canyon Dam) on the factors directly influencing RBT and HBC populations

(e.g., facilitating exotic fish species immigration) and indirectly by influencing other emerging 

issues like macrophyte shifts, benthic invertebrate productivity, and nutrient dynamics. This 

could be done through either bioenergetics- based assessments built on the multi-stage life 

history models or through simulation models. The design of these studies and 

communication/integration of the results into the adaptive management program would benefit 

greatly from development the conceptual models recommended earlier. 
26

Literature cited

Cuhel, R.L. and C. Aguilar. 2013. Ecosystem transformations of the Laurentian Great Lake 

Michigan by nonindigenous biological invaders. Annual Review of Marine Science 

5:289-320.

Hilwig, K.D. and M.E. Andersen. 2011. Summary of nonnative fish control options, monitoring 

strategies, and research needs for Grand Canyon, Arizona. Administrative Report. U.S. 

Geological Survey, Reston, VA. 

Johnson, B.M., Martinez, P.J., Hawkins, J.H., and Bestgen, K.R. 2008. Ranking predatory threats 

by nonnative fishes in the Yampa River, Colorado via bioenergetics modeling: North 

American Journal of Fisheries Management, 28:1941–1953.

Kennedy, T.A., J.D. Muehlbauer, C.B. Yakulic, D.A. Lytle, S.W. Miller, K.L. Dibble, E.W. 

Kortenhoeven, A.N. Metcalfe and C.V. Baxter. 2016. Flow management for hydropower 

extirpates aquatic insects, undermining river food webs. BioScience 

doi: 10.1093/biosci/biw059.

Korman, J., M.D. Yard, and C.B. Yackulic. 2016. Factors controlling the abundance of rainbow 

trout in the Colorado River in Grand Canyon in a reach utilized by endangered humpback 

chub. Canadian Journal of Fisheries and Aquatic Sciences 73(1):105-124.

McClintock, B.T., White, G.C., Burnham, K.P. & Pride, M.A. 2008: A generalized mixed effects 

model of abundance for mark-sight data when sampling is without replacement. - In: 

Thompson, D.L., Cooch, E.G. & Conroy, M.J.(Eds.); Modeling demographic processes 

in marked populations. Springer, New York, New York, USA, pp. 273-292.

McFadden, J. E., T. L. Hiller, and A. J. Tyre. 2011. Evaluating the efficacy of adaptive 

management approaches: is there a formula for success? Journal of Environmental 

Management 92(5): 1354–1359.

Peterson, J.T., P.D. Scheerer, S. Clements. 2015. An evaluation of the efficiency of minnow 

traps for estimating the abundance of minnows in desert spring systems. North American 

Journal of Fisheries Management. 35: 491-502.

Rogowski, D.L., R.J. Osterhoudt, L.K. Winters, and P.N. Wolters. 2016. Colorado River fish 

monitoring in Grand Canyon, Arizona – 2015 annual report. Unpublished report 

submitted to USGS Grand Canyon Monitoring and Research Center by Arizona Game 

and Fish Department, Flagstaff, AZ. Cooperative Agreement # G13AC00086.
27

Scheerer, P.D., J.T. Peterson, and S. Clements. 2015. 2014 Warner Sucker Investigations (Lower 

Twentymile Creek). Annual Progress Report, Fish Research Project Oregon. Oregon 

Department of Fisheries and Wildlife, Corvallis, Oregon.

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. The Southwestern 

Naturalist 52:130-137.

Williams, B. K., J. D. Nichols, and M. J. Conroy. 2002. Analysis and management of animal 

populations. Academic Press, San Diego, California, USA.
28

Appendix A. 2016 Protocol Evaluation Panel - Fisheries Program Review agenda.

Start End Topic

Tuesday, August 02, 2016

8:00 8:30 Welcome, introductions, workshop agenda, goals, ground rules

8:30 8:50 Historic Colorado River ecosystem and fish

8:50 9:30 Program overview, fisheries issues and policies

9:30 10:00 Tribal perspectives 

10:00 10:15 Break

10:15 11:00 Rainbow trout population dynamics and early life history studies 

11:00 11:45 Arizona Game and Fish Lees Ferry Rainbow Trout Monitoring and Creel

11:45 14:00 Travel to Lees Ferry

14:00 18:15 Boat safety orientation, Boat trip up-river, with presentations at stop-points

18:15 19:30 Disembark at campsite, campsite orientation, dinner

19:30 20:30 After dinner discussion, Natal Origins and trout movement

Wednesday, August 03, 2016

8:00 9:00 Informal discussion: Emerging issues: Green Sunfish, Brown Trout

9:00 1300 Break camp and return to Flagstaff

13:00 13:20 Formal presentation, with discussion: Food base

13:20 13:40 Formal presentation, with discussion: Bioenergetics

13:40 14:00 Influence of warming temperatures on trout recruitment and size

14:00 14:30 Formal presentation, with discussion: Zuni perspectives

14:30 14:45 Break

14:45 15:15 Stakeholder Perspectives (Colorado River Energy Distributors Association)

15:15 15:45 Formal presentation and discussion: Little Colorado River HBC

15:45 16:35 Formal presentation and discussion: Humpback chub population dynamics

16:35 17:00 Recap, discussion

Thursday, August 04, 2016

8:00 8:30 Formal presentation and discussion: Trout/chub interactions

8:30 9:00 Formal presentation and discussion: HBC aggregations

9:00 9:30 Formal presentation and discussion: Chute Falls Translocation

9:30 10:00 Arizona Game and Fish system-wide fish monitoring

10:00 10:45 Discussion: nonnative fish detection, monitoring HBC populations on lower 

river

10:45 11:00 Break

11:00 12:00 Questions from panelists to scientists and discussion

12:00 12:30 Final (review/summary) discussion

12:30 13:30 Lunch and break time at GCMRC

13:30 17:00 Panel meets in closed session at GCMRC,
29

Appendix C. Questions and issues provided to the PEP by the angler stakeholders August 2, 2016

1. Approaches to identify the root cause(s) of the unstable trout populations in Lees Ferry;

2. The highest priority actions to stabilize and enhance the quality of the aquatic food base and the 

Lees Ferry trout fishery;

3. The appropriate metrics to trigger TMF’s, stocking, and other management actions;

4. The most appropriate methods and level of effort to effectively monitor progress towards 

achieving the goals outlined in the Lees Ferry Recreational Trout Fishery Management 

Recommendations, August 2015;

5. Important data gaps that need to be filled and uncertainties that need to be resolved; and

6. The need to develop or refine an existing Stock Assessment Model to:

a. measure progress towards reaching the goals contained in the Lees Ferry Recreational 

Trout Fishery Management Recommendations, August 2015,

b. determine the suitability of the metrics identified in the Recommendations, and

c. evaluate the effectiveness of increasing harvest as a tool for managing the trout fishery.

7. A method or strategy for characterizing the overall health of the aquatic ecosystem including 

aquatic food base, native and nonnative fish, water quality and habitat quality/availability.
30

Appendix C. Questions and issues provided to the PEP by the Colorado River Energy Distributors 

Association, August 3, 2016.

The following are issues and questions for the panel meant to stimulate discussion. My work for the 

Colorado River Energy Distributors Association provides them with an environmental perspective on 

research and monitoring efforts in the AMP as they pertain to influences on dam operations. The 

following is a very brief list of what constitutes a very large topic. (My thoughts follow in parentheses.)

 The impacts of the Modified Low Fluctuating Flow operating regime on HBC survival, growth 

and reproduction are contained in a variety of research and monitoring efforts and reports, 

including those in the Near Shore Ecology studies by Pine and Finch.

The NSE study appears to conclude that the Grand Canyon population of young HBC is doing quite well 

utilizing a variety of available near shore habitats under a wide range of flow conditions. Will the PEP be 

attempting to reach a conclusion after reviewing this material as to its comprehensiveness and 

quality and whether more research and monitoring should be prioritized to determine flow impacts 

on growth and survival? And if so, what types of research and monitoring?

(My hypothesis about HBC relation to river flows consists of having little worry. The research 

and monitoring could continue to dig deeper into their relationships; however, for purposes of 

developing recommendations on dam operations, the data are pretty conclusive that river flows 

have little effect on their growth and survival. River temperatures do have effects on growth and 

probably on their survival at the early stages as cold temperature does make them more 

susceptible to predation.)

 Actions needed to prevent future green sunfish (and other nonnatives) infestations, 

Last year, a population of green sunfish was discovered in a backwater downstream of the dam. Great 

concern was expressed about allowing this population of aggressive, predatory fish to persist and 

eradicating this population was believed to be a necessary step; therefore, an eradication project was 

implemented using rotenone. Future influx of warm water nonnative fish from Lake Powell would appear 

to be a significant possibility. Can the PEP offer opinions on the necessity for monitoring detection 

of entrainment, ideas on an adequate monitoring program to detect future fish entrainment from 

Lake Powell, what habitats downstream to monitor for their presence and point to research 

ongoing or planned on future preventative measures?

(My thought on this is to pursue physical modifications of the present backwater used by the GSF 

to create a flow-through system. This will move the fish downstream to Lake Mead, an existing 

habitat already used by GSF. There are other backwaters that GSF could hang in which could be 

similarly modified; but these may be sufficiently few and of small consequence to make much 

difference. Also, I think we could implement some more intense monitoring downstream of the 

dam to provide early detection of nonnative warm water fish coming through the dam. 

Smallmouth bass are the biggest concern.)

 Research on the value of temperature control and oxygen maintenance using dam bypass tubes

Bypass tubes on Glen Canyon Dam and many other dams exist at a lower elevation than the hydropower 

intakes. Does the PEP see advantages to pursuing research efforts to determine the efficacy of their 
31

use to ameliorate temperature and oxygen conditions downstream of dams? If so, can the PEP offer 

some research approaches to establishing their efficacy?

(We would like to see if there are advantages to fish populations by use of the bypass tubes since 

their use for other purposes are many. If we can establish a collective benefit to fish and these 

other uses, perhaps this will be sufficient to justify their use.)

 Importance of establishing HBC origins in lower canyon. 

Recent fish monitoring in the lower Grand Canyon have detected various life stages of humpback chub. It 

is currently unknown where these fish originate but there is much speculation. We think knowing their 

origin is important to future efforts to increase alternative habitat use and thereby secure the population 

against catastrophic losses. Does the PEP think some research and monitoring approaches should be 

employed to help us determine their origins and if so, what ideas do they suggest short of actually 

sacrificing individuals?

(The lower canyon is the location where humpback chub were originally identified but we do not 

know their numbers or origins. We believe some today originate within Havasu Creek and 

possibly one or more main stem spawning group. If we can identify their origins, there may be a 

way to enhance those populations. This enhances the overall canyon population and can further 

justify down- or delisting the species.)

 The rainbow trout population in the Colorado River below the dam has fluctuated widely over the 

last 10 years at least an order of magnitude.

Over the last few years, the food base for the trout population has morphed from one consisting 

primarily of Gammarus to one consisting more of black flies and midges. During the 3 decades 

following dam closure, Gammarus populations were high and persisted under high fluctuating flows, 

providing an abundant food base both within the Lees Ferry reach and downstream as drift. 1) Does 

the PEP have any ideas on how we could approach obtaining answers to why this has occurred 

and its ramifications to the ongoing food supply for trout and downstream fish populations 

(e.g., HBC). 2) Does the PEP have any ideas on what linkage there may or may not be between 

fall HFEs and foodbase impacts compared to spring HFEs and foodbase impacts? What would 

be the most effective monitoring protocols to determine whether there are linkages?

(Some believe that High Flow Experiments coincide with the change in Gammarus domination. 

There is some evidence that the recurring scouring during HFEs does not allow sufficient time for 

their recovery. Since the drop in their numbers coincides with the advent of HFEs, there is at least 

a high suspicion. Also, conducting spring HFEs, immediately prior to the growing season may 

have less impact on the food base than one conducted in the fall, prior to winter. There have been 

a preponderance of fall HFEs.)

 The value of using other trout strains to enhance the fishery.

There are hundreds of strains of rainbow trout developed over the last 150 + years, each with a different 

set of tolerances, capabilities, behaviors, etc. We see the Lees Ferry trout population as dominated by the 

Bel Aire strain, primarily due to it being a good hatchery product and are concerned that this may be 

attempting to put a “square peg in a round hole.” This strain may not be appropriately suited to the 

conditions prevailing below Glen Canyon Dam yet we continue to try modifying conditions to suit this 
32

strain. Is the PEP aware of any efforts to marry trout strains to river conditions and if so, consider 

reviewing the suitability of various trout strains to be a worthwhile research topic?

(I have conducted two such studies and have managed to locate strains that may be better in tune 

with the type of fishery demanded by Lees Ferry anglers and the riverine conditions below the 

dam. The Bel Aire strain is not known for having the capability to reach a large size but it is 

easier to catch than others! Both studies are on file with GCMRC. I would like to know if others 

have attempted to marry strains with dam tailwater conditions or if this is even a worthwhile 

research topic given other priorities.)
33

Appendix I Acronyms

ADMB – AD model-builder software

AGFD – Arizona Game and Fish Dept.

CMIN – Core Monitoring Information Needs

CRe or CRE – Colorado River Ecosystem

FNU - Formazin Nephelometric Units

GCDAMP - Glen Canyon Adaptive Management Program

HBC – Humpback Chub

HFE – High Flow Experiment

JCM – Juvenile Chub Monitoring 

JS – Jolly Seber model

LCR – Little Colorado River

LTEMP – Glen Canyon Dam Long-Term Experimental and Management Plan

MLFF – modified low fluctuating flows

MUX - Multiplexer

NEI – Net Energy Intake

NO – Natal Origins

NSFS – Nonnative fish suppression flows

PIT - Passive Integrated Transponder

PBR – Paria River to Badger Rapid

PEP – Protocols Evaluation Panel

RBT – Rainbow Trout

RD- Robust Design

RIN – Research Information Needs

RTELSS – Rainbow Trout Early Life Stage Survey

SSQs – Strategic Science Questions

TCD - Temperature Control Device

TMF – Trout Management Flows