GRAND CANYON MONITORING AND RESEARCH 

CENTER

Protocols Evaluation Program 

Draft Report of the Aquatic Protocol Evaluation Program 

Panel 

November 28, 2001 

Panel: 

Paul Anders 

Mike Bradford (Chair) 

Paul Higgins 

Keith H. Nislow 

Charles Rabeni 

Cathy Tate 

1
Executive Summary 

 In May, 2001 a panel of 6 scientists was convened to review the aquatic resources 

program of the Grand Canyon Monitoring and Research Center (GCMRC, ‘the Center’) 

as part of the Protocol Evaluation Program (PEP). The panel was asked to determine if 

the research and monitoring programs for Colorado River aquatic biological resources 

were adequate to evaluate the status of aquatic resources in relation to the interim

qualitative management goals. In addition, the panel considered whether the monitoring 

programs were sufficient to evaluate Adaptive Management experiments, particularly 

those that involved changes to the operation of the Glen Canyon dam. Finally, responses 

were provided to a list of specific questions given to the panel. 

Overall, the panel was impressed by the quality of the work that has been conducted, and 

the dedication of researchers working in the Grand Canyon. Much has been learned. But, 

an adequate monitoring program is not yet in place. 

The panel recommends that the Center urgently needs to specify the linkages between the 

qualitative management goals and the results from current and proposed monitoring 

programs. This process likely result in more focussed monitoring activities, and will 

expose the uncertainties that remain to be resolved. The panel supports the ongoing 

process of assembling existing data, and urges the quantitative analysis of those data to 

determine the utility of those metrics currently in use for long-term monitoring. 

A program designed to monitor long-term trends in the ecosystem may not be suitable for 

the evaluation of short-term responses to flow experiments. The latter will likely have to 

be evaluated with a combination of management and process-oriented research. 

Individuals of the panel took the lead in conducting more detailed review for each major 

component of the Grand Canyon aquatic ecosystem. The following are key 

recommendations from those reviews: 

1. Water Quality: A water quality program that monitors physical and biological 

parameters of the Colorado River in Grand Canyon should be established. This 

program could be tied to physical sampling sites at non-boat access points 

associated with USGS gauging stations. 

2. Food Base: The food base program needs to be critically reviewed because the 

current level of understanding about the linkages between lower trophic levels 

and food availability of native fishes is not adequate to interpret food base data 

in relation to the management goal. Lower trophic levels can also be used to 

monitor ecosystem changes. GCMRC needs to explicitly identify the goal of the 

food base program, determine what metrics to use to monitor the lower trophic 

levels, and decide what level of detection of change is required. Sufficient data 

and experience exists to design a program that meets the identified needs with 

appropriate power. 

2
3. Humpback Chub: The Panel recommends that further work be conducted to 

develop a conceptual model of the metapopulation biology of chub in the GCE to 

provide a context for a long-term monitoring program. Consideration should be 

given to the inclusion of genetic concerns in the monitoring program. GCMRC 

needs to develop explicit linkages between the results of annual monitoring and 

the management goals to ensure that the monitoring programs produce results 

appropriate to review progress to the goals. The Panel supports the completion 

of the current review of existing data, and the development of population models 

as these programs will yield sufficient information to make decisions about 

sampling programs for chub. 

4. Other Native Fish: The Panel was concerned that there no plan for monitoring 

the status of the 3 other extant native fish of the GCE. The Panel supports the 

ongoing synthesis of existing information and attempts to develop a population 

model for flannelmouth sucker as the first steps for developing a program for 

this species. The Center should develop explicit linkages between management 

goals and monitoring programs, and once all available data for the non-native 

species have been assembled, review options for monitoring these species. 

5. Exotic Fish: For the GCE below Lee’s Ferry, the management goals for nonnative fish are related to their impacts on native species. The Panel was 

impressed by the efforts to develop a program to estimate the abundance of 

salmonids in the Colorado River, but felt some effort should be (re-)allocated to 

the other components of risk to native species, especially with respect to 

predation. There is no explicit program for warm-water exotic fish species. The 

Panel suggests that the species should be ranked for their potential for impacting 

native species, and that monitoring metrics be developed for the important 

species that address potential risk to native fish. Thorough analysis of available 

data should assist in the evaluating the feasibility of monitoring programs for 

these species. 

6. Management Issues: The panel observed considerable variation in the analytical 

effort expended, the timeliness of reporting, and the availability of standardized 

databases among programs for aquatic resources. A standardized annual 

reporting cycle is a key component of any monitoring program. The Panel 

recommends that the contracting process needs to be much more tightly 

controlled, and wonders whether greater ‘in-house’ capability is required at 

GCMRC to achieve long-term consistency and quality in the monitoring 

program. 

3
Chapter 1. INTRODUCTION 

The construction of Glen Canyon Dam on the Colorado River has affected the 

physical and biological attributes of resources downstream in Grand Canyon (Webb et al. 

1999). Despite nearly two decades of monitoring and applied research there remains 

considerable scientific uncertainty about effects of Glen Canyon Dam on the physical 

environment and dynamics of biological components of the aquatic ecosystem of the 

Colorado River (NRC 1999). In 1996 the Secretary of the Interior’s Record of Decision 

(ROD) on the operation of Glen Canyon Dam authorized the long term monitoring and 

research and experimentation on river ecosystem and dam operation management 

options. The Record of Decision called for the formulation of the Glen Canyon Dam

Adaptive Management Group (AMWG) as a Federal Advisory Committee to guide the 

development of the adaptive management program, review results of monitoring and 

applied research activities, and make recommendations to the Secretary of the Interior 

about the long term operation of Glen Canyon Dam. As part of the ROD the Grand 

Canyon Monitoring and Research Center (GCMRC) was established to coordinate/conduct monitoring and research on the influence of operation of Glen Canyon 

Dam on the physical, biological (aquatic and terrestrial) and cultural resources of the 

Colorado River ecosystem (NRC 1999). The goals of aquatic monitoring activities were 

to: 1) provide surveillance on key ecological index variables associated with the 

qualitative management goals and 2) to provide information on the effects of dam

operations on the ecosystem. 

One component of the development of a monitoring and research program is 

independent peer review of monitoring and research protocol. The Protocol Evaluation 

Program (PEP) to assess monitoring and research activities to identify strengths and 

weaknesses and to make recommendations for reliable and cost effective long-term

monitoring and research program for the CRE. On May 7, 2001, GCMRC convened a 

six member peer review panel with expertise in aquatic ecology, water quality, fish stock 

assessment, and monitoring program design to conduct the Aquatic Protocol Evaluation 

(see Appendix Table 1). The review was conducted in two stages. In the first stage, the 

PEP panellists were hosted on a seven-day raft trip from mile 0 to mile 225 of the 

Colorado River (May 8 - May 15, 2001). The PEP panellists were accompanied on the 

trip by GCMRC staff, independent scientists conducting monitoring and research on the 

physical environment, aquatic ecology, and fish populations of the study area. This trip 

greatly facilitated direct interaction between GCMRC staff, scientists conducting 

monitoring and research on the physical environmental, aquatic ecology, and fish 

populations of the study area. It also benefited the panel members by providing site 

specific experience and appreciation of the scope and practical issues relevant to 

conducting aquatic monitoring and research in the Colorado River ecosystem (CRE). 

Information transfer during this trip occurred in a variety of ways including: 

1) Plenary presentations (all panel + all contractors) to describe the fundamental 

purpose, general findings, assessment of limitations, and required future directions of 

field of research in the CRE (Physical Science Program: Ted Melis, GCMRC; 

Aquatic Food Base Program: Joe Shannon, Northern Arizona University, Flagstaff 

4
AZ; Fish Studies: Carl Walters, UBC, Conceptual Model: Josh Korman, Ecometric 

Research; Background of Environmental Studies: Adaptive Management, and the 

Role of PEP, Barry Gold, GCMRC) 

2) Panel convened sessions (all panel + individual researchers) to allow less formal 

discussion of the individual programs and protocol (Humpback Chub/Flannelmouth 

sucker stock assessment; Carl Walters, UBC; Non-native fish populations Bill 

Persons, Arizona Game and Fish; Mainstem fish sampling, Mellisa Trammel, SWCA 

Inc. Flagstaff AZ., Little Colorado River Chub Program Lew Coggins USFWS, 

Flagstaff AZ,) 

3) Adhoc informal discussion between panel members and contractors. 

4) Review of technical reports provided to the panel by GCMRC representatives. 

On the day following the raft trip (May 16, 2001), a half day workshop was held at 

the GCMRC facility in Flagstaff so that additional presentations could be made to the 

panel (Allan Haden; bioenergenetics of Humpback chub in the Little Colorado River; 

Mike Yard, GCMRC, water quality; Carl Walters, chub stock sythesis model). Several 

members of the Technical Working Group were also present. 

In the second stage of the review panellists undertook a detailed review of available 

technical documents and prepared assessments of the protocol for specific aquatic 

monitoring and research program areas. For the purposes of discussion in the evaluation, 

the aquatic monitoring program was arbitrarily subdivided into five primary program

areas: 1)Water Quality; 2) Food Base; 3) Humpback chub; 4) Other Native Fish; and, 5) 

Non-Native Fish. These program areas were indirectly linked to qualitative goals of the 

program as they relate to aquatic ecosystem (Adaptive Management Working Group, 

Draft Strategic Plan 2001). The fundamental objective of the Aquatic PEP was to identify 

the strengths and weaknesses in each program area and to supply recommendations for 

required activities to address documented shortcomings. Each program area was 

evaluated to assess the degree of understanding about key ecological processes, the 

expected statistical reliability of monitoring, and the ability of the current monitoring and 

research effort would allow evaluation of management goals associated with the aquatic 

ecosystem. For the protocol evaluation the Panel considered the following four primary 

questions: 

1) Are there well-defined linkages between ecosystem response indicators and the 

management goals? 

There are significant uncertainties associated with choosing appropriate measurement 

variables and designing monitoring programs that truly reflect ecological response and 

provide acceptable levels of statistical reliability. Choice of indicator variables will be 

largely based on current understanding of key interactions for the ecosystem indicators. 

Subjective decisions have to be made about what indicator variables to measure and this 

can influence the perception of response to changes in dam operations. For example, 

selection of a early life index such as the abundance young of the year for long lived fish 

populations such as humpback chub can be risky if there is some other factor that acts 

later in life which controls the number of fish that recruit to the spawning population. 

5
2) Is there sufficient scientific understanding about the response of the key indicator 

variables to be confident that selected measurement variables used in monitoring 

program are appropriate and can be reliably measured? Is the ecologically 

significant effect size known? 

Monitoring programs follow a typical ontogenetic pattern of development that 

evolves with time as more is learned about what is appropriate to measure and how to 

those measurements are collected. The first phase of monitoring is where a 

comprehensive inventory of the components of the ecosystem is collected. This 

information is useful because it provides basic information such as species composition 

and documents spatial variation in assumed key indicators variables. In the second phase 

of monitoring basic sampling continues and additional detailed studies are conducted to 

fill data gaps, and refine sampling protocols where weaknesses are detected. Process 

research can produce a deeper knowledge of the interactions among ecosystems 

processes. The results of monitoring and research must be closely linked so that new 

information is integrated into the monitoring protocol to improve the statistical reliability 

of monitoring protocol or aid in the identification of new monitoring variables. These 

studies provide managers information about what are the appropriate variables to monitor 

and what sampling protocol is most likely to allow judgment whether management 

objectives are met. The third phase of monitoring is where scientists and managers are 

confident that there is sufficient scientific understanding and experience in measuring 

key ecological indicator variables. At this point, long term data collection begins. The 

need for research is not eliminated but rather monitoring becomes a process of iteration 

between collecting routine information and more focused research to better understand 

the impacts of management actions. 

3) Does the current sampling strategy allow sufficient statistical reliability to protect 

managers from adverse or irreversible impacts? Does the current protocol allow 

reliable detection of “signal” of the impacts of dam operations through the “noise” 

of natural variation in ecological variables or confounding effects of factors other 

than habitat alteration dam operations? 

Ecological communities undergo wide fluctuations in both space and time and because of 

this it is has proven difficult to design and implement reliable monitoring programs that 

provide reliable statistical inference. Distinguishing ecological changes that result from

the operation of Glen Canyon Dam from all other sources of natural variation therefore 

requires understanding of both the magnitude and the structure of variance in key 

ecological indicator variables. Consideration of the relative contribution of spatial and 

temporal components of variance in relation to total variance is an important 

consideration for the design of such programs for two reasons: 1) it determines how 

available resources for replication in space and time should be allocated ; and 2) it 

determines the magnitude of treatment effects that can realistically be differentiated from

unexplained sources of variation. 

6
4) Does the monitoring provide required information to support a weight-of-evidence 

approach to strengthen inferences resulting from monitoring? 

Monitoring will provide inferences about trends in abundance or the response of indicator 

variables to changes in dam operation. However, because of incomplete knowledge 

about the response of the ecosystem to management actions, difficulties in detecting 

responses, and the high likelihood of surprise, or unexpected responses, there will usually 

be a need to support data from the monitoring of key indicators with inferences through a 

weight-of-evidence approach. This approach involves systematic description of 

hypotheses about the expected response of each component of the ecosystem to the 

management action, and the assembly of all data available data to evaluate those 

hypotheses. 

 

This report is divided into eight sections. Sections 2 though 6 address protocol 

evaluation and provide recommendations for each aquatic monitoring program areas. 

While not specified in the original scope of the protocol evaluation, the panel recognized 

that implementation was influenced by other broader implementation, management and 

institutional issues. Section 7 addresses those considerations and the recommendations 

of the panel. Written questions were also posed to the panel associated with particular 

aspects of the aquatic monitoring program and the implementation of adaptive 

management. The panel’s responses to the questions are provided Section 8 of the report. 

7
Chapter 2. Water quality 

Recommendation: A water quality program that monitors physical and biological 

parameters of the Colorado River in Grand Canyon should be established. This program 

could be tied to physical sampling sites at non-boat access points associated with USGS 

gauging stations. 

This section addresses Goal 7 of the April 2001 Strategic Plan of the Glen 

Canyon Dam Adaptive Management Workgroup, which is to “Establish water 

temperature, quality and flow dynamics to achieve GCDAMP ecosystem goals.” The 

“ecosystem goals” addressed by this panel includes the biological goals as related to food 

base and fish and also the potential to use water quality as an indicator of ecosystem

change as a result of changes in dam operation. 

A robust water-quality monitoring program can act as a “barometer” to assess 

linkages among water quality parameters (temperature, turbidity, nutrients, carbon, 

suspended sediment) and aquatic food base and fish. Water quality can be defined in 

terms of the physical, chemical, and biological characteristics of the river ecosystem. To 

date, water quality monitoring has focused more on the physical measures (temperature, 

suspended sediment, turbidity, and specific conductance) with some monitoring of 

nutrients and carbon as part of the food base program. While these physical measures 

affect species distribution, biological processes (e.g., metabolism, primary production, 

nutrient dynamics), instream habitat, predation, etc., nutrients (nitrogen and phosphorus) 

and carbon (dissolved and particulate forms) are important because they “fuel” the food 

web (i.e., the food base and fish). Additionally, monitoring water quality can provides 

supplementary information for a “weight of evidence” approach for identifying plausible 

mechanisms that cause changes in the aquatic resources in response to dam operations. 

A comprehensive long-term water-quality monitoring program currently does not 

exist. With the exception of the physical measures mentioned above, water quality 

sampling has been primarily tied to the food base sampling sites and sampling has not 

been conducted to develop a long term consistent data base at time and spatial scales 

relevant to impacts of dam operations. Changes in water chemistry can cascade 

throughout the food web. For example, the type of phytobenthos assemblage 

(Cladophora versus a mixture of algae, macrophytes, and moss) was related to the 

seasonal variation in nutrient concentrations and flow regime downstream of Glen 

Canyon Dam from 1995-1998 (Benenati et al., 2000); the dominant type of phytobenthos 

assemblage, in turn, affected the invertebrate assemblage. In addition, the form (e.g., 

dissolved versus particulate, nitrate versus ammonia) of nutrients and carbon at any point 

along the Colorado River Ecosystem is a function of upstream inputs, lateral inputs (from

backwaters or springs), tributary inputs and biological processes (e.g., uptake of nutrients 

by algae). Future studies should include a more thorough examination of these changes in 

water chemistry throughout the Colorado River Ecosystem (upstream to downstream). 

8
Specific Water-Quality Program Recommendations 

1. Water-quality objectives should be clearly articulated as they relate to food base 

and fish (Management Objectives 7.1 and 7.2). Only then can a water-quality 

monitoring program be designed to appropriately address these objectives. 

2. Use the existing turbidity (surrogate indicator of light) and temperature networks 

as a starting point for additional water-quality monitoring. Adding key nutrient and 

carbon sampling to this network will serve two purposes: 1) to provide information 

on the physical and chemical factors that directly and indirectly affect the food web, 

and 2) to detect changes in water quality along the entire river system. At a 

minimum, consider building on the routine sampling conducted by the physical 

program at the four accessible sites al Lee’s Ferry, Paria River, Bright Angel Creek 

and Diamond Creek. By using these sites that have discharge measurements, 

concentrations and flux (loads) of sediment, nutrients, and carbon can be measured 

in the long term. 

3. Establish regular temporal sampling (at minimum use physical program 

sampling sites and schedule) and begin spatial sampling along the Colorado River 

and at the mouth of tributaries on at least a seasonal basis. We suggest that 

tributaries should be included for water-quality monitoring, due to their potential 

affect on mainstem water quality (e.g. sediment from Paria River). This minimal 

sampling design can be used to: 

a. Address the spatial and temporal variation of water-quality parameters 

and discharge as they relate to food base and fish. 

b. Address whether the system meets the legally-defined State water-quality 

standards where appropriate (also a part of Management objective 7.2). 

4. After examining existing nutrient data, we determined that a better low-level 

analysis of nutrients in needed. The technology to analyze nutrients at lower levels 

(1-10 μg/L range for N and P) is widely available and it is strongly recommended 

that this be utilized to provide better resolution of changes in nutrients 

concentrations. Also, a Quality Assurance/Quality Control protocol needs to be 

developed as a part of the water-quality program 

5. Measurements of carbon should include all forms [dissolved organic carbon, fine 

particulate matter, coarse particulate matter (organic drift)] if feasible. At a 

minimum the dissolved organic carbon and the particulate material collected on the 

glass fiber filter should be analyzed. 

6. Consider adding diurnal measurements of dissolved oxygen to the routine 

monitoring sites to measure autotrophic/heterotrophic metabolism if resources 

permit. Metabolism could be used as a biological response to nutrient and carbon 

dynamics. Along with this measurement, chlorophyll should also be measured in the 

9
water column. Use of oxygen probes for extended periods (weeks) can be 

problematic due to fouling. However, if the probes can collect dissolve oxygen for a 

two-day period monthly (i.e., service probe and download data for the first two-day 

period from the previous sampling trip) then a long-term record of metabolism can 

be collected throughout the river system (see monitoring primary 

production/community metabolism in Chapter 3). 

7. Consider using benthic organisms as an indicator of water-quality changes if this 

is an important water-quality objective and resources are available. This would 

require a different sampling design and taxonomic resolution than what has been 

used in past but would be valuable to assess changes in water quality over time and 

with changes in dam operation (see Food base as indicators of system health or 

integrity in section 3). 

 

8. Link the water-quality sampling in the Grand Canyon Ecosystem to the Glen 

Canyon Dam sampling and the Physical Program sampling. Changes in the water 

released from the dam and tributary inputs can have profound downstream effects. 

These databases need to be linked. 

10
Chapter 3: Food Base 

Recommendations: The food base program needs to be critically reviewed because the 

current level of understanding about the linkages between lower trophic levels and food 

availability of native fishes is not adequate to interpret food base data in relation to the 

management goal. Lower trophic levels can also be used to monitor ecosystem changes. 

GCMRC needs to explicitly identify the goal of the food base program, determine what 

metrics to use to monitor the lower trophic levels, and decide what level of detection of 

change is required. Sufficient data and experience exists to design a program that meets 

the identified needs with appropriate power. 

This chapter addresses Goal #1: “Protect or improve the aquatic food base so that 

it will support viable populations of desired species at higher trophic levels” 

The five management objectives relating to this goal strive to attain or maintain 

primary producers (algae and macrophytes) and secondary producers (benthic 

invertebrates) at different locations for different fishes along the all sections of the river. 

The terms of references for the Aquatic PEP, however, deals with native fishes below 

Lee’s Ferry, and thus is concerned with the accompanying food base for the fishes 

occurring there. The well being of the trout populations have been addressed by other 

PEPs and will be considered here only as they impact native fishes. 

The PEP Panel was impressed with recent and ongoing research conducted on 

lower trophic levels in the Colorado River and some of its tributaries. While these 

studies were not often directly oriented toward answering specific monitoring questions, 

they will be important in determining possibilities for a meaningful and efficient 

monitoring program. 

A long-term monitoring program for the food base does not presently exist. This 

is understandable because the research needed to ensure a successful monitoring program

has not yet been completed. The panel does not necessarily consider the goal of 

monitoring the food base for native fishes a priority at this time because of the 

unanswered questions dealing with the native species life histories, population dynamics 

and habitats. That is, there is not enough known about many of the life requirements and 

ecology of native fish species in this ecosystem to concentrate so much on one aspect – 

their food. The panel was concerned that the assumed linkages between food base and 

fishes have not been empirically established. While increased primary and secondary 

production (food base) may relate to increased native fish production other consequences 

are also likely- the most important being that a maintaining or attaining a healthy food 

base may benefit non-native species which are possible competitors with, or predators on, 

native species. However, if the GCMRC deems this goal worthy, or might revisit it after 

suitable research, we offer the following suggestions. 

The stated objective dealing with food base is to ensure adequate food resources 

available for native fishes, yet our conversations with GCMRC personnel and 

Cooperators suggest an interest in using primary and secondary producers as indicators of 

11
ecosystem processes or ecosystem health. The panel addressed both aspects; food base 

and biological integrity. These topics are in some ways mutually exclusive and will 

require different approaches. However, the panel assumed that the monitoring objective 

is the same: to obtain ecologically useful data of known precision such that trends in 

those data can be detected over time. This fundamental assumption that the objective 

of food base monitoring has a good relation to the management objective, such that a 

detected change in the object of monitoring signifies an ecological change of some

importance. Finally, we adhere to the philosophy that simple and inexpensive ecological 

indicators are the best insurance against problems of ever-changing professional and 

technical staff, political winds, and fluctuating budgets. 

We agree that managing dams to benefit native fishes would be enhanced if we 

had a sound understanding of the benthic algal and invertebrate communities and their 

response to different flow and sediment regimes. However this understanding will 

require considerable research before it can be incorporated into a regular monitoring 

program. There are many potential indicators of “food base” for the system. We 

suggest that whatever approach is considered the GCMRC should use the existing 

historical data, excellent in some cases but limited in others, to examine for spatial 

and temporal variability. Next GCMRC should determine the effort involved to 

achieve any particular ability to statistically detect changes (statistical power), and 

if possible, determine the sensitivity of any particular measurement to potential 

alterations in dam operation. A good start to this end is work like that reported by 

Stevens et al. (1997) where algal and invertebrate biomass on the Colorado River were 

examined at specific habitat types at 11 sites bimonthly for a year. Data from this project 

should be used to examine the effort necessary to sample over a large area to obtain the 

ability to detect changes over time. 

Food for Native Species: 

 A fish-food monitoring program could be more specifically targeted if the 

nutritional preferences and requirements of native fishes were better known. If there is a 

desire to understand the implications of changes in the food base that might be associated 

with management actions more research must be directed to understanding food-fish 

linkages. Some progress has been made using stable isotopes of C and N has been made 

(Angradi 1994; Shannon 2001;G. Allan Haden, unpublished MS) both in the mainstem

river and in tributaries, especially the LCR. However, stable isotope research is evolving 

rapidly, especially with respect to the complexities of C isotopes, and there may be a 

need to revisit these results in the near future (Finlay 2001). Research utilizing Cesium 

isotopes (Rowan and Rasmusson 1996) along with C and N to better understand the 

amount as well as the source of food paths should be considered. An effort should 

be made to analyze fish stomachs that have been recently collected. Bioenergetics 

modeling, such as the recent study by on humpback chub in the LCR (Haden 

unpublished MS) could be pursued to roughly understand limits the GCE 

environment may have for native fish feeding. 

12
We recommend the continued evaluation of fish condition indices – perhaps 

developing a standard weight for all native species – may be a better and more 

precise indication of the adequacy of the food base that now exists. The decline in 

weight-at-length observed by Meretsky et al. (2000) for chub over the past 20 years is 

cause for concern, and may be related to feeding conditions. Other venues may be 

analysis using proximate composition (i.e. lipids, see Marshall et al. (2001) for an 

example of how lipid composition is related to reproductive success), or RNA/DNA 

ratios. 

Since there are scientific as well as statistical uncertainties associated with any 

approach for study the relation of food base to trends in abundance of fish populations 

the best approach is likely a fully integrated one, utilizing data on the abundance of prey 

available to fish in the GCE, the apparent food habits as indicated by stomach content 

analysis, and indicators from the fish themselves, including isotopes, growth and 

condition, and body composition. 

Because the food habits of specific life stages of most native species are not well 

known a broad look at the potentially available food is required for a monitoring 

program. The best indicator of potential energy available is a measure of production – 

both primary and secondary – which is a measure of organic matter creation over time 

(mass/area/time). Neither measurement is routinely carried out in a monitoring program, 

especially one with the spatial extent of the Colorado River. 

Monitoring Primary Production (Community metabolism) - Estimating total stream

metabolism is often used to evaluate production or the potential food base. Two methods 

have been tried on the Colorado River during the experimental flood of 1996 – an open 

stream method (Marzolf et al. 1999) and enclosed chambers method (Brock et al. 1999). 

Both were able to detect the effects of the experimental flood in P/R (the ratio of primary 

production to community respiration), gross and net primary production. Both 

approaches might be evaluated as endpoints for monitoring primary producers, as they 

are relatively easy and inexpensive to perform. As with other monitoring tools, initial 

efforts are required to evaluate variability in both space and time, and power analysis 

must be conducted to determine the changes that can be detected. The key question to 

be resolved by research is whether primary production is actually related to the well 

being of native fishes. 

Monitoring Secondary Production: Directly measuring secondary production of even a 

single species to estimate energy available to fishes is a daunting task. Regular, at least 

monthly, multiple quantitative samples over at least a year, rigorous determinations of 

sizes or weights and an excellent understanding of life histories are required. We know 

of no examples where secondary production is used in a regular monitoring program, 

although it has been successfully carried out in the Colorado River in a research effort by 

Blinn et al. (1994). It is unlikely this effort could be sustained in a long-term monitoring 

program. 

13
Biomass (mass/area) is often used as a surrogate for production as it often has 

some relation to production, and is relatively easy to obtain. Algal biomass can be 

estimated by in-situ measurements of lengths of strands, harvesting and weighing, or 

indirectly by estimating chlorophyll content. Invertebrate biomass is estimated by 

quantitative sampling of the river bottom, removing invertebrates from associated debris 

and obtaining a dried weight. The problems associated with estimating biomass with 

any reasonable precision in a system as large and dynamic as the Colorado River are 

likely large. However, Colorado River researchers (e.g., McKinney et al 1999) have 

shown that when taxonomic level is kept relatively coarse a sample size somewhat <100 

is sufficient to obtain reasonable variations. While 100 samples (Hess samples in this 

case) seems like a lot, identifying only to the level of algae or macrophyte for 

primary producers and Gammarus, Chironomidae, Gastropoda and Oligochaetes 

for secondary producers keeps efforts and costs to a minimum while presenting data 

at a sufficient resolution to understand benthic biomass that is available for fishes. 

One caution for directly relying on a biomass approach is the order of magnitude 

variation in the turnover rate of benthic organisms under different habitat 

conditions. For example, turnover rate (i.e. production/biomass ratio) of 

chironomids in lotic environments can vary between 10 to >250. Without 

knowledge of site specific estimates of spatial variation in turnover in CRE, as well 

as the impact of dam operations on habitat conditions that drive turnover rates, 

projections of benthic productivity are highly uncertain. 

Monitoring Drift: Research on the river has indicated a shift in energy sources 

longitudinally along the Colorado River below Glen Canyon Dam (Shannon 2001), and 

from tributaries (Angradi 1994), some of which may be from outside the main channel. 

Significant allochthonous sources would complicate the use of primary production 

measurements as the sole measure of river productivity. A way to address this concern is 

by monitoring drift. Drift, composed of algae, detritus and invertebrates that have been 

either washed into the river or detached from the river substrate and are being carried by 

water currents, has been used as an indicator of river productivity. Because particulate 

organic matter is likely important to downstream filter-feeding invertebrates (e.g., 

Simuliidae and some Chironomidae) drift estimates of coarse particulate organic 

(CPOM) and fine particulate organic matter (FPOM) would seem prudent. A start on a 

monitoring program for particulates can be obtained from the recent work on the 

Colorado River by Blinn et al. (2001), and Shannon et al. (1996). The most appropriate 

methodology for collecting drift (CPOM) is a depth and flow integrated sample across 

the channel as described by McKinney et al.(1999). 

 

Advantages of drift as an indicator of system productivity are that the 

sample is relatively simple to collect, it integrates processes over a wide spatial area, 

and thus likely will have moderate intersample variation, allowing a reasonable 

number of collections. A drift program could be conducted at land-based access 

points that are currently used for physical science monitoring. Research questions 

to be addressed before knowing if this approach is feasible for the Colorado River 

include relating production to drift, and examining existing data on sample 

variability. 

14
Finally, the interpretation of invertebrate biomass or drift density is contingent on 

an understanding of the degree to which the system is ‘bottom-up’ or ‘top-down’ 

controlled. That is, determining whether invertebrate abundance is limited by its food 

sources, or by grazing pressures from fish will influence how a management action might 

affect invertebrate abundance. Unfortunately, the response of intermediate trophic levels 

in tightly coupled systems is quite unpredictable (e.g., Power 1990). 

Food base as indicators of system health or integrity. 

The use of food-base organisms, benthic invertebrates, is a common and 

widespread approach to evaluating the biotic integrity of riverine systems. The benthic 

community is assumed to integrate numerous environmental features including water 

quality, quality of nutrients and carbon, physical habitat conditions, biotic interactions, 

and flow regime. While the most-used practice of having regional reference conditions 

to compare against obviously cannot be used in the Colorado River, a system whereby 

species composition is monitored for changes over time is eminently reasonable. The 

approach can be tailored to resources in terms of frequency of sampling, number of sites, 

and type(s) of habitats sampled. The most sensitive, and most difficult, system would 

encompass the presence or relative abundance of all taxa. However, even relatively 

simple indices such as ratios of Gammarus/Chironomidae/Simuliidae or some other 

dominant invertebrate groups would be valuable in indicating changing conditions. The 

value of long-term monitoring of invertebrates downstream from a large dam (Flaming 

Gorge Dam) is demonstrated in recent paper by Vinson (2001). This paper examined 

about 50 years of invertebrate data that included pre-dam and post-dam and pre and post 

thermal restoration. His major conclusion was “Changes in dam operation done long 

after dam construction may not be effective in restoring native species because the new 

community may have considerable tolerance to new operations”. One caveat brought out 

in this study was that the difficulty in examining long-term trends because data were 

collected by different investigators and at varying taxonomic levels. Thus, establishing 

a robust systematic program is critical to examining changes in biological 

communities over time. 

Finally, because primary and secondary producers are closely related to 

substratum conditions the food base monitoring program could be linked to highresolution physical habitat modeling presently being conducted. Also, linking the 

food base monitoring program with the terrestrial invertebrate sampling program 

would provide a better invertebrate species list for the Grand Canyon Ecosystem. 

15
Chapter 4 Humpback chub 

Recommendations- The Panel recommends that further work be conducted to develop a 

conceptual model of the metapopulation biology of chub in the GCE to provide a context 

for a long-term monitoring program. Consideration should be given to the inclusion of 

genetic concerns in the monitoring program. GCMRC needs to develop explicit linkages 

between the results of annual monitoring and the management goals to ensure that the 

monitoring programs produce results appropriate to review progress to the goals. The 

Panel supports the completion of the current review of existing data, and the 

development of population models as these programs will yield sufficient information to 

make decisions about sampling programs for chub. 

The Humpback chub (HBC) is an endemic cyprinid (minnow) species, that has 

the distinction of being the first fish species listed under the Endangered Species Act 

(ESA). The listing was prompted by concerns over decreases in range and abundance, 

which have been attributed to anthropogenic changes physical and biotic environment of 

the Colorado River (Douglas and Marsh 1996). Consequently, there has been 

considerable work conducted on HBC that has lead to a large body of knowledge on the 

biology of the species (see Valdez and Ryel 1995, Gorman and Stone 1999). Most HBC 

in the Grand Canyon are found in the region of the Little Colorado River (LCR), 

although smaller numbers of mainly adults are scattered throughout the mainstem

Colorado River. Consistent successful reproduction appears to occur only in the LCR, 

although there are occasional reports of spawning and the presence of early life stages at 

other locations in the mainstem (Valdez and Ryel 1995). 

The management objectives (Goal 2.1 to 2.5) for humpback chub (HBC) are 

generally driven by endangered species considerations and call for the establishment and 

maintenance of viable populations, and the ‘removal of jeopardy’. Although the 

management target of a ‘viable population’ is difficult to define quantitatively, the likely 

monitoring needs will include the determination of the absolute abundance, trends in 

abundance, and measures of recruitment and other biological indicators of population 

status. 

The Panel did note a lack of an explicit consideration of genetic issues in the 

HBC management goals. Genetic considerations can constitute an important basis for 

conservation. Any strategy for the conservation of a particular species or component 

subpopulations should be, at least in part, determined by knowledge or inference 

regarding that species’ genetic structure (Franklin 1980). Such information can provide 

insight into the value and importance of individual subpopulations relative to a species’ 

genetic diversity, and population viability and persistence. However, genetic structure, 

and population persistence and viability are inexorably linked with census population 

size (N), effective population size (Ne), and the number of breeders (Nb) available in a 

particular population at any given time. 

The effective population size (Ne) for a population to retain its evolutionary 

potential sets a lower limit for viable population size (e.g. minimum viable population, 

16
MVP, Soule 1987). Franklin (1980) suggested two primary considerations when 

determining a minimum Ne for perceived population viability: 1) immediate danger in 

small populations due to inbreeding; and 2) loss of quantitative genetic variation that 

could limit future evolutionary change in the longer term. Franklin (1980) also argued 

that in small populations the rate of change in additive genetic variation is essentially 

determined by genetic drift minus the rate of gain due to mutation. The rate and potential 

directionality of genetic drift in turn is profoundly influenced by population and effective 

population size. 

Although the principle that conservation of quantitative genetic variation is an 

important factor in managing endangered species is generally accepted, disagreement 

over appropriate Ne values continues (Franklin 1980; Shaffer 1987; Lande and 

Barrowclough 1987; Lande 1995; Franklin and Frankham 1998). Franklin (1980), 

Shaffer (1987), and Lande and Barrowclough (1987) provided theoretical arguments to 

suggest a minimum Ne of 500 for population viability and persistence. Lande (1995) 

argued that because only a fraction of newly generated mutations are beneficial (i.e. 

useful in providing adaptive potential for evolutionary change), an Ne of 5,000 is 

necessary to maintain evolutionary potential. Franklin and Frankham (1998) reviewed 

these and other arguments for an Ne of 5,000 and concluded that an Ne of 500-1,000 

appears appropriate at this time. However, Lynch and Lande (1998) suggest that this 

number should be revised upwards to a range from 1000 to 5000. 

It should be noted that the number Ne is generally much less than N, the census or 

total number of adults that could spawn. The difference is caused by fluctuating 

population sizes, sex ratios among spawners, and variation in the survival of offspring 

from particular matings, and subpopulation extinctions (Avise 1994). Based on recent 

census estimates, genetic concerns may be significant for HBC, and researchers may 

want to obtain estimates for Ne to monitor this surrogate viability metric. 

The Panel concludes that significant uncertainties about the population biology of the 

chub need to be resolved before a long-term monitoring program for demographic or 

genetic concerns can be implemented. Specifically, the relative roles of the LCR-region 

fish and some of the smaller aggregations in the mainstem to overall population viability 

is not clear. This uncertainty might be represented by 2 strawman hypothesis about the 

population biology: 

1. The only successful spawning and subsequent recruitment of HBC occurs in the Little 

Colorado River. Some spawning adults reside in the LCR, but perhaps most migrate 

to the LCR from the adjacent reach of the mainstem. Most recruitment results from

juveniles that spend 2-3 years in the LCR. Juveniles that leave the LCR at small size 

(<100mm) likely experience low survival and contribute little to the population. 

Individuals that migrate or are displaced long distances from the LCR do not return to 

the LCR to spawn. These individuals may attempt to reproduce but recruitment does 

not occur. 

17
This scenario is an extreme ‘source-sink’ metapopulation model where there is only 

one source of new individuals (the LCR) and a large ‘sink’ area (much of the 

Mainstem), where individuals are effectively lost from the reproductive population. 

If this hypothesis is confirmed, the appropriate monitoring program would involve 

estimating the size of the LCR spawning population. Supplemental sampling to 

estimate the abundance of juveniles might provide an early warning to changes 

in the adult population. The Panel sees limited value in extensive surveys to 

estimate the size of the mainstem population (a difficult task), especially at times 

of year when the LCR spawning population becomes remixed with fish in the 

mainstem. Occasional (but nonetheless rigorous and repeatable) surveys of the 

mainstem might be appropriate for checking changes in the distribution of 

adults, and the occurrence of mainstem spawning or recruitment. Estimates of 

the effective population size for genetic monitoring would be derived from LCR 

spawning population estimates.

2. The second hypothesis would propose that there are one or more spawning subpopulations in the Colorado mainstem contributing some individuals to the overall 

recruitment. These other aggregations may still be sinks, in that immigration from the 

LCR to the mainstem populations may occur. However, overall population viability is 

enhanced by the presence of these other spawning locations because of the 

opportunity to ‘spread the risk’ of a population failure at any single location. There 

may also be genetic benefits to multiple, somewhat isolated, populations. 

Under this scenario, monitoring related to the management goal of maintaining a 

viable population of HBC necessarily entails estimating the abundance of adult fish 

throughout the drainage. Sampling chub in the mainstem Colorado River is not an 

easy task because they are relatively scarce, and occupy habitats (deep water, bedrock 

ledges) that are difficult to sample. It was suggested to the Panel that previous 

sampling efforts may not be appropriate for estimating relative or absolute abundance 

of chub because they were focussed on the known aggregations of fish, not in 

surveying the whole river in a statistically robust manner. Simulation studies based 

on the analysis of the variability in existing data indicate that a very large number of

samples (ca. 500) are needed per year to obtain reasonable estimates of relative 

abundance that might be used in trend analysis. These results highlight the need to 

resolve the uncertainty about population structure before embarking on a 

mainstem program as described above. Consideration will have to be given to 

the degree of genetic isolation and mixing for any genetic conservation goals for 

HBC. If in fact hypothesized humpback chub aggregations turn out to be 

maintained by geographically exclusive spawning and rearing, estimates of N, 

Ne, and Nb should be applied separately to each chub aggregation in the GCE. 

Review of Current Activities- The panel used a multiagency documented entitled 

‘Fisheries Monitoring Activities in the Colorado and Little Colorado Rivers within Grand 

Canyon During 2001’ as the basis for our review of the existing monitoring program for 

HBC. The current (2000-2001) monitoring program consists of a very intensive sampling 

18
to obtain a spring estimate of the number of spawners in the LCR, a second intensive 

effort to estimate abundance of HBC in the mainstem near the LCR some 6 months later, 

and possibly scattered sampling throughout the mainstem, either as part of directed 

efforts, or incidental to other programs. Additional sampling in the LCR for sub-adult 

fish in the fall has also been proposed. 

It was not clear to the Panel how all of these components would be integrated into 

a monitoring program that addresses the management objectives for chub. In particular, 

the LCR spring program and the summer-fall mainstem sampling appear to be trying to 

estimate the abundance of the mostly the same group of fish. One possibility would be to 

redefine the management goal of maintaining ‘a viable population’ to the maintenance of 

an abundance of reproductive individuals. Then, the ‘viable population’ should be 

assessed by monitoring trends in spawner abundance. The number of individuals 

contributing to subsequent generations, both in a genetic and demographic sense, will 

determine the persistence of the population over time. 

The Panel believes that the resolution of the population biology of HBC to be 

a critical information need for the implementation of a long-term monitoring 

program. A useful first step would be to explore the use of geochemical markers on 

scales of HBC caught in different locations of the Colorado River to determine if all 

adult fish had originally been spawned (and perhaps reared as juveniles) in the LCR 

(hypothesis 1), or if some of the non-LCR fish were the survivors of mainstem (or 

other tributary) spawning events (hypothesis 2). Recent work by Thorrold et al. (2001) 

provide an good example of this approach. There may be potential in using scale archives 

to determine the distribution of spawning in the pre-dam era, if distinct geochemical 

signatures exist for various waterbodies. Upon resolution of these uncertainties a 

conceptual model of the biology of the chub can be developed, and appropriate 

monitoring programs designed. 

The use of existing information- Recently, significant efforts have been undertaken to 

assemble and review the results of the past decade of sampling for HBC to determine 

whether these data could form the baseline for a monitoring program, be used in a 

population model, and to aid in the development of future programs. Concern was 

expressed to the Panel about the utility of past data, because of changing techniques, 

sampling intensity and the orientation of past programs for goals other than monitoring 

population abundance. The Panel strongly encourages the completion of the assembly 

of past data into a single database, including the documentation, where possible, of 

details of sampling to enable future researchers to comprehend the complexities of 

the data that has been collected. 

Historical capture data for HBC have recently been integrated into a model to 

estimate recruitment by examining the relative abundance of chub grouped by length 

classes. Once a model of this type is fully parameterized it potentially can be used for 

forward simulations to make predictions about future trends in the population, and 

impacts of habitat change on those trends. From material presented to the Panel, it was 

evident that there may be significant limitations to this approach for chub, as the 

19
historical database are results from a variety of programs over the past two decades that 

have changed almost continuously with respect to sampling procedures and gear types. 

Further, the use of a length-based, rather than age-based model reduces the sensitivity of

the approach to detect small changes in recruitment. 

The Panel was also appraised of the development of a ‘Stock Synthesis Model’ 

that makes use of the large PIT tag database to estimate population trends and year-class 

strengths. This model will be used to integrate results from the intensive tagging 

programs recently initiated. The Panel encourages the development, documentation 

and review of the HBC stock synthesis model, as it appears to have potential to 

provide reliable estimates of abundance and cohort strength for chub.

The Panel was made aware of a very recent reconstruction of catches of young 

chub in the lower LCR from a variety of sampling programs conducted in the spring 

months from 1984-1998. These data have the potential to provide an index of cohort 

strength from the LCR, and provide information on the relative abundance of other native 

and non-native fishes. Since long-term trend data for HBC are lacking, the Panel 

recommends that these data be thoroughly examined for their utility as a ‘real-time’ 

indicator of recruitment, and consideration be given to the continuation of the 

program. If the proposed fall sampling of young chub is successful, it may be worth 

running both the lower LCR spring program and the fall program in parallel for a 

few years to allow the calibration and linking of data to extend the length of the 

series. These data may also have utility to cross-validate the stock-synthesis model, 

or could be used as an additional source of information to refine year-class 

estimates. 

In the spring of 2001 an intensive, structured, marking program was initiated for chub 

in the LCR. This program should yield a reasonably accurate estimate of the number of 

adult chub in the LCR at the time of spawning. Such estimates would be the cornerstone 

of an assessment program under the single-spawning population hypothesis described 

above. The 2001 population assessment should be documented and reviewed after its 

completion. Some issues the Panel identified during its review are: 

1. Whether the timing of the sampling mid-May and re-sampling in June will yield 

reasonable estimates of the total number of spawning fish, given the complexities 

that arise because of the immigration and departure of some spawners 

(especially larger ones) from the LCR. 

2. Bias caused by tag loss (either through the mortality or emigration of repeatedly 

handled fish, or expulsion of tags). In controlled experiments 5-10% of PIT tags 

are lost soon after application; higher figures might be expected in the field. 

3. Whether this program needs to be conducted annually, given the longevity of 

adult fish and the likely slow changes in the abundance over time. 

The Panel was concerned about the impacts of handling and tagging of fish in the 

LCR. The intensity of the program results in some fish being handled repeatedly, and the 

timing of the program results in handling of recently spawned spent fish that may not as 

20
robust as in other times of the year (Meretsky et al. 2000). The panel was not made aware 

of any studies to assess the impacts of capture and tagging on chub, but experience with 

many other fish suggests these impacts cannot be dismissed, especially given the harsh 

nature of the LCR environment. We recommend that a fish handling protocol be 

developed that considers the relative impacts on the LCR chub population of an 

intensive marking program, and describes the appropriate techniques for capture, 

handling, anaesthesia, tagging, recovery and release. Experiments with captive fish 

may assist in development of the protocol. 

A second part of the proposed 2001 program is the sampling and tagging of small 

chub (<200mm) in the LCR to provide population estimates of the pre-adult cohorts. This 

program should yield a year-class or recruitment index that will provide insight into the 

cause of trends in the adult population. Year-class strength can potentially be used to 

identify relations between habitat and recruitment, although these types of analyses are 

often unsuccessful because the causative link is usually unknown and spurious 

correlations are not infrequent. The 2001 sampling will be a pilot program, and the 

assessment of the results should include a consideration of the factors identified by the 

adult program, especially with respects to the effects of tagging small chub. 

In summary—Two decades of investigation on the biology of humpback chub has left a 

body of information that is perhaps unparalleled for a non-game fish. The Center is thus 

well-positioned (after investigation of some of the outstanding uncertainties listed above) 

to design a monitoring program that should allow the evaluation of the management goals 

with reasonable reliability. 

The Center should refine the links between management goals for HBC and 

each of the monitoring activities by specifying how the outputs from monitoring will 

be used in decision making. Quantitative analyses of past and currently collected data 

should yield estimates of the precision of the various programs, allowing calculations of 

the power of different types and intensities of monitoring programs to detect change in 

the population. 

Finally, it should also be recognized that there may a large distinction between 

monitoring the chub population for ESA considerations, and monitoring to detect 

changes that may occur in response to the operation of the Glen Canyon Dam, or other 

management actions that change chub habitat (physical or biological). In particular, it has 

been hypothesized that the main linkage between GCD operations and chub result from

changes the survival of juvenile chub that emigrate from the LCR at small size. The 

proposed programs and current programs need to be critically reviewed to determine if 

they are likely to be successful in detecting increasing recruitment from the mainstem as 

a result of a habitat manipulation. This problem is exacerbated by the observation that 

recruitment from the LCR is (and has probably always has been) highly variable, because 

of the extreme nature of that environment. Monitoring the fate of juvenile chub that leave 

the LCR may require more focussed research-type programs, preferably with sufficient 

pre- and post-treatment years of sampling to detect any changes that may have occurred 

as result of dam operations. 

21
Chapter 5. Other native fish 

Recommendations- The Panel was concerned that there no plan for monitoring the status 

of the 3 other extant native fish of the GCE. The Panel supports the ongoing synthesis of 

existing information and attempts to develop a population model for flannelmouth sucker 

as the first steps for developing a program for this species. The Center should develop 

explicit linkages between management goals and monitoring programs, and once all 

available data for the non-native species have been assembled, review options for 

monitoring these species. 

Management goal 2.8 is the maintenance of viable populations of the other native 

fish species of the GCE, the flannelmouth (Catastomus latipinnis) and bluehead suckers 

(C. discobolus) and the speckled dace (Rhinichthys osculus). Razorback suckers 

(Xyrauchen texanus) have been virtually extirpated from the GCE and will not be 

considered in this review of monitoring programs. 

As with the other taxa, the Panel was not presented with an explicit plan of how 

results from present and future monitoring activities would be used to evaluate progress 

towards the management goals. In fact, there does not appear to be a coherent program of 

field activities for these three native species that would constitute the basis of a 

monitoring program. Certainly the elevated status of the humpback chub (Gila cypha) 

and the razorback sucker under the US Endangered Species Act imposes elevated 

priority to assessment and protection of these species. However, from ecological, 

conservation, and biodiversity protection perspectives, flannelmouth and bluehead 

suckers and speckled dace constitute species no less worthy of equitable research, 

management, and protection. Therefore, the Panel recommends consideration of 

directed, proactive attention to these native species, prior to possible population 

declines currently exhibited by other native fish populations in the GCE. 

Flannelmouth and bluehead suckers and speckled dace currently appear to be 

represented by reasonable numbers of fish, however absolute abundances are not 

available, making it difficult to evaluate the significance of genetic conservation concerns 

for these species. 

As with the humpback chub, there is a great deal of uncertainty about the 

population structure for these species, the location of major spawning areas, and the 

interchange of individuals among aggregations. Sampling of these species appears to be 

largely the result of incidental catches for other programs, rather than directed efforts to 

address key uncertainties, or rigourous programs to generate data suitable for monitoring. 

Thus, the Panel recommends directing significant resources to the collection of 

important basic biological information for these species. 

The panel encourages the continued development of the ‘stock synthesis’ 

model for flannelmouth suckers. If successful, the model could provide a means to 

evaluate past natural and management-induced variation in abundance. If a link between 

habitat (i.e., flow, or physical and biotic conditions) and recruitment can be established, 

22
the model can be used for gaming management policy alternatives. While the data may 

limit the potential for this application, the exercise should result in a thorough summary 

of the available information. The Panel also encourages the use and documentation of 

the quantitative sample design program (as developed by C. Walters) for the 

development monitoring programs consistent with detection requirements of the 

adaptive management program. 

An additional concern of the Panel involves analysis of fish data collected from

backwater habitats. A great deal of effort has been expended on sampling backwaters for 

larval and juvenile fishes in the mainstem, which has been summarized in the review by 

Hoffnagle (2000). The Panel recommends the backwater fish data be reanalyzed 

with the express goal of evaluating the utility of this information as a real-time 

recruitment index. 

Some of the native fishes use tributaries to the Colorado River as spawning 

habitat, and the Panel recommends consideration be given to the use of an upstream

migration collection weir, as widely used with spawning salmonids, to effectively 

capture, mark, and estimate the number and biological attributes of spawning native 

fishes. Alternative, passive counting devices also exist (using sonar or resistivity) that 

may prove useful in estimating abundances. Bright Angel Creek is an obvious candidate 

for pilot studies of this approach. While the proportion of the total spawning population 

being monitored by the approach may be small and variable, the implementation of an 

‘index stream’ program does provide some hard data that can complement less intense 

programs on other tributaries or the mainstem. Collection of increased numbers of fish 

could also provide useful population age class structure and spawning periodicity 

information. In addition, access to these aggregations provides the opportunity to collect 

samples for use in isotopic or elemental analyses. Such analyses could possibly usurp the 

need for longer-term, iterative mark-and-recapture studies currently used to delineate 

habitat use and distribution of native fishes in the mainstem Colorado River and its 

tributaries. 

23
Chapter 6- Non-native Fishes 

Recommendations- For the GCE below Lee’s Ferry, the management goals for nonnative fish are related to their impacts on native species. The Panel was impressed by the 

efforts to develop a program to estimate the abundance of salmonids in the Colorado 

River, but felt some effort should be (re-)allocated to the other components of risk to 

native species, especially with respect to predation. There is no explicit program for 

warm-water exotic fish species. The Panel suggests that the species should be ranked for 

their potential for impacting native species, and that monitoring metrics be developed for 

the important species that address potential risk to native fish. Thorough analysis of 

available data should assist in the evaluating the feasibility of monitoring programs for 

these species. 

As presented to the Panel, the focus of the non-native fishes monitoring program

in the overall aquatic resources monitoring program is on the extent to which these fishes 

pose a risk to native fish species (management objective 2.6). Non-native fishes that 

pose threats can be categorized into two groups, coldwater and warmwater non-natives, 

with major differences in distribution and natural history that will likely make their 

responses to changes in dam operations very distinct. The Panel therefore considered 

them separately throughout. 

Coldwater Non-Natives

Coldwater non-native fishes that are well established in the Grand Canyon reach 

of the Colorado River are two species of salmonids, rainbow trout (Onchorhynchus 

mykiss) and brown trout (Salmo trutta). It is not anticipated that any other coldwater 

salmonids are likely to invade the system. Maintenance of a naturally-reproducing 

rainbow trout population, while potentially a major threat to native fishes, is a 

management goal for the section of the Colorado from Glen Canyon Dam to the mouth of 

the Paria River. There is no similar management goal for brown trout. Abundances of 

both species are thought to be increasing, with estimates of ~ 1 million trout in the Grand 

Canyon reach of the Colorado River (Bill Persons, Arizona Game and Fish, Phoenix, 

Arizona; pers. comm). We will focus on the dominant species, rainbow trout, with a 

section on special issues concerning brown trout. 

From the information provided a number of expected responses of non-native 

salmonids have been identified (see Table 6.1). Based on these potential effects, Panel 

attempted to whether current monitoring efforts are sufficient to detect changes in the 

threat to native fishes from coldwater non-natives. Interactions between non-native and 

native fishes may take several forms, including predation, competition, and parasitism. 

We will focus on monitoring changes in the predation risk posed by coldwater nonnatives, as the most obvious route of impact. We cannot comment on the potential for the 

transmission of parasite or disease organism among species. 

24
Table 6.1 Proposed responses non-native salmonids to changes in dam operations 

Eggs and Alevins Small 

Juveniles 

Large 

Juveniles 

Adults 

Low Steady 

Flows 

Increased survival 

due to reduced 

exposure/scourin

g of redds 

Increased 

survival due to 

availability of

stable 

nearshore 

habitats; 

Increased 

dispersal 

? ?

Temperature 

Control 

(Increased to 

favor native 

fish) 

Decreased 

survival due to 

reduced oxygen 

in redds 

Suboptimal 

growth due to 

increased 

energy 

expenditures 

Suboptimal 

growth due to 

increased 

energy 

expenditures 

Suboptimal 

growth due to 

increased 

energy 

expenditures 

Sediment 

Augmentation 

Decreased 

survival due to 

smothering 

Decreased 

growth due to 

decreased 

foraging 

efficiency 

Decreased 

growth due to 

decreased 

foraging 

efficiency 

Decreased 

growth due to 

decreased 

foraging 

efficiency 

Spike Flows Decreased 

survival due to 

redd scour 

? ? ?

Predation Risk Posed By Non-Native Coldwater Fishes—Monitoring changes in the 

abundance of non-native coldwater fishes alone is insufficient to understand the 

predation risk imposed on native fishes. Monitoring changes in predation risk requires 

more detailed understanding of biotic and abiotic factors. In the following sections we 

review monitoring efforts in the context of a generalized predation risk equation: 

Per Capita Risk to Native Fish = f(Predator Density, Per Capita Predation Rate, Spatial 

and Temporal Overlap between Predators and Native Fish) 

Monitoring Issues 

Predator Density

The current monitoring plan is focused on detecting changes in trout density and 

distribution. Overall, the panel was impressed by the amount of effort and organization 

involved in this program, and felt that it provided a model for other programs, 

particularly in terms of clearly-stated goals, standardized sampling methodology, and 

25
informative, useful data summaries showing analyses to date. In fact, it might be useful 

at this point in the program to assess, using power analysis, whether adequate 

monitoring of trout abundance and distribution might be accomplished with less 

sampling effort. 

One issue we felt could be more rigorously addressed is the interrelationship 

between trout density, recruitment, growth, and dispersal. This relationship is 

particularly important in assessing any potential change in risk resulting from a change in 

dam operations. For example, it was suggested to the Panel that experimental low steady 

flows had increased the survival of young juvenile rainbow trout by increasing the 

availability of stable nearshore habitat. However, these young juveniles are not likely a 

predation threat to native fishes. If trout recruitment is strongly density-dependent, 

which has been demonstrated in many previous studies in other systems, then increased 

survival of young juvenile trout may have no influence on overall risk to native fishes. 

Similarly, if trout growth is highly density-dependent (Bohlin et al. 1994), and the ability 

of trout to prey on non-natives is size-dependent (see next section), high trout densities 

may actually reduce predation risk, by reducing the number of large, highly piscivorous 

individuals in the population. We suggest that efforts to use existing data to assess 

these functional relationships would be well worthwhile. 

Per Capita Predation Rates

Per Capita predation rate on any particular prey type depends on overall consumption 

rates, along with the proportion of the particular prey type in the diet. 

The panel feels that insufficient attention has been given to this aspect of nonnative influences on native fishes. Without knowing the propensity of trout to prey on 

natives, it is very difficult to assess predation risk. The panel was informed that a large 

number of trout stomach contents (>800) had been collected in association with fish 

sampling activities. We strongly suggest that these samples be analyzed, and the data 

brought to bear on this issue. Other factors that influence consumption may also be 

directly linked to changes in dam operations. For example, trout consumption rates are 

strongly influenced by temperature. The effects of dam operations that modify stream

temperatures may therefore influence overall risk to non-native fishes. Bioenergetics 

models have proven to be very effective tools for assessing the influence of temperature 

change on potential consumption by trout in other tailwater fisheries (Filbert and 

Hawkins 1995), due to relatively limited diel temperature fluctuations in these systems. 

Also, several recent papers have discussed the effect of changes in turbidity on trout 

consumption rates (Swetka and Hartman 2001). We suggest that this information be 

used in assessing potential changes in suspended sediment concentrations resulting 

from changes in dam operations, and should be tied directly into output of the 

physical program. 

Spatial overlap between predators and prey; spatial and temporal heterogeneity in 

predation risk

Distributions of both trout and native fishes appear to be very spatially 

heterogeneous in the Grand Canyon section of the Colorado River. In particular, 

26
humpback chub appear to be highly aggregated (although there is some contention about 

this point). Recent work dealing with the impact of predators on migratory river fishes 

indicates that the majority of total predation on a population may occur infrequently, and 

at limited spatial locations (Peterson 2001). We urge the monitoring program to 

develop protocols that can quantify the spatial overlap between predators and prey, 

particularly during critical and vulnerable life history stages of native fishes such as 

larval and juvenile dispersal. Predation on fishes with distinct migration/dispersal 

episodes may be difficult to document without knowing the timing and spatial extent of 

these episodes. For example, the impact of rainbow trout predation on humpback chub 

populations may be largely determined by predation on juveniles leaving the Little 

Colorado River. We additionally urge that diet and environmental (temperature and 

suspended sediment) data also be targeted towards these potential overlap zones. 

Brown trout: special concerns

In addition to rainbow trout, brown trout have been increasing in abundance, and 

becoming more widely distributed in the Grand Canyon section of the Colorado River. 

Brown trout populations have some distinct issues from rainbow trout in the river. For 

example, while rainbow trout are believed to be able to spawn successfully in the main 

channel, Brown trout spawning is thought to occur mainly in tributaries, particularly in 

Bright Angel Creek. Monitoring the extent to which brown trout spawn in locations 

other than Bright Angel is likely to be important in determining whether proposed 

mitigation strategies, particularly the use of blocking weirs for predator control, are 

likely to be affected. 

Warmwater Non-Native Fishes 

The potential effects of changes in dam operations on warmwater non-native fishes pose 

a special challenge for monitoring. At present, cold thermal regimes currently 

maintained by the operation of Glen Canyon Dam strongly limit warmwater non-native 

abundance, likely reducing any negative impact on native fishes. However, there is 

considerable concern that proposed changes in dam operations designed to benefit native 

species may also benefit these warmwater non-natives, who may in turn negatively affect 

native species. The panel was charged with evaluating how well the current monitoring 

program would be able to detect these changes resulting in altered dam operations and 

experimental flows. 

At present there is no specific monitoring program targeted toward warmwater 

non-native fishes. Part of the challenge facing any warmwater non-native program is the 

diverse array of species that have historically or currently occur in the Grand Canyon 

section of the Colorado River. These include large piscivores (channel catfish, black 

bass, striped bass), small invertivores (redside shiner and fathead minnow) and large 

detritivores (common carp). Individual stock assessments on each of these species is 

likely to be unfeasible, and many not be necessary. However, at least coarse-scale 

detection of trend in abundance for those species that are likely to pose the greatest threat 

to native species is essential. 

27
We suggest several steps towards the development of a warmwater nonnative monitoring program. First, existing catch per unit effort (CPUE) data on 

warmwater non-natives needs to be compiled, documented, and subjected to 

analysis to determine the level of change in population abundance that could be 

detected, given observed spatial and temporal variability and current sampling 

procedures. The GCRMP could then use the results of this analysis, along with 

existing knowledge and best professional judgment concerning threats to native 

species to target certain species for intensive monitoring. For example, a species 

which is highly piscivorous, able to be sampled with high precision, and whose 

abundance tracks the abundance of other warmwater species, would be an ideal target for 

intensive monitoring. The GCMRP also needs to decide whether this monitoring 

program should be targeted toward documenting changes in abundance at a given 

point, or towards documenting changes in distribution (i.e. upstream extent). 

Once a method for monitoring changes in abundance has been established, 

additional considerations of risk to native species can be considered (see previous section 

on coldwater non-natives). Like trout, there are well-established bioenergetic models for 

several warmwater non-natives (particularly black bass and striped bass) that can be used 

to model predation risk as a function of both abundance and temperature. Some of these 

additional considerations could even be targeted in the initial stages of the monitoring 

program. This could include intensive monitoring of warmwater non-natives in the 

vicinity of native fish aggregations and important spawning tributaries, potentially 

including gut content analysis. 

One important point of distinction between warmwater and coldwater non-natives 

is that predation may not be the only, or even the dominant mode of interaction with 

native species. Due to biological and ecological similarities between natives and nonnatives, competition and parasitism may be equally as important. Therefore, it is 

important that in addition to monitoring for population trends, additional research 

be considered that focuses on aspects of warmwater non-native populations that are 

likely to influence the range of potential interactions. 

28
Chapter 7. Management and institutional issues 

Recommendations: The panel observed considerable variation in the analytical effort 

expended, the timeliness of reporting, and the availability of standardized databases 

among programs for aquatic resources. A standardized annual reporting cycle is a key 

component of any monitoring program. The Panel recommends that the procurement 

process needs to be much more tightly controlled, and wonders whether greater ‘inhouse’ capability is required at GCMRC to achieve long-term consistency and quality 

in the monitoring program. 

In the first chapter we described the necessary ontogeny of monitoring programsfrom the initial description of the resources of concern, to the in-depth research on the 

processes and metrics of interest to the final decisions about the nature of the long-term

monitoring program. Each of the aquatic components we reviewed was at a different 

point along this trajectory. 

In many cases enough experience and data has been gained to allow development 

of explicit links between the management goals and monitoring outputs. In each of the 

preceding chapters we have noted that these links are required to permit the full 

development of the monitoring program. The management objectives and goals are 

currently qualitative, but are sufficiently described to permit the Center to determine the 

types of metrics (e.g., number of adult chub, abundance or diversity of invertebrates) and 

how they would be used analytically to describe performance with respect to the 

management goals. While the types of metrics and their use might change in time, the 

Panel feels the Center should devote considerable attention to exactly how the 

monitoring results will be used with respect to the management goals. This exercise 

should comprise a thorough review of the results collected to date, and will assist in 

the refinement of the long-term program. This exercise would also require more 

tightly defined hypotheses about the linkage between dam operations and the 

management goals 

The process of establishing monitoring programs would be greatly assisted by 

stronger leadership by GCMRC. The Panel felt the program would benefit from an 

enhanced ‘in-house’ capability for quantitative analysis and synthesis, to make 

greater use of existing data, and to integrate results across disciplines (and 

contractors). We observed inconsistencies in the level of analytical effort among 

program elements, and recommend analytical effort of the quality and level of detail 

consistent with the existing rigor of many of the field data collection programs. It is 

particularly important that existing and future data be archived and analyzed in a 

manner consistent with the goal of long-term monitoring. The Panel notes the need 

for timely reporting, improved accessibility of data resulting from monitoring programs, 

and to the extent practical, standardization of data entry forms, database formats, and 

annual reports which can increase program efficiency and utility. We have often noted 

the need for database development, and laud the attempts that are underway to assemble 

existing information. The Panel wonders whether database management should be a 

role for the Center itself, rather than contractors.

29
Long-term monitoring requires long-term stability in the study design, sampling 

protocol, analysis and reporting requirements. The Panel gained the impression that the 

process of executing the work with short-term contracts was not meeting these 

requirements, and was not a particularly effective use of resources. The Panel thought 

that the Center should play a larger role in the design of the monitoring program, detailed 

articulation of sampling protocol, and the interpretation of results. Following this, the 

panel recommends that the Request For Proposal’s used in the solicitation process 

and resulting contracts should be more focussed to include specifics on the sampling 

program, have a standard report framework and rigidly enforced data assembly 

and reporting timelines. Consideration should be given to longer term contracts to 

permit continuity in data collection. 

Our final comment lies somewhat outside the purview of the Panel’s charge, but 

was a concern that overshadows many of the issues that we have commented on. The 

Panel was concerned about the nature of the Adaptive Management Program with respect 

to its likelihood of success in providing new information about the response of the GCE 

to management actions. A successful Adaptive Management program will result from a 

coupling of a planned management experiment sufficient to evoke a change in the 

ecosystem, and a monitoring program reliable enough to detect that change. For the GCE 

the adhoc or stochastic (but not random) nature of baseline hydro operations of Glen 

Canyon Dam, and the important role of this variability on detecting ecosystem or trophic 

indicator responses is of great concern. Assuming that adaptive management is 

predicated on statistically powerful documentation of baseline ecosystem conditions, 

excessive baseline system variability (relative to perceived treatment effect scales) may 

provide a perilous context in which to detect treatment effects at desired levels of 

resolution. Secondly, the time scale of ecological responses for some taxa could span 

many years, both for the equilibration of lower trophic communities to be reached, and 

for the effects of change to be manifest in the longer lived organisms. We concur with 

NRC (1999), who call for explicit articulation 1) of what the core experiment is, and 2) 

the hypotheses to be tested by the experiment; such an articulation will allow a 

determination of the likelihood of success of the detection of the hypothesized effects. 

30
Chapter 8: Panel Responses to Questions Posed by GCMRC 

1. What are the appropriate indicators to be monitored to adequately track trends in 

fish and aquatic food base resources? Given funding constraints, what are the 

fewest, most important, overarching indicators to monitor? 

a. Is the approach associated with the food base appropriate? 

b. Would diet analysis be more informative/useful or should it be a combination of 

survey and consumption, and how can we adequately address the spatial scale 

question in Grand Canyon?

Chapter 2 and 3 provide details on options for monitoring programs of varying levels 

of intensity. The most basic and cheapest monitoring program for the lower trophic levels 

would entail a small number of fixed sampling stations, located at land-access points, 

where basic water quality parameters, and carbon and invertebrate drift would be 

estimated on a monthly or seasonal basis. 

Because the relation between estimates of abundance of lower trophic levels and fish 

population abundance or recruitment is not well understood, we have proposed measures 

to directly use fish-based indicators (including diet analysis) to measure the effects of the 

lower trophic levels on fish abundance. 

2. How should sample sites be selected? 

Geomorphic reaches? 

Using tributaries as demarcation points? 

Completely random? 

No generalizations are possible here, as the sampling design will depend on the 

variability of the attribute being sampled over space and time as well as the goals of the 

program. Randomized or stratified random designs are required for whole-river 

estimates of populations or densities, but for long-term trend monitoring of variables 

such as nutrients, temperature, and drift, fixed sites are suitable and logistically more 

practical. Standard sampling regimes often make use of stratified designs to subdivide the 

sampling area into more homogenous regions to reduce the variance in the final 

estimates. Stratification is usually based on a priori knowledge of how the variable of 

interest is distributed. Whether that stratification should be based on geomorphic reaches, 

at tributaries or other features depends on whether the organism’s distribution is related 

to these strata. 

3. Concerns have been expressed that past fish researchers in Grand Canyon (and 

the program under which they were funded) did not adequately analyze, 

synthesize, and integrate their data. What is the PEP's view of the status of 

information assessment for native and non-native fishes in Grand Canyon? Is it 

sufficient to serve as a basis for recommendations on future management actions, 

particularly those that may involve high risk to these species? 

Throughout the review the Panel has noted the need for long-term databases that 

collate information collected to date, and it supports recent efforts to bring such 

31
information together. While most of the past work was not focussed on long-term

monitoring needs there is much to be gained from the re-analysis of existing data, either 

1) help define/re-define hypotheses about the effects of dam operations on key physical 

and biological monitoring variables with data; 2) to ensure that monitoring data is 

generated in a form comparable to current and future programs; or 3) for ‘components of 

variation’ analysis to assist in the design of future programs. The Panel strongly supports 

current efforts to assemble and examine the data collected to date for its utility in the 

monitoring context. 

A great deal has been learned about the GCE. However, many other cases have 

shown us that the most consistent result of large-scale ecosystem manipulations is that of 

surprise or unexpected responses. That is, no amount of research and investigation will 

yield completely reliable predictions about the responses of organisms to changes in their 

environment. However, the panel felt that more has yet to be learned about the ecosystem

and continued efforts to understanding the response of the aquatic community to dam

operations will likely reduce risk of adverse impacts. The expected responses can be 

bounded, and particular attention can be paid to negative consequences, and the resilience 

of populations and ecosystems to manipulations that did not turn out as planned. 

4. Is there a large benefit to be gained from measurements (water quality, 

macrobenthos, phytobenthos, physical habitat, fish, stable isotopes, microbes, 

etc.) being collected at the same times and places? If so, should a common or 

integrated sampling design be applied to all resource groups? 

 

The sampling depends on the time and spatial scale of the variability of the distribution 

of the organism, and the goals of the program. For example, if the goal is a food web 

study, then there is obvious benefit to sampling at the same space and time scale as the 

foraging organism. This linkage allows more direct (certain) relation of abiotic 

conditions, primary and secondary response indicators providing a stronger weight of 

evidence to resulting inferences. However, for monitoring, there is a need for 

consistency over time and space (and methodology). Most monitoring programs involve 

fixed stations because these are the logistically easiest to implement, and have the highest 

likelihood of assuring continuity. In the strict statistical sense there is a shortcoming for 

fixed stations (i.e. repeated measures design), because the level of inference about the 

results is restricted to those sites, not the whole reach or river. This comment mainly 

applies to the objects of sampling that are relatively sessile, not time and space integrated 

variables such as temperature or drift. In summary it seems unlikely that a common 

sampling design can be expected for all resource groups, but where it is possible linkage 

of the sampling can help to provide more defensible inferences. 

5. Can a protocol be developed that will monitor trends effectively year to year in 

the Canyon regardless of the hydrology, other natural events that occur, or 

management actions implemented in any given year? [Is there too much noise in 

this system to track trends specific to dam operations?]

32
All natural systems vary from year-to-year, and in the GCE there is an unusual form of 

variation imposed by the operations of the dam. Whether the response to a management 

action can be detected depends on the natural variation, the sampling or measurement 

variability and the size and duration of the management perturbation. For the lower 

trophic levels there is probably sufficient information already available to assess the 

likelihood of detecting changes that result from management actions, and the fish 

programs should yield similar information soon. Usually, the outcome from these 

analyses is that it is often very difficult to detect changes in the taxa of most interest (i.e. 

adult fish; Korman and Higgins 1997). Multiple lines of evidence, including the results of 

monitoring of a variety of biota, as well as focussed investigations on the hypotheses 

being tested by the management action will be required to judge the outcome of an 

experiment. 

6. If, as is currently being discussed, fish (HBC) recruitment trends are only evident 

two to three years after a designed management action is taken, what can be 

accomplished in the intervening years without altering the developing trend? 

a. Emphasis in assessing native fish and the rainbow trout fishery has 

shifted strongly to stock assessment and stock synthesis. For the humpback 

chub, recruitment does not occur until age 3 or 4, and not until 2-3 years 

after fish are first marked. Hydrology of the Colorado River is, and will 

remain, unpredictable in the years between reproduction and recruitment. 

Thus, it is not a treatment that can be applied consistently in the years 

between reproduction and recruitment. If the primary question being 

addressed is, what is the relationship between dam operations, i.e. 

hydrology, and recruitment, how do we parse out the effects of different dam 

operations and tributary inputs in the relationship? 

 The significance of these issues depends on the hypotheses being tested about the 

relation between chub recruitment and dam operations. For example, if dam operations 

are expected to assist the survival of larval and age-0 fish only, dam operations in the 

intervening years are not as important because their effects will be limited to the first 

year of the chub’s life. But, if dam operations are hypothesized to affect all pre-recruit 

years, then the full effect of the experiment on a single cohort will not be realized unless 

the operating regime is continued for 3-4 years. 

The Panel was surprised that one-year flow experiments have been used and were 

being considered for future experiments useful for evaluating the relation between dam

operations and aquatic ecosystems. While some information about physical processes 

affecting fish (temperature, stranding) and those of the most rapidly growing organisms 

might be obtained, most components of the ecosystem will take longer (perhaps 

generations) to fully respond to changes in the physical and biological components of the 

ecosystem to flow regime. Further, any one-year experiment is completely confounded 

with the natural events of that year, and will have to be repeated a number of times to 

average out those effects. Much more information will be generated by repeating the 

management action in successive years. 

33
b. Movement to stock assessment and stock synthesis has resulted in 

movement away from measurements of native fish species, particularly 

humpback chub, in early life stages. Is this prudent, assuming that the 

majority of mortality from dam operations is visited upon humpback chub in 

the first year of life and the major responsibility of the Glen Canyon Dam 

Adaptive Management Program (GCDAMP) is to determine the effect of 

dam operations on native fish and other resources? 

There are other cases in fisheries where the trade-off between estimating 

recruitment as entry into the adult population and year-class strength as indicated by the 

indices of the abundance of the early life stages has been examined. The former is a 

measure of the variable that is of real interest (new adult fish), while the latter is more 

timely, but is often more difficult to do properly. There is also the possibility of

considerable variation in survival after the early life stage and actual recruitment that can 

hinder the utility of juvenile indices. It should be possible to evaluate this trade-off 

between these strategies quantitatively using juvenile information from the backwater, 

mainstem sampling, LCR trammel program and the stock synthesis model. 

7. How do we assure a trend is related to a specific management action and not 

other influences affecting the resource? Type I and Type II error. 

Adaptive management in the GCE is a spatially unreplicated experiment as there is no 

‘control’ river from which one can estimate the effects of large-scale factors such as 

decadal-scale changes in climate that could affect the aquatic ecosystem. The only 

method to control for external influences is to vary the treatments in randomized blocks 

over time (which could be an ‘on-off’ cycle) to avoid the coincidence of a treatment and 

a particular source of natural variation. In cases where the influence of natural variation 

is well known, it may be possible to collect ancillary data and use these as additional 

explanatory variables in the analysis to help remove their effects. 

 

Adaptive Management questions. 

8. A primary purpose of science in the GCDAMP is to assess the relationship 

between dam operations and responses of target resources. Most of the funding 

advocated by managers seems to be for what they deem core monitoring, with 

much less emphasis on research. Many scientists argue that status and trend of 

resources can be measured effectively by core monitoring, but much of the cause 

and effect relationships will need to be addressed through experiments and 

associated research. Is there a process known to the PEP that would facilitate 

resolution of these issues between scientists and managers? 

Adaptive management has been widely advocated in the CRE as the ‘process’ for 1) 

reducing scientific uncertainty about the response of the aquatic ecosystem to dam

operations; 2) the integration of research and management activities to most effectively 

34
manage water resources and aquatic conservation objectives (NRC 1999). Flow 

experiments have been explicitly proposed to empirical assess the relation of key 

ecosystem response indicators. Core monitoring in adaptive management programs 

provide time series of changes in the relative state of key aquatic resources and allow 

correlation of responses to dam operations. However, alone, this information is unlikely 

to provide enough information to make informed decisions about dam operations and 

aquatic conservation. We have identified many instances where additional research is 

required to before a monitoring program can be established, so requirement for research 

still exists. For planned flow experiments, we have also suggested that the routine longterm monitoring may not be sufficiently powerful to detect expected responses. 

To resolve these problems, there is a need for better linkage between research and 

research through experimental manipulation, and managerial research to learn how to 

effectively deal with uncertainty and design management approaches to reduce it (see 

Underwood 1994). Experiments should be framed as tests of hypotheses, as defined by 

research and monitoring is required to provide the data needed to test them. Thus for the 

Adaptive Management program there should be a mix of both monitoring and directed 

research studies. 

9. Are management objectives appropriate? 

Management objectives are policy determinations based on an array of values- the Panel 

was not charged with the review of the objectives. The Panel did note that, given limited 

resources, the management goals and their monitoring activities may have to prioritized. 

In all cases, there is a need to link the management objectives to the metrics that result 

from monitoring programs. 

10. How important is it to attempt replication in large-scale experiments like beachhabitat building flows? How much of the response in target variables might be 

attributed to driving variables other than dam operations? How does one 

compare tradeoffs between repeating large-scale experiments and the cost of 

conducting such experiments? 

The need for replication depends on the extent to which the ecosystem response 

varies with the management action, the magnitude of ‘noise’ or variability unrelated to 

the treatment, and the inherent time-scale the responding variable to the management 

action. For some variables (especially physical ones) replication may not be needed, 

however, the detection of responses in biological variables will almost always require 

replication. Since ecosystems may take some years to adjust to an altered physical 

regime, treatments should be replicated in successive years rather than isolated events. 

To justify conducting large scale replicated experiments the proponents of such 

an approach must show how deliberate flow manipulations will generate new information 

about the relative effectiveness of management actions or about hypotheses about 

ecological processes and thereby improve future management of the dam. Peterman and 

Peters (1998) suggest three general types of analyses can be conducted to quantify the 

35
value of information produced in adaptive management programs: 1) expected value of 

incorporating uncertainty; 2) expected value of collecting sample information; and 3) 

expected value of perfect information. The reasoning behind using the value of 

information calculations is to estimate whether it is worthwhile to acquire new data about 

how the ecosystem will respond to management actions and thus add value to 

management decisions in terms of net economic performance or some other manner of 

assessing utility (i.e. conserving a threatened species). Value of information calculations 

therefore are useful to help screen for opportunities to conduct adaptive management. 

Where it appears to be worthwhile to conduct experimental management actions 

the next step is to construct a management policy accounting framework for the 

evaluation of alternative experimental approaches (including baseline non-adaptive 

policies experimental design options). To be effective this policy accounting framework 

must: 

1) evaluate management actions based on explicit definition of benefits (and costs); 

2) account for the dynamic nature of fish populations and other aquatic and riparian 

resources and the influence of flow management actions on those dynamics; 

3) permit management actions to be constrained by economic, social or political 

factors; 

4) account explicitly for uncertainty as to the effects of management actions and 

uncontrolled environmental factors; and, 

5) define explicit linkages between management policies, operational monitoring, 

and assessment programs 

In this management policy accounting framework, dynamic models for predicting 

physical and ecological response to instream flow changes are developed and used to 

simulate how managers learn from implementing different experimental management 

strategies. By structuring the models to treat uncertainty as a dynamic variable of 

inherent in the management system, they can be used to compare different strategies for 

assessment and management and to design deliberate strategies for reducing uncertainty 

over time (Walters 1994). This analysis usually involves developing a conceptual model 

that incorporates the physical-ecological response model and an observation/management 

model that simulates how managers collect and respond to information. The model is 

then used in a Monte Carlo framework to investigate how realistic levels of natural 

variation and measurement error to establish the performance of a given proposed 

management experiment. The basic idea behind these evaluations to determine whether 

ecological uncertainty can be reduced by conducting the experiment and how reduced 

uncertainty influences expected long term net economic and ecological benefits from

management (Walters and Green 1997). To evaluate the net value of alternative designs 

for instream flow experiments managers must be able to compare the short term costs of 

conducting flow experiments and monitoring programs to the long term net benefits that 

accrue from managing based on the experimental results (Walters and Green 1997). 

11. Control or suppression of non-native species, primarily fish, has been advocated 

in conjunction with modified dam operations, particularly with a temperature 

36
control device. How effective does the panel think such actions could be in Grand 

Canyon? Which non-native fish would be most susceptible? 

To scope these questions the Panel suggests a simple population model of native fish be 

used to game (experiment) the response of fish populations to various management 

actions. While many parameters will have to be guessed at, the exercise should provide 

order-of-magnitude impacts of each management action on the target population. The 

relative risk of each exotic species could be estimated, and the likelihood that a proposed 

predator control program might succeed could be estimated. Brown trout appear to be the 

easiest predator species to control, and actions on this species could probably be justified 

for other reasons (i.e., elimination of exotic species in National Parks). Consideration 

might also be given to the removal of non-native fish from the Little Colorado River, 

given its importance for the recruitment of chub. 

37
References: 

Angradi, T. R. 1994. Trophic linkages in the lower Colorado River: multiple stable 

isotope evidence. Journal of the North American Benthological Society. 13: 479-496. 

Avise, J.C. 1994. Molecular Markers, Natural History and Evolution. Chapman and Hall. 

Benenati, E.M., J.P. Shannon, D.W. Blinn, K.P. Wilson, and S.J. Hueftle. 2000. 

Reservoir-river linkages: Lake Powell and the Colorado River, Arizona. Journal of the 

North American Benthological Society 19:742-755. 

Blinn, D. W., J. P. Shannon, K. P. Wilson, C. O’Brien, and P. L. Benenati. 1999. 

Response of benthos and organic drift to a controlled flood. Pgs:205-216 In: R. H. Webb, 

J. C. Schmidt, G. R. Marzolf, R.A. Valdez, Eds. Pgs 259-272 In: The controlled flood in

the Grand Canyon. American Geophysical Union, Washington D.C. 

Bohlin, T., C. Dellefors, U. Faremo, and A. Johlander. 1994. The energetic equivalence 

hypothesis and the relation between population-density and body size in stream-living 

salmonids. American Naturalist. 143(3): 478-493. 

Brock, J. T., T. V. Royer, E. B. Snyder, and S. A. Thomas. 1999. Periphyton metabolism:

A chamber approach Pgs. 217-224. In R. H. Webb, J. C. Schmidt, G. R. Marzolf, R.A. 

Valdez, Eds. The controlled flood in the Grand Canyon. American Geophysical Union, 

Washington D.C. 

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. 

Filbert, R.B. and C.P, Hawkins 1995. Variation in condition of rainbow trout in relation 

to food, temperature, and individual length in the Green River, Utah. Transactions of the 

American Fisheries Society 124(6): 824-835. 

Finlay, J.C. 2001. Stable-carbon-isotope ratios of river biota: implications for energy 

flow in lotic food webs. Ecology 82:1052-1064. 

Franklin, I. R. 1980. Evolutionary change in small populations. Pages 135-150 In: M. E. 

Soule and B. A. Wilcoz, eds. Conservation Biology: An evolutionary-ecological 

perspective. Sinauer, Sunderland MA. 

Franklin, I. R., and R. Frankham. 1998. How large must populations be to retain 

evolutionary potential? Animal Conservation. 1:69-73. 

Gorman, N.B. and D.M. Stone. 1999. Ecology of spawning humpback chub in the Little 

Colorado River, near Grand Canyon, AZ. Env. Bio. Fishes 55:115-133. 

38
Haden, G. A., D. W. Blinn, J. P. Shannon, and O.T. Gorman. Food resource limitations 

of the humpback chub (Gila cypha) an endangered cyprinid fish in the Little Colorado 

River, Arizona, USA. (unpubl. manus.) 

Hoffnagle, T. L. 2000. Backwater fish communities in the Colorado River, Grand 

Canyon 1991-1999. Draft Final Report. Arizona Game and Fish Department. Flagstaff 

AZ. 

Korman, J. and P.S. Higgins. 1997. Utility of escapement time series data for monitoring 

the response of salmon populations to habitat alteration. Canadian Journal of Fisheries 

and Aquatic Sciences 54:2058-2067 

Lande, R. 1995. Mutation and conservation. Conservation Biology 9:782-791. 

Lande, R. and G. F. Barrowclaw. 1987. Effective population size, genetic variation, and 

their use in population management. Pages 87-124 in: M. E. Soule, editor. Viable 

populations for Conservation. Cambridge University Press, Cambridge, UK. 

Lynch, M., and R. Lande. 1998. The critically effective size for a genetically secure 

population. Animal Conservation 1:70-72. 

Marzolf, G. R., C. J. Bowser, R. Hart, D. W. Stephens and W. S. Vernieu. 1999. 

Photosynthetic and respiratory processes: an open stream approach. Pgs: 205-216 In: R. 

H. Webb, J. C. Schmidt, G. R. Marzolf, R.A. Valdez, Eds. The controlled flood in the

Grand Canyon. American Geophysical Union, Washington D.C. 

McKinney, T., A.D. Ayers, and R.S. Rogers. 1999. Macroinvertebrate drift in the 

tailwater of a regulated river below Glen Canyon Dam, Arizona. The Southwestern 

Naturalist 44:205-210. 

Marshall, C.T.et al. 1999. Total lipid energy as a proxy for total egg production by fish 

stocks. Nature 402:288-290. 

. 

Meretsky, V.J. and 5 coauthors. 2000. Spatiotemporal variation in length-weight 

relationships of endangered humpback chub: implications for conservation and 

management. Trans. Am. Fish. Soc. 129:419-428. 

McKinney, R.S. Rogers, A. D. Ayers and W. R. Persons. 1999. Lotic community 

responses in the Lees Ferry reach. Ppg 249-258 In R. H. Webb, J. C. Schmidt, G. R. 

Marzolf, R.A. Valdez, Eds. The controlled flood in the Grand Canyon. American 

Geophysical Union, Washington D.C. 

NRC 1999. Downstream: Adaptive Management of Glen Canyon Dam and the Colorado 

River Ecosystem. National Academy Press, Washington D.C. 

39
Peterman R.M. and C. N. Peters 1998. Decisions analysis: taking uncertainties into 

account in forest resource management p105-128 In: Sit ,V. and B. Taylor [eds]. 1998. 

Statistical Methods for Adaptive Management Studies. Res. Br. B.C. Min. For. Res. Br., 

Victoria, B.C.; Land Manage. Handbook No.42. 

Peterson, J.H. 2001. Density, aggregation, and body size of northern pikeminnow preying 

on juvenile salmonids in a large river. Journal of Fish Biology 58:1137-1148. 

Rowan, D. J., & Rasmussen, J. B. 1996. Measuring the bioenergetic cost of fish 

activity in situ using a globally dispersed radiotracer (137Cs). Can. J. 

Fish. Aquat. Sci. 53: 734-745 

Schaffer, M. L. Minimum viable population sizes for species conservation. BioScience 

31(2):131-134 

Shannon, J. P. 2001. Factors affecting the aquatic community in the Colorado River 

through Grand Canyon, Arizona. Ph.D. Dissertation Northern Arizona University. 87pp. 

Shannon, J. P., D. W. Blinn, P.L. Benenati and K. P. Wilson. 1996. Organic drift in a 

regulated desert river. Canadian Journal of Fisheries and Aquatic Sciences. 53:1360-

1369. 

Soule, M. E. 1987. Editor. Viable populations for conservation. (Introduction pgs 1-10) 

Cambridge University Press, Cambridge, UK. 

Stevens, L. E., J. P Shannon, and D. W. Blinn 1997. Colorado River benthic ecology in 

Grand Canyon Arizona, USA: Dam, tributary and geomorphological influences. 

Regulated Rivers: Research and Management 13: 129-149. 

Sweka, J.A. and K.J. Hartman. 2001. Effects of turbidity on prey consumption and 

growth in brook trout and implications for bioenergetics modeling. Canadian Journal of 

Fisheries and Aquatic Sciences. 58(2): 386-393. 

Thorrold, S. et al. 2001. Natal homing in a marine fish metapopulation. Science 291:297-

298. 

Underwood, A.J. 1994. Ecological research and (and research into) environmental 

management. Ecological Applications 591:232-247. 

Valdez R.A. and R.J. Ryel. 1995. Life history and ecology of the humpback chub in the 

Colorado River, Grand Canyon, Arizona. Final Rept. Bur. Reclamation. Contract No. 0-

CS-40-09110. 

Vinson, M.R. 2001. Long-term dynamics of an invertebrate assemblage downstream

from a large dam. Ecological Applications 11:711-730. 

40
Walters. C.J. 1994. Use of gaming procedures in evaluation of management experiments. 

Canadian Journal of Fisheries and Aquatic Sciences 51:2705-2714. 

Walters, C., and R. Green. 1997. Valuing large-scale management experiments for 

natural resources. Journal of Wildlife Management 61:987-1006. 

41
Table 1 Field of expertise and institution of Aquatic Protocol Evaluation Panel Members 

Name Field of Expertise Institution 

Paul Anders 

Fish ecology, 

Population genetics 

Department of Fish and Wildlife 

Resources, 

University of Idaho 

Mike Bradford (chair) 

Fish ecology, 

Population dynamics 

Fisheries and Oceans Canada and 

Simon Fraser University, 

Vancouver, B.C. 

Paul Higgins 

Fish ecology 

Monitoring design 

B.C. Hydro 

Vancouver, B.C. 

Keith H. Nislow 

Aquatic ecology, 

Experimental design 

USFS and Univ. Mass. 

Amherst, Mass. 

Charles Rabeni 

Aquatic Ecology 

Fisheries Ecology 

USGS, and Univ. Missouri 

Cathy Tate 

Aquatic ecology, 

Fisheries ecology 

Water Quality 

USGS, Denver 

42
Table 2 Contributions and institution of other participants in the 7 day field trip 

associated with the Aquatic Protocol Evaluation (May 8 to May 15, 2001) 

Name Activity Institution

Lew Coggins 

Little Colorado River 

Humpback Chub 

Stock Assessment Program

United States Fish and 

Wildlife, 

Flagstaff, Arizona 

Barry Gold (p/t) 

Environmental Studies 

Background 

Adaptive Management, and 

Role of PEP panel 

GCMRC 

Flagstaff, Arizona 

Stewart Jack (p/t) Observer 

United States Fish and 

Wildlife, 

Pinetop, Arizona 

Josh Korman Conceptual Model 

Ecometric Research, 

Vancouver, B.C. 

Dennis Kubly (p/t) Observer 

United States 

Bureau of Reclamation 

Ted Melis (p/t) 

Physical Science 

Program Coordinator 

GCMRC 

Flagstaff, Arizona 

Bill Persons 

Non-Native Fish Stock 

Assessment 

Arizona Game and Fish 

Phoenix, Arizona 

Barbara Ralston 

A/Biological Program 

Coordinator 

GCMRC 

Flagstaff, Arizona 

Joe Shannon 

Aquatic Food 

Base 

Northern Arizona 

University, 

Flagstaff, Arizona 

Melissa Trammell 

Native Fish 

Biology 

SWCA, Inc 

Flagstaff, Arizona 

David Topping 

Physical Science 

Program

USGS 

Flagstaff, Arizona 

Carl Walters 

Native Fish Stock 

Assessment 

University of British 

Columbia, Fisheries Center, 

Vancouver, B.C. 

Mike Yard 

Water Quality, 

Fisheries Biology 

GCMRC 

Flagstaff, Arizona 

43