Southwest Biological Science Center, Grand Canyon Monitoring and Research Center

Study Plan—Biological Resource Responses to Fall Steady 

Experimental Flows Released from Glen Canyon Dam, 

2009–12 

Planning Document—February 2010

U.S. Department of the Interior

U.S. Geological Survey
ii

U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

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Contents

Executive Summary.........................................................................................................................................................1

Background .....................................................................................................................................................................3

Need for Study.............................................................................................................................................................3

Provisions of the Environmental Assessment and Biological Opinion.........................................................................3

Previous Experiments and Studies ..............................................................................................................................4

Experimental Design .......................................................................................................................................................9

Fall Steady Flows.........................................................................................................................................................9

August to September Transition in Discharge .............................................................................................................9

High-Flow Experiments..............................................................................................................................................10

Ongoing and Proposed Studies.....................................................................................................................................11

Objectives ..................................................................................................................................................................11

Data Synthesis and Integration..................................................................................................................................13

Reporting and Synthesis............................................................................................................................................15

Project 1—Nearshore Ecology (Bio 2.R15.09)..............................................................................................................16

Project 2—Stock Assessment of Grand Canyon Native Fish (BIO 2.R7.10–11)...........................................................21

Project 3—Aquatic Food Base (Bio 1.R1 and 4) ...........................................................................................................25

Project 4—Monitoring Lees Ferry Fishes (Bio 4.M1.09)................................................................................................28

Project 5—Supplemental Water Temperature Data Collection .....................................................................................31

Project 6—Support and Enhancement of Ecosystem Modeling Efforts (R12.P1.10)....................................................33

References Cited...........................................................................................................................................................36

Appendix A—Nearshore Ecology Proposal...................................................................................................................39
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1

Study Plan—Biological Resource Responses to Fall 

Steady Experimental Flows Released from Glen Canyon 

Dam, 2009–12

Executive Summary

Experimental steady releases from Glen Canyon Dam in September and October 2008 through 2012 

(fall steady experimental flows, FSEF) were prescribed by a 2008 environmental assessment and an 

associated biological opinion. The Grand Canyon Monitoring and Research Center (GCMRC) prepared 

this science plan at the request of the Glen Canyon Dam Adaptive Management Work Group to examine

the effects of FSEF on downstream resources. Four ongoing projects are collecting data that will be 

used to assess possible impacts of these flows on biological resources: (1) the nearshore ecology project, 

(2) stock assessment of native fish populations, (3) aquatic food base monitoring, and (4) monitoring of 

early life stages of rainbow trout. Given uncertainties regarding the extent and degree of nearshore

warming that will occur as the result of fall steady flow operations, we propose the collection of new 

water temperature data in association with these flows. Physical and biological data will be integrated 

and synthesized using an ecosystem model to evaluate whether this management action had impacts on 

the ecosystem as a whole. A description of the sediment-monitoring program is not included in this 

document. However, the effects of the discharge regime on sediment resources are well understood, and 

the GCMRC Physical Sciences and Modeling Program could evaluate and report on the response of 

sediment resources to fall steady flows, should it be of interest to managers. 

The GCMRC also has been asked to recommend flow parameters because the environmental assessment 

and biological opinion did not establish specific release rates for FSEF. Findings from recent studies 

indicate that lower flows result in greater abundance of backwater habitats, which are thought to be used 

by juvenile native fish, including the endangered humpback chub (Gila cypha). Thus, steady flows of 

about 8,000 cubic feet per second (cfs) for the remainder of the experiment (2010 through 2012) would 

likely maximize backwater habitat in addition to maximizing the potential for nearshore warming, also 

thought to benefit native fish. If water releases must be moved into other months of the year to 

accommodate these steady flows, it is recommended that releases in July and August not be increased. 

Daily peak discharges during July and August are already relatively high and further increases will 

increase sediment transport and sandbar erosion, which are undesirable side effects.
2
3

Study Plan—Biological Resource Responses to Fall 

Steady Experimental Flows Released from Glen Canyon 

Dam, 2009–12

Background

Need for Study

Regulation of the Colorado River by Glen Canyon Dam has eliminated spring snowmelt flood peaks, 

which historically occurred from April through early July, and increased discharge in summer, fall, and 

winter (Topping and others, 2003). The Bureau of Reclamation (Reclamation) has released or will 

release experimental steady flows from Glen Canyon Dam in September and October of 2008 through

2012 (fall steady experimental flows, FSEF) to partially mimic the steady and low flows that 

historically occurred annually from July to March. It is hypothesized that steady flows during the fall 

will benefit native fishes by stabilizing and warming the nearshore habitats that are occupied by juvenile 

(less than 150 mm total length) life stages of endangered humpback chub (Gila cypha) (Stone and 

Gorman, 2006). Fall steady flows may also affect other downstream biological resources, including the 

food base for native and nonnative fish.

The Glen Canyon Dam Adaptive Management Work Group (AMWG) requested that the Grand Canyon 

Monitoring and Research Center (GCMRC) develop a science plan for investigating the effects of 

FSEF. Glen Canyon Dam Adaptive Management Program participants, including natural resource 

managers and other stakeholders, want to know if the 2008–12 fall steady flows will affect humpback 

chub and other biological resources. One of the tenets of adaptive management is that learning about 

managed ecosystems can and should be gained by monitoring ecosystem responses to management 

actions (Williams and others, 2007; Souchon and others, 2008). Additionally, evaluation of natural 

resource responses to the 2008–12 FSEF is required by a 2008 environmental assessment (EA) (U.S. 

Department of the Interior, 2008). The studies outlined here will examine the effects of FSEF on 

downstream biological resources to advance adaptive management and ensure compliance with Federal 

environmental regulations.

Provisions of the Environmental Assessment and Biological Opinion

In February 2008, Reclamation released an EA (U.S. Department of the Interior, 2008) that built upon

an earlier environmental impact statement for Glen Canyon Dam operations (U.S. Department of the 

Interior, 1995). The 2008 EA describes two flow experiments: (1) a 60-hour experimental high-flow 

release from Glen Canyon Dam in March 2008 and (2) steady releases in September and October of 

2008 through 2012. The exact release volumes of the second experiment (FSEF) were not specified in 

the 2008 EA. As a result, in addition to examining the effects of the FSEF on biological resources, the 

GCMRC was asked by the AMWG to make recommendations for the volume of the fall steady flows, 

which are presented here. Recommendations for flows needed to evaluate whether a change in the lower 

limit of discharge, which, since 1996, has occurred between August and September, are also provided. 
4

Evaluating the impacts of changing the lower limit of discharge on biological resources also was raised 

in the EA. 

A 2008 biological opinion (BO) released by the U.S. Fish and Wildlife Service (U.S. Fish and Wildlife 

Service, 2008) called for two conservation measures that are addressed in this plan in response to the 

experimental flows. The conservation measures under the 2008 BO include the nearshore ecology 

project and a study of the impacts of flow transition, that is, the impacts of the flows fluctuating in 

August followed by reduced, steady flows in September during the experimental period. The BO 

suggested that the long-term impacts of the experimental flows would benefit humpback chub by 

creating and improving rearing habitats and increasing growth and survival. The BO also calls for 

monitoring the impacts of the March 2008 HFE and the fall steady flows on humpback chub.

There was not sufficient time to prepare this plan and implement the activities described herein during 

the 2008 FSEF; the GCMRC and its cooperators were preparing to undertake a substantial body of 

research associated with the March 2008 high-flow experiment (HFE) in February when the EA was 

released. However, there were ongoing studies during the 2008 FSEF, including a pilot project to start 

collecting data for the nearshore ecology project. Additionally, select biological resources were studied 

in association with the March 2008 HFE, and final reporting for all projects is nearly complete (Melis 

and others, 2010). Some baseline data from these studies are available and will be incorporated into the 

longer term studies.

Previous Experiments and Studies

Stable and low discharge is expected to benefit native fish in the Colorado River below Glen Canyon 

Dam by improving the quality of nearshore habitats that are occupied by juvenile life stages of native 

fish. Warming of nearshore water temperatures, stability of nearshore environments, and increases in 

food resources are the main habitat parameters that are hypothesized to improve with stable and low 

discharge. A number of these hypotheses have been investigated and the findings are summarized 

below.

Nearshore Water Temperature

The water temperature of nearshore habitats in the Colorado River is influenced by a variety of factors, 

especially the temperature of releases, air temperatures, the residence time of water in the mainstem, and 

the residence time of water in the nearshore environment (Korman and others, 2006; Wright and others, 

2008). The elevation of Lake Powell and the thickness of the epilimnion have a major influence on 

release temperatures. In particular, the temperature of water discharged from Glen Canyon Dam during 

the summer of 2005 was 4°C warmer relative to the summertime average from 1989 to 2000 because of 

low Lake Powell elevations. The mainstem water temperatures observed between Glen Canyon Dam 

and the Little Colorado River in 2005 were warmer than temperatures observed in 2000, despite 

fluctuating flows in 2005 and steady flows in 2000, because of the lower elevation of Lake Powell in 

2005 (B. Ralston, U.S. Geological Survey, written commun., 2009).
5

If air temperatures are warmer than water temperatures, heat energy is transferred from air to water and 

the water warms. Since 1994, water temperatures at Diamond Creek (river mile1 (RM) 226, or 386 km 

below the dam) averaged 7.5°C warmer relative to releases in July but only 4°C warmer in October 

(Voichick and Wright, 2007; Wright and others, 2008). If air temperatures are cooler than water 

temperatures, then heat energy is transferred from water to air and the water cools; in December, water 

temperatures at Diamond Creek are on average slightly cooler (<1°C) than dam release temperatures.

The amount of mainstem warming or cooling that occurs is positively related to water residence time, 

and the primary determinant of residence time is discharge volume (residence time decreases as 

discharge volume and average velocity increase). For example, water temperatures at Diamond Creek 

were 10°C warmer relative to releases in June 2000, when discharge was a constant 8,000 cubic feet per 

second (cfs), but only 5°C warmer during June of 1997, when discharge was a relatively constant 

25,000 cfs (Vernieu and others, 2005).

If the residence time of water is sufficiently long, water temperatures of nearshore habitats can be 

different from the mainstem. For example, Korman and others (2006) found that water temperatures 

along high-angle shorelines—where water velocity is fast and residence time is short—were no different 

than the mainstem river across all months studied (mid-August through mid-November of 2004; three

reaches were sampled: RM -3.5, RM 44.6, and RM 64.5). In contrast, daytime water temperatures in 

backwaters (longest water residence time) and low-angle shorelines (intermediate residence time) were 

about 2 and 1°C warmer, respectively, relative to mainstem temperatures in August. In September, 

when air temperatures were cooler but water residence time presumably was longer because of lower 

discharge volume and fluctuation range (10,000 to 18,000 cfs in August versus 5,000 to 10,000 cfs in 

September and October), water temperatures in backwaters and low-angle shorelines were about 3 and 

2°C warmer than mainstem temperatures, respectively. However, in October, average daily air 

temperatures were cooler than water temperatures, and, as a result, water temperatures in these habitats 

were the same or slightly cooler than the mainstem. Thus, September and October represent a period of 

transition during which nearshore warming declines and eventually ceases, at least when discharge is 

fluctuating.

Mainstem and nearshore water temperatures for 42 miles of the Colorado River (RM 30 to 72) were 

measured using an aerially deployed thermal infrared sensor on July 21, 2000, around 1 p.m. local time

as part of the low summer steady flow (LSSF) experiment (B. Ralston, U.S. Geological Survey, written 

commun., 2009). Resolution of these data were 1 m2 and the total area of habitat within 2 and 4 m of 

shore were 446 ha and 804 ha, respectively. Water temperatures were warmer closer to the shore and 

ranged from 9 to 30°C (mainstem temperatures in this reach were about 13°C at the time), indicating 

significant nearshore warming can occur during the summer months when discharge is constant.

However, 67 percent and 75 percent of the nearshore habitat within 2 and 4 meters of the shoreline, 

respectively, had water temperatures that were actually the same or slightly cooler than the mainstem.

Unfortunately, thermal infrared images providing a comprehensive picture of nearshore water 

temperatures have not been collected during fluctuating operations at the same time of year as the low 

summer steady flow experiment, so it is difficult to put these data into context. That is, it is unclear 

whether nearshore habitats will gain increased water temperatures during steady flows relative to 

fluctuating flows.

 1 By convention, river mile (RM) is used to describe distance along the Colorado River in Grand 

Canyon: Lees Ferry (located 15.7 miles downstream of Glen Canyon Dam) is the starting point, as RM 

0, with mileage measured for both upstream (-) and downstream directions.
6

Stability of Nearshore Habitats

Constant and low discharge might benefit fish by stabilizing nearshore habitats, if, for example, daily 

fluctuations in discharge, stage, and/or velocity makes foraging/feeding less profitable relative to when 

discharge is stable (for example, more energy is expended foraging during fluctuations). The 2000 low 

summer steady flow experiment (constant discharge of 8,000 cfs from June through August) warmed 

and stabilized nearshore environments (B. Ralston, U.S. Geological Survey, written commun., 2009), 

but there is no evidence that this management action is responsible for the decade-long increasing trend

in adult humpback chub (Coggins and Walters 2009). The Grand Canyon humpback chub population 

began its current uptick as the result of increasing recruitment of the cohorts spawned after about 1998.

Inferences with respect to the native fish response to the 2000 experiment are weak because of reduced 

sampling efforts in the years before 2000 and low numbers of native fish present in the system in 2000, 

limitations that reduce the statistical power of comparisons that were made (B. Ralston, U.S. Geological 

Survey, written commun., 2009). Further, no process-level measurements of fish growth, such as otolith 

daily increments or RNA/DNA ratios, were made during this experiment, so the fish response was only 

evaluated by comparing catch rate data in 2000 with the years before and after, and by comparing the 

strength of the 1998–2000 cohorts after they recruited into the adult population relative to the strength 

of cohorts from years before or after.

There was no clear response of biological parameters to short-duration flow treatments that were 

implemented in 2005. During September and October 2005 fluctuating (7,000 to 9,000 cfs) and steady 

releases (8,000 cfs) were alternated on 2-week intervals. Backwater and mainstem habitats throughout 

the Colorado River ecosystem were sampled for water-quality parameters, invertebrate biomass, and 

fish relative abundance in early September (fluctuating) and again in late September (stable). Turbidity, 

which is negatively related to primary production, was significantly lower during the steady discharge 

treatment, but this decrease was likely because of tributary spates during the fluctuating treatment rather 

than the stable discharge treatment itself. Zooplankton concentrations were higher during the fluctuating 

treatment while relative abundance of bluehead suckers (Catostomus discobolus) was higher during the 

steady treatment. There were no statistically significant differences across flow treatments for biomass 

of the 11 benthic macroinvertebrate taxa collected, and there were no treatment effects on the relative 

abundance of the other 10 fish species collected (Ralston and others, 2007). This sampling effort was 

not repeated during the second pair of fluctuating-stable discharge treatments that occurred in October

2005, so it is tenuous to ascribe the differences that were observed in biological parameters to the flow 

treatments. Further, no process-level measurements, such as rates of primary production or fish growth, 

were made during this experiment.

Juvenile humpback chub catch rates measured by the nearshore ecology project’s pilot study in August 

2008 during fluctuating flows were higher relative to catch rates from September 2008 during steady 

flows. However, large numbers of humpback chub, especially 2- and 3-year-old fish, were captured on 

both trips, likely because of flooding in the Little Colorado River from July to September that moved 

humpback chub into the mainstem (discharge of the Little Colorado River at Cameron, Arizona, was 

above 1,000 cfs for a duration of least 2 days on five different occasions from July to September 2008).

Little Colorado River spates, which periodically move humpback chub into the mainstem, will likely 

complicate interpretation of catch rate/abundance data collected by the nearshore ecology project 

throughout the remainder of the FSEF.
7

Otolith (inner ear bone) data highlights the importance of using process-level measurements to 

document biological responses to the FSEF. Korman and Campana (2009) found that steady flow 

releases conducted 1 day/week (Sunday) in January through March of 2003 through 2005 led to 

measurable increases in growth (presumed to correlate with measured otolith responses) of young-ofyear rainbow trout (Oncorhynchus mykiss) below Glen Canyon Dam. Because this was documented in 

the Glen Canyon Dam tailwaters reach (RM 0 to -15) in winter when nearshore temperatures were likely 

no different from the mainstem, this study indicates that stability of nearshore habitats without 

concomitant warming can benefit rainbow trout. It is possible that steady flows in September and 

October, a time when nearshore warming is likely modest, will also benefit juvenile humpback chub 

simply by stabilizing nearshore environments. However, results obtained from trout may not be directly 

comparable to other fishes, including humpback chub. 

Food Resources

Constant discharge will increase available food resources if algae and invertebrate growth rates are 

higher when discharge is constant or if accumulation of algae and invertebrate biomass is higher during 

steady flows relative to fluctuating flows (Production is total biomass accumulation per unit time, 

P=Growth Rate*Biomass). The two most likely mechanisms whereby stable discharge could increase 

algae and invertebrate growth rates are through (1) warming nearshore habitats and/or (2) delivering 

nutrients to algae and food particles to invertebrates should constant water velocities support higher 

growth rates relative to water velocities that fluctuate on a daily basis. Experiments at the Artificial 

Stream and Pond Research Facility at the Loyola University Chicago directly evaluated these two 

mechanisms and found strong support for mechanism 1 (temperature), but results were actually contrary 

to mechanism 2 (stable water velocity) (Kennedy and others, U.S. Geological Survey, written commun., 

2009).

Net primary production of Colorado River algae and individual growth rates of larval black flies were 

more than twice as high in 15oC streams relative to 10oC streams, indicating minor increases in the 

amount of nearshore warming (that is, 5oC) can lead to substantial increases in algae and invertebrate 

growth rates (see figs. 1a and 2a). In contrast, net primary production was about 50 percent lower in 

streams with constant daily velocity (15 cm/second) relative to streams with either low (velocities of 22

to 44 cm/second within a day) or high daily velocity fluctuations (11 to 67 cm/second within a day; see 

figs. 1b and 2b). Individual growth rates of larval black flies were lowest in the stable flow streams on 

the two occasions these measurements were made, but the differences were not statistically significant.

There were no significant interactions between water velocity and temperature for any of the response 

variables evaluated. Growth and production in stable flow streams was likely lower than fluctuating 

streams because the rate of nutrient and food delivery was lower in stable streams. That is, the water 

velocity of the stable treatment streams was lower than the average water velocity of fluctuating 

treatment streams. This aspect of the experimental design is similar to the FSEF, with stable discharge 

(velocity) in September and October being lower than discharge (velocity) in July and August. It should 

be noted that the water velocities evaluated are lower than reach-average velocities in the Colorado 

River. Regardless, these results indicate water temperature has a strong and positive effect on algae and 

invertebrate growth rates while stable water velocities do not (Kennedy and others, U.S. Geological 

Survey, written commun., 2009).
8

Accumulation of algae and invertebrate biomass might be higher during steady flows if rates of 

sloughing and downstream export are higher when discharge is fluctuating. However, rainbow trout and 

humpback chub have been documented to forage on drifting food items (Valdez and Ryel, 1995; 

McKinney and Speas, 2001), so increases in benthic biomass because of a decrease in sloughing may 

actually reduce the quantity of drifting food items that are available to these species. Benthic biomass 

data are inherently variable (Stevens and others, 1997) and it seems unlikely that 2 months of steady 

flows in the fall, a time when primary production is decreasing and steady-flow mediated increases in 

nearshore warming are likely minimal (Korman and others, 2006), will lead to a detectable 
9

accumulation of algae or invertebrate biomass. However, algae and invertebrate drift data are less 

variable and easier to collect than benthic biomass data, so we propose evaluating drift response to the 

FSEF and using these data to make inferences about potential biomass accumulation.

Experimental Design

Fall Steady Flows

Selecting a discharge for the FSEF and determining whether discharge should vary across years of the 

experiment depends on what science questions are of greatest interest to managers. Our assumption is 

that managers are most interested in determining whether steady flows in the fall have a positive impact 

on the recruitment of juvenile humpback chub into the adult population. Varying the discharge of stable 

flows across years would allow scientists to evaluate whether discharge volume affects the degree of 

nearshore warming or habitat selection by juvenile humpback chub. However, identical steady discharge 

across the remaining years of this experiment would simplify interpretation of humpback chub 

recruitment data. That is, having the same stable discharge across the remaining years of the experiment 

would make it easier for scientists to attribute any trends in humpback chub recruitment observed in 

subsequent years to the steady flow experiment.

We believe managers are also interested in maximizing the amount of backwater habitat available 

during the steady flows, and recently published findings based on data collected in 2008 demonstrate 

that there is generally greater abundance of backwater habitat at lower flows (Grams and others, 2010).

In October 2008, there was about 26 percent greater area of backwater habitat at 10,000 cfs than at 

12,000 cfs and an additional 50 percent more habitat at 8,000 cfs than 10,000 cfs. Based on these 

results, there may be reason to implement the lowest possible discharge of 8,000 cfs, if there is a desire 

to maximize the quantity of backwater habitat. It is important to recognize that the amount of backwater 

habitat available in fall 2010 and thereafter will depend on the morphology of the sandbars that create 

the habitat. The results of Grams and others (2010) are based on morphology measured in October 2008 

and, therefore, cannot be used to predict the amount of habitat that will be available. However, because 

the relation between habitat quantity and discharge was similar in February 2008, before the HFE, and 

October 2008, 6 months after the HFE, we believe that it is reasonable to assume that the relation will 

be similar in 2010 through 2012. In other words, we believe that there should still be more habitat at 

8,000 cfs than higher discharges, even if the total amount of habitat is different in 2010 than it was in 

2008. The only time the relation is expected to be different is for the first few months following a high 

flow, when backwater habitat size is not expected to vary as a function of discharge (Grams and others, 

2010).

If water releases must be moved into other months of the year to accommodate these steady flow levels, 

then it is recommended that releases in July and August not be increased, as daily peak discharges

during these months are already relatively high. Further increases will increase sediment transport and 

sandbar erosion, an undesirable side effect because it would reduce backwater area.

August to September Transition in Discharge

Determining whether the transition from the high discharges of August to lower discharges of 

September has a negative impact on organisms downstream is of longstanding interest to managers. The 

BO calls for study of this topic, stating the following:
10

...transitions from August to September in some years have consisted of a transition from a lower 

limit of 10,000 cfs in August to an upper limit of 10,000 cfs in September. Such a transition results 

in a river stage level that is below the varial zone of the previous month’s flow, and may be 

detrimental to fishes and food base for fish. Reclamation has committed to adjusting daily flows 

between months to attempt to attenuate these transitions such that they are more gradual, and to 

studying the biological effects of these transitions, in particular to humpback chub.

However, studying potential effects of these transitions on food base or fish would require a series of 

experimental transition flows that would confound and complicate interpretation of data from the 

ongoing FSEF. Previous research on stranding in Grand Canyon, which was conducted during the 1980s 

when daily changes in discharge were much greater than presently allowed (that is, change from 25,000 

to 5,000 cfs in roughly 6 hours), revealed that only a small percentage of backwaters contain isolated 

pools when discharge is drastically reduced over a short time period (Maddux and others, Arizona Game 

and Fish Department, written commun., 1987). Humpback chub (0.2 percent) and native fishes 

collectively (4 percent) represented a small percentage of the 1,923 fish that were stranded in isolated 

pools during a systemwide survey conducted from October 19–21, 1984 (Maddux and others, Arizona 

Game and Fish Department, written commun., 1987). The average size of native fish stranded was also 

small (<55 mm), indicating that adult native fish are not susceptible to stranding. The GCMRC has 

concluded that the comprehensive study by the Arizona Game and Fish Department (Maddux and 

others, Arizona Game and Fish Department, written commun., 1987) provides sufficient information for 

managers to make an informed decision about whether transitions should be gradual (to reduce potential 

stranding of native fish) or if transitions can be abrupt (because changes in monthly volume are much 

more gradual now than during Maddux study). As a result, the GCMRC concludes that additional study 

of stranding is not warranted.

If managers are interested in studying the effects of abrupt transitions in monthly volume on food base 

or fish growth, the GCMRC is ready to help design the necessary experimental hydrographs. But any 

transition experiments and associated studies should be conducted after 2012 when the FSEF will be 

completed. Conducting this research after 2012 would allow transition studies to benefit from the 

experience and insights gained by FSEF studies (that is, what techniques worked, whether process-level 

measurements sensitive enough to detect transition effects, etc.). Further, designing transition 

experiments would not be constrained by the ongoing FSEF.

High-Flow Experiments

The number and size of backwaters has greatly diminished since the March 2008 HFE (T. Kennedy, 

U.S. Geological Survey, personal observations, 2008, 2009). In April 2008, immediately after the HFE,

there were at least six large backwaters between the Little Colorado River and Lava Chuar (the reach for 

the nearshore ecology project), and they were all present across the full range of April flow fluctuations.

A year later, there was only one backwater in this reach that was present across the full range of flow 

fluctuations in July 2009 (M. Yard, U.S. Geological Survey, personal observations, 2009). There are 

three other backwaters in this reach, but they are only isolated during the night when discharge is low; 

however, during the day when discharge is high, the return-current channel bar is overtopped. As such, 

the nearshore ecology project is evaluating the interactions between flows, fish growth, and habitat type 

in a reach where the amount of backwater habitat is minimal. If managers are interested in having more 
11

and larger backwaters available for the nearshore ecology project to evaluate, a HFE could be conducted 

should the sediment trigger be reached before October 2011, when fieldwork for the nearshore ecology 

project is scheduled to end. We propose consulting with Reclamation on this issue in early 2010 after 

the results of the March 2008 HFE have been reported and the effects of experiment on backwater 

habitat are known.

Ongoing and Proposed Studies 

Objectives

Collectively, the studies we describe in the next section will evaluate the components and linkages of 

the Colorado River ecosystem that managers are most interested in evaluating with respect to stable 

discharge (see especially daily flow variation and nearshore habitat stability components of fig. 3).

These studies are as follows:

1. Nearshore ecology project (see appendix A for the complete project description)

2. Stock assessment of Grand Canyon native fish

3. Aquatic food base monitoring

4. Rainbow trout monitoring

5. Supplemental water-temperature data collection

6. Ecosystem modeling efforts

Projects 1 through 5 emphasize process-level measurements because previous studies focusing on static 

measurements, with the exception of HFEs, have had minimal success detecting impacts of shortduration flow experiments (that is, fall steady flow experiments of 2005, see Ralston and others, 2007).

Finally, under Project 6, ecosystem-modeling efforts will incorporate much of these data and allow for 

comparison with different flow scenarios. 
12
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Data Synthesis and Integration

We will use several lines of evidence to determine whether humpback chub benefit from stable flows in 

September and October because of the significance and importance of this issue. Over the next 5 years, 

there will be hourly variation in flow rates (related to diel variations in energy demand) during summer 

months (modified low fluctuating flows, MLFF, June through August) and lower, steady experimental 

flows during the fall (FSEF, September and October). 

The centerpiece of this data synthesis and integration is the nearshore ecology project (Project 1), which 

seeks to determine the use and relative importance of nearshore habitat to humpback chub and other 

fishes and addresses strategic science questions (SSQs) 1.1, 1.7, 4.2, 5.4, and 5.6. This project will 

quantify abundance, survival, habitat use, growth, and natal source of selected native and nonnative 

juvenile fish over two flow periods (summer MLFF and FSEF). This project will evaluate humpback 

chub response by measuring differences in static measurements (catch rate, abundance, and occupancy 

data) and process-level measurements (proxies for fish growth—otolith daily increments, RNA/DNA 

ratios) during fluctuating flows of July and August relative to these same measurements during stable 

discharge in September and October. These measurements will evaluate the short-term effect of 

interactions between flow, fish habitat selection, and growth, and will help inform analysis of humpback 

chub recruitment trends. Because of the importance of the nearshore ecology project, a complete project 

description is presented in appendix A.

If stock-assessment analysis (Project 2) finds that humpback chub recruitment trends from cohorts 

spawned during 2008 through 2012 are strongly positive, this may provide support that steady flows in 

September and October benefit humpback chub. During the remaining years of the experiment there are 

likely to be differences in annual volumes, tributary activity, and other factors that will affect humpback 

chub recruitment success and may confound data interpretation. As such, we propose that the same 

stable discharge occur the remaining years of the experiment to minimize the number of confounding 

factors that will complicate interpretation of these recruitment data. We are not evaluating interactions 

between native and nonnative fish (that is, competition and predation) because previous studies have 

evaluated these interactions (Yard and others, in press; Kennedy and others, U.S. Geological Survey, 

unpub. data, 2010), and we do not expect there to be a strong interaction between the proposed July–

October flows and competition or predation. Yard and others (in press) found turbidity had a strong 

influence on the degree of piscivory by rainbow trout, and tributary activity will have a far greater 

impact on turbidity than steady flows. Further, the nearshore ecology project pilot study attempted to 

quantify differences in predation risk among habitat types and across flows in August and September 

2008, but the results were inconclusive and the work was extremely time consuming. Thus, our 

humpback chub projects focus on studying the short-term interactions between flows, habitat use, and 

fish growth, and the long-term effect of these interactions on recruitment. 

Food base data (Project 3) will provide additional insights into mechanisms underlying any native fish 

response and seeks to determine whether and to what degree flow regimes impact the rates of primary 

production and/or invertebrate drift. Project 3 specifically relates to SSQ 3.5. The food base project 

focuses on process-level measurements at locations that are easy to access (Lees Ferry and Diamond 

Creek). Frequent measurement of these parameters, which is only possible at easy to access locations, 

will greatly increase the strength of our inferences with respect to flow. Work in Lees Ferry will be 

especially informative because tributary sediment and carbon inputs, which have a far greater impact on 
14

algae production and organic drift than do the proposed flows, are minimal in this reach. We are not 

proposing food base data collection in association with the nearshore ecology project because fieldwork

for food base was reduced starting in 2009 to complete sample processing, data analysis, and reporting.

Monitoring of rainbow trout populations (Project 4) will provide insights into the impacts of flow on 

fish and addresses, in part, SSQs 3.6, 4.2, 5.4, and 5.6. Work by Korman (Gloss and Coggins, 2005;

Korman and Campana, 2009) has provided the most conclusive evidence to date of the relationship 

between dam operations and fish vital rates (that is, growth and survival). Frequent and low-cost 

measurements, and the lack of tributary activity and other complicating factors, make it easier to 

identify the nature of flow/trout interactions in Lees Ferry relative to sites downstream. This work will 

be continued because understanding the rainbow trout response to experimental flows will help inform 

scientists about native fish response at downstream locations, where tributary activity will make it 

harder to separate the effects of flow.

We propose additional water temperature data collection (Project 5) because one of the primary 

mechanisms whereby stable flows might benefit native fish is by increasing nearshore warming. This 

project is not in GCMRC’s fiscal years 2010 to 2011 work plan and would require supplemental 

funding. These data will be critical for evaluating the degree of nearshore warming that occurs with 

stable flows across summer and fall and for informing analysis of native fish growth rates among habitat 

types.

Finally, we propose that ecosystem-modeling efforts (Project 6) underway in 2011 and 2012 will 

include data analysis methods and integration of physical and biological research data into models for 

response of aquatic ecosystem indicator variables to possible management actions. The goal of this

modeling effort is to provide screening of alternative adaptive management proposals for improving 

responses of performance indicators such as abundance of humpback chub. These models are likely to 

be developed in an Ecopath with Ecosim (EwE) platform in cooperation with Carl Walters (University 

of British Columbia) and Josh Korman (Ecometric Research, Inc.). We believe that this project provides 

a good framework for separating the effects of flow from other variables such as nonnative fish 

abundance, changes in food resources, or tributary hydrology. 

The ecosystem modeling effort will focus and integrate key SSQs and Science Advisor (SA) questions,

including indentifying linkages between food web changes and fish population changes in response to 

flow actions below Glen Canyon Dam:

SSQ 3-5 How is invertebrate flux affected by water quality (for example, temperature, nutrient 

concentrations, turbidity) and dam operations? 

SA 1 What are the most limiting factors to successful HBC adult recruitment in the mainstem: 

spawning success, predation on YoY and juveniles, habitat (water, temperature), pathogens, adult 

maturation, food availability, competition?

In addition, modeling efforts will address responses of native fish to mechanical removal of nonnative 

fish, fall steady flows, and backwaters created by experimental high flows: 
15

SSQ 1-2 Does a decrease in the abundance of rainbow trout and other cold- and warmwater 

nonnatives in Marble and eastern Grand Canyons result in an improvement in the recruitment rate of 

juvenile HBC to the adult population? 

SSQ 5-1 How do dam release temperatures, flows (average and fluctuating component), 

meteorology, canyon orientation and geometry, and reach morphology interact to determine 

mainstem and nearshore water temperatures throughout the CRE?

Development and testing of EwE models for food web interactions in the aquatic communities will 

occur in the Lees Ferry and Little Colorado reaches of Grand Canyon. This will involve continued 

development and fitting to historical abundance trend data of EwE models developed during FY2009 in 

cooperation with GCMRC scientists. Model parameter estimates will be refined using information 

provided by GCMRC cooperators, and formal parameter estimation procedures will be applied to 

estimate key production parameters by fitting the models to historical fish population trend data for 

1990 through 2009. 

The Grand Canyon Ecosystem Model (GCEM), developed in the late 1990s through collaboration 

between Ecometric Research and the GCMRC (see Walters and others, 2000), will be used to 

reconstruct historical changes in the Colorado River food base for native and nonnative fish associated 

with changes in diurnal flow regimes and turbidity conditions caused by tributary sediment inputs. The 

EwE food web models need to be fitted to historical abundance trend data, and that model fitting will be 

misleading unless the EwE models are provided with realistic time forcing data on past changes in 

primary and secondary (insect, amphipod) production owing to change in turbidity. The GCEM model 

will be run with historical tributary sediment inputs and refined estimates of regrowth rates of primary 

producers following periods of low productivity because of high turbidity to provide monthly estimates 

for 1990 through 2009 of food biomass likely to have been available to native and nonnative fish in 

reaches of Grand Canyon near and below the Little Colorado River. 

Ongoing collaboration with University of Florida and State University of New York at Syracuse will 

evaluate pilot study results from flannelmouth sucker (Catostomus latipinnis) otolith analyses and

employ geochemical signatures in water and native fish otoliths to infer natal origin, tributary habitat 

use, and migration patterns. The project will conduct pilot analyses of flannelmouth sucker otoliths and 

water samples collected in fiscal year 2008. Preliminary analyses of the water samples suggest 

promising uniqueness among Colorado River tributaries for describing patterns in flannelmouth sucker 

otoliths associated with ontogenetic shifts in tributary versus Colorado River occupancy. These analyses 

above will tie into the nearshore ecology project with the objective of troubleshooting field methods and 

data analysis procedures, with particular emphasis on assessment of changes in native fish dispersal and 

survival rates in relation to changes from fluctuating to fall steady flows.

Reporting and Synthesis

Results of individual projects will be presented in the various reports or publications that are listed in 

each project description. We will also produce an overall summary report to be delivered by January 

2013 that summarizes and synthesizes the results of all projects with respect to the FSEF. The cost to 

produce this report (workshop with relevant scientists and managers, 2 to 3 months salary for one GS-12

to GS-14 scientist to lead writing, and publication costs) is estimated to be about $50,000. 
16

Proposed Studies

Project 1—Nearshore Ecology (Bio 2.R15.09)

Start Date

October 2008

End Date

September 2012

Principal Investigators

W.E. Pine, III (University of Florida), J. Korman (Ecometric Research, Inc.), K. Limburg (State 

University of New York, Syracuse), M. Allen (University of Florida), T.K. Frazer (University of 

Florida), in cooperation with M.D. Yard, L.G. Coggins, Jr., and C.J. Walters (GCMRC)

Geographic Scope

The mainstem Colorado River in Grand Canyon below the mouth of the Little Colorado River.

Project Goals

The primary goal of the nearshore fish ecology study is to relate river flow variables and ecological 

attributes of nearshore habitats to better understand the relative importance of the biotic and abiotic 

attributes of these habitats to juvenile (less than 200 mm total length) native and nonnative fishes. 

The fall steady experimental flow (FSEF) related objectives that are addressed by this project are:

• Develop sampling approaches and analytical methods to use for determining abundance, density, or 

occurrence of native and nonnative fishes among different nearshore habitat types.

• Assess past and current data and integrate data across multiple sources and disciplines to determine 

small-bodied and juvenile fish nearshore habitat selection at local, geomorphic, and landscape 

scales. 

• Determine whether discharge regime (i.e., fluctuating vs. steady discharge) affects nearshore habitat 

selection, movement, growth, and survival of native and nonnative fishes.

Need for Project

The life history requirements of HBC in the mainstem Colorado River are not well understood. Habitat 

selection by HBC and whether those habitats are affected by dam operations are of particular interest to 

the GCDAMP and managers. To help meet these information needs, this project will determine whether 

native fish vital rates (i.e., survival and growth) differ among habitat types and/or flow regimes.

Findings from this project will provide information on native fish habitat requirements and guide future 

GCDAMP recommendations for the Department of the Interior to consider as management or 

experimental actions.
17

Strategic Science Questions

Primary SSQs addressed:

SSQ 1-7 Which tributary and mainstem habitats are most important to native fishes and how can 

these habitats best be made useable and maintained?

SSQ 4-2 How important are backwaters and vegetated shoreline habitats to the overall growth and 

survival of YoY and juvenile native fish? Does the long-term benefit of increasing these habitats 

outweigh short-term potential costs (displacement and possibly mortality of young humpback chub) 

associated with high flows?

SSQ 5-4 What is the relative importance of increased water temperature, shoreline stability, and 

food availability on the survival and growth of YoY and juvenile native fish?

SSQ 5-6 Do the potential benefits of improved rearing habitat (warmer, more stable, more 

backwater and vegetated shorelines, more food) outweigh negative impacts due to increases in 

nonnative fish abundance?

Information Needs Addressed

RIN 2.1.3 What is the relationship between size of HBC and mortality in the LCR and the 

mainstem? What are the sources of mortality (that is, predation, cannibalism, other) in the LCR and 

the mainstem?

RIN 2.1.4 What habitats enhance recruitment of native fish in the LCR and mainstem? What are the 

physical and biological characteristics of those habitats?

RIN 2.4.3 To what degree, which species, and where in the system are exotic fish a detriment to the 

existence of native fish through predation or competition?

RIN 4.2.6 To what extent are RBT below the Paria River predators of native fish, primarily HBC?

At what size do they become predators of native fish, especially HBC, that is, how do the trophic 

interactions between RBT and native fish change with size of fish?

RIN 2.4.4 What are the target population levels, body size and age structure for nonnative fish in 

the Colorado River ecosystem that limit their levels to those commensurate with the viability of 

native fish populations?

RIN 12.9.1 What is the impact on downstream resources of short-term increases to maximum flow, 

daily fluctuations, and downramp limits?

RIN 2.6.6 How is the rate of mortality for flannelmouth sucker, bluehead sucker, and speckled dace 

in the Colorado River ecosystem related to individual body size? What are the sources of mortality 

for flannelmouth sucker, bluehead sucker, and speckled dace in the Colorado River ecosystem?

RIN 4.2.5 To what extent is there overlap in the Colorado River ecosystem below the Paria River 

of RBT habitat and native fish habitat?
18

RIN 7.4.1 What is the desired range of seasonal and annual flow dynamics associated with 

powerplant operations, BHBFs, and habitat maintenance flows, or other flows that meet GCDAMP 

goals and objectives?

EIN 2.1.1 How does the abundance and distribution of all size classes of HBC in the LCR and 

mainstem change in response to an experiment performed under the Record of Decision, 

unanticipated event, or other management action?

EIN 2.1.2 How does the year class strength of HBC (51 – 150 mm) in the LCR and mainstem 

change in response to an experiment performed under the Record of Decision, unanticipated event, 

or other management action?

EIN 2.4.1 How does the abundance and distribution of nonnative predatory fish species and their 

impacts on native fish species in the Colorado River ecosystem change in response to an experiment 

performed under the Record of Decision, unanticipated event, or other management action?

EIN 2.6.1 How does the abundance, distribution, recruitment and mortality of flannelmouth sucker, 

bluehead sucker and speckled dace populations in the Colorado River ecosystem change in response 

to an experiment performed under the Record of Decision, unanticipated event, or other 

management action?

SIN 8.5.4 What is the role of turbidity and how can it be managed to achieve biological objectives?

Methods and Tasks

The nearshore ecology study will incorporate findings from ongoing studies and develop new sampling 

and analytical approaches that examine the effects of the March 2008 high-flow experiment on 

nearshore habitats and address the effects of modified low fluctuating flows (MLFF), including 

September–October fall steady experimental flows (FSEF), on juvenile HBC and other native fishes. 

The specific methods that the cooperator will use to address these issues are:

1. Investigate sampling methods to estimate fish habitat use, growth, and survival. Estimation of 

juvenile abundance, survival rate, growth rate, and habitat use is fundamental to resolving 

uncertainties in the conceptual model and the two key research questions outlined and identified 

above. We propose sampling trips in late July and late August to characterize abundance, habitat 

use, growth, and survival rate of juvenile fish over the summer under MLFF flow fluctuations. 

These trips would be followed by sampling trips in early September and late October to 

characterize juvenile fish responses during the MLFF-FSEF transition, and FSEF period.

Differences in abundance in each habitat type, between each sampling trips would be used to 

estimate habitat specific, reach-wide survival rates across flow events. We propose two basic 

sampling approaches for estimating these characteristics: (1) reach-wide abundance estimation 

(RWAE); and (2) robust-design mark-recapture (RDMR) at replicate sites.

2. Site selection. We will use existing data and models from the GCMRC physical science program 

to quantify habitat availability over the study reach that contains the RDMR sites, habitat 

availability within the sites, and how habitat changes with flow. The existing GCMRC shoreline 
19

GIS database and other surveys will be used to stratify habitat into classes such as talus slopes, 

open sand bars, vegetated sand bars, cobble bars, and backwaters. We hypothesize that unstable 

habitat types (sand bar-mediated backwaters) will be used only minimally during the summerunsteady flow period, but that use of these habitats will increase during the fall-steady period 

when flows are stabilized. If this difference in habitat use were ecologically important, we would 

also predict increase in growth and survival during the fall-steady flow period relative to the 

summer because habitats may offer more favorable conditions, such as food and higher 

temperature.

3. Effects of Fall Steady Flows on Native Fish Habitat Use. Any mark-recapture approach to 

estimating abundance and density depends on recapturing sufficient numbers of marked 

individuals to draw inferences on the parameters of interest. Closed population models generally 

have fewer parameters (and assumptions) than open models and are thus better able to estimate 

parameters of interest (capture probability and abundance) when recaptures are low. We will 

evaluate the closure assumption in our mark-recapture experiments using methods similar to 

Korman and others (2009). Additionally, recaptures of fish marked on previous trips will 

provide useful information on growth and movement (e.g., movement into backwaters during 

periods of steady flow) between sampling trips and associated flow conditions. The nearshore 

ecology project pilot sampling data from 2008 should provide some information on closure and 

also provide information on capture probability which is necessary to fully assess how violation 

of the closure assumption biases abundance estimates. This project will evaluate occupancy 

models (MacKenzie and others, 2005) and sonic tags to support habitat use assessment. This 

project will utilize otoliths (inner ear bones) from native fishes, such as flannelmouth sucker and 

humpback chub to investigate habitat use and origin of fish by using microchemistry to identify 

unique isotopes. Otoliths may also prove useful for determining growth and survival rates of 

humpback chub and other fishes.

Links/Relationships to Other Projects

This project utilizes habitat information developed largely by the GCMRC Physical Sciences and 

Modeling and the Data Acquisition, Storage, and Analysis (DASA) programs. The results of this project 

will help evaluate responses of small size classes of fish to various dam release flows, and so will 

provide some of the information needed to assess the status and trends of humpback chub in the

mainstem Colorado River.

Logistics 

This project will utilize four trips, one each in July, August, September, and October, for three years

(2009-2011), subject to permit approval. All four trips are to be motor supported. The first three are 

scheduled to launch in the motor season, but the October trip will require authority from Grand Canyon 

National Park to use motors during the non-motor season. Sampling in October supports investigation of 

the possible effects of steady flows on fish habitat use and so authority to conduct the trip has been 

requested.

Products/Reports

Annual reports of project results will be delivered in December 15 of each year of the fieldwork, 2009-

2011. A final, synthetic report will be delivered by September 2012.
20

Budget

FY 2010: $552,825

FY 2011: $556,911
21

Project 2—Stock Assessment of Grand Canyon Native Fish (BIO 2.R7.10–11)

Start Date 

2007

End Date 

Ongoing

Principal Investigators

Fisheries Biologist, U.S. Geological Survey, Grand Canyon Monitoring and Research Center, and C.J. 

Walters, University of British Columbia

Geographic Scope

Colorado and Little Colorado Rivers in Glen, Marble, and Grand Canyons

Project Goals

This project will provide annual updates of size composition and capture rates of humpback chub 

(HBC) and other Grand Canyon fish to the Glen Canyon Dam Adaptive Management Program 

(GCDAMP) and other managers. Reporting will include retrospective time series to allow for 

comparison with previous years’ data. The assembled HBC data from the Grand Canyon fish 

monitoring projects will be incorporated into updates of the Age-Structured Mark-Recapture (ASMR) 

model every 3 years (the next ASMR update will be published in 2012).

This project will lead the analyses of existing fish capture information recommended by the 2009 

Protocol Evaluation Panel (PEP) for Grand Canyon Fishes. The goal of these analyses is to evaluate 

whether the fish monitoring project changes recommended by the PEP, especially to reduce some 

efforts and increase others, are consistent with the available data.

This project will seek to develop and implement methods for making the HBC database available 

electronically. Data serving must be done in a manner consistent with USGS Fundamental Science 

Practices.

Need for Project 

Native fish populations in Grand Canyon are key resources of concern influencing decisions on both the 

operation of Glen Canyon Dam and other non-flow actions. To inform these decisions, it is imperative 

that accurate and timely information on the status of native fish populations, particularly the endangered 

HBC, be available to managers.

Several adaptive experimental management actions are being contemplated to better understand the 

mechanisms controlling the population dynamics of native fish and to identify policies that are

consistent with management goals. The stock assessments generated from this project will support 

assessment of implemented experimental actions. This information is therefore crucial to

• inform the program as to attainment of identified goals, 
22

• provide baseline status and trend information to be used as a backdrop to understand the 

mechanisms controlling native fish population dynamics, and 

• evaluate the efficacy of particular management policies in attaining program goals. Finally, 

results from this project are potentially useful in assessing changes to Federal Endangered 

Species Act listing status of HBC in the Colorado River.

Strategic Science Questions

Primary SSQ addressed:

SSQ 1-1 To what extent are adult populations of native fish controlled by production of young fish 

from tributaries, spawning and incubation in the mainstem, survival of YoY and juvenile stages in 

the mainstem, or by changes in growth and maturation in the adult population as influenced by 

mainstem conditions?

Additional SSQ addressed:

SSQ 1-8 How can native and nonnative fishes best be monitored while minimizing impacts from 

capture and handling or sampling?

The Adaptive Management Program Science Advisors have articulated the following science question, 

which is partially addressed by this project:

SA 1 What are the most limiting factors to successful humpback chub adult recruitment in the 

mainstem: spawning success, predation on YoY and juveniles, habitat (water, temperature), 

pathogens, adult maturation, food availability, competition?

Information Needs

RIN 2.2.8 What combination of dam release patterns and nonnative fish control facilitates 

successful spawning and recruitment of humpback chub in the Colorado River ecosystem?

RIN 2.4.2 Determine if suppression of nonnative predators and competitors increases native fish 

populations.

Methods and Tasks

To provide HBC status and trend information, the Grand Canyon Monitoring and Research Center 

(GCMRC) mark-recapture database will be annually updated with the most recent data collected during 

routine monitoring efforts including mainstem electrofishing and netting and the Little Colorado River 

monitoring efforts (see GCMRC/AMP 2011-12 work plan for additional details). Following this update, 

the HBC mark-recapture database will be reanalyzed using (where appropriate) both open and closed 

mark-recapture-based abundance estimators to provide the most current information on HBC status and 

trends. In particular, the ASMR models (Coggins and others, 2006a and 2006b; Coggins, 2007; Coggins 

and Walters, 2009) will be used to determine trends in HBC abundance and recruitment over multiyear 

time scales. Over annual time scales, this project will assemble and deliver summaries of annual catch 

rate and size-class composition of HBC and other species from the Little Colorado River (LCR) and 
23

mainstem to the GCDAMP and managers. It will also deliver other species metrics, likely to include 

results of closed population estimates and juvenile abundance from the LCR.

This project was reviewed by the 2009 PEP for Grand Canyon Fishes. The panel recommended that 

because of the inherent variability in the ASMR (for example, estimates of growth and mortality rates 

limit its ability to detect fine scale changes), preparing annual updates of the model was an inefficient 

use of personnel time, especially for the long-lived HBC. The PEP also observed that the ASMR has 

only limited sensitivity to detect small annual population changes, and that it requires tremendous 

personnel and computer resources to generate. Based on these observations, the PEP recommended that 

the ASMR be updated every 3 to 5 years. Because the GCMRC is planning to prepare the next State of 

the Colorado River Ecosystem in Grand Canyon (SCORE) report in FY2011, the GCMRC will 

accelerate this recommendation for the next iteration and include an update of ASMR in the FY2011 

SCORE report. In the future, the GCMRC intends the next iteration of the ASMR following the FY2011 

update will be scheduled for FY2014, consistent with the PEP recommendation. Updates will include 

not only estimates of HBC abundance and recruitment from ASMR, but also summaries of annual 

catch-rate and size composition estimates from LCR hoop net sampling, summaries of annual catch-rate 

and size composition estimates from mainstem Colorado River hoop and trammel net sampling, and 

closed population abundance estimates of HBC adults and rearing juveniles in the LCR as these data are 

available. Finally, the applicability of similar techniques to those described above will be evaluated to 

assess stocks of flannelmouth sucker and bluehead sucker.

The GCMRC fisheries biologist will work with agency and cooperative personnel to evaluate the utility 

of the remote passive integrated transponder (PIT) tag antenna project to provide information useful in 

determining movement rates of HBC into and out of the LCR, empirical capture probability estimates of 

LCR hoop het sampling, and PIT tag recapture information for inclusion in ASMR.

The 2009 PEP for Grand Canyon Fishes made a series of recommendations that direct shifting 

monitoring efforts to decrease efforts in the LCR and increase efforts in the mainstem of the Colorado 

River, subject to an analysis of the existing data to see if their recommendations are consistent with the 

data. The GCMRC fisheries biologist working on this project will be responsible for assembling and/or 

conducting the analyses necessary to evaluate the recommendations. AZGFD and USFWS personnel to 

support this effort will also conduct data analyses of individual projects. If the recommendations are 

found to be warranted, the shift to different monitoring will be initiated in FY2011; these projects are 

described elsewhere in Goal 2 of this work plan. If the data analyses are not found to support the 

recommendations, projects will revert to the work plans described for FY2010. The full analysis of all 

the data will not be required in FY2011, so there will be some shifting of the fisheries biologist time to 

other projects.

Links/Relationships to Other Projects

The status and trend of the Grand Canyon HBC population are two of the key metrics utilized in 

GCDAMP to evaluate the success of the GCDAMP and actions undertaken under the sponsorship of the 

GCDAMP. Therefore, annually updating the HBC catch rates and size-class composition and updating 

ASMR model runs every 3 years is related to many other GCDAMP work plan elements, especially 

experimental actions such as the March 2008 High Flow Experiment (described in a separate science 

plan) or removal of nonnative fish. The annual HBC population status will be important to projects 

studying biotic and abiotic aspects of the systemincluding the aquatic food base, riparian vegetation 
24

mapping, and nearshore ecology projectsbecause changes in the parameters measured by these 

projects can be compared to trends in the HBC population to search for relevant correlations. 

Logistics 

There are no logistical needs for this project.

Products/Reports 

• This project will be the lead for retrospective analysis of the fish catch rate data, especially for 

HBC. The analyses will also be supported by AZGFD and USFWS personnel as part of the 

reporting for their respective projects. Under this project GCMRC will convene an annual fish 

meeting to review these analyses and see if the 2009 PEP recommendations are consistent with 

project changes in FY2011. 

• The next scheduled update of the ASMR model will be in FY2011 to coincide with the next 

SCORE report, with the next update to occur in FY2014.

• Annual reports of the status and trends of HBC will be delivered to the GCDAMP committees 

by December 15 of each year. These updates will include summaries of annual catch-rate and 

size composition estimates from LCR hoop net sampling, summaries of annual catch-rate and 

size composition estimates from mainstem Colorado River hoop and trammel net sampling, and 

closed population abundance estimates of HBC adults and rearing juveniles in the LCR as these 

data are available.

• This project will pursue making the HBC data base information available electronically. This 

will be done in a manner consistent with USGS Fundamental Science Practices.

Budget

FY 2010: $110,877

FY 2011: $103,776
25

Project 3—Aquatic Food Base (Bio 1.R1 and 4)

Start Date

2006

End Date

2010

Principal Investigators

T.A. Kennedy (GCMRC), R. Hall (University of Wyoming), E. Rosi-Marshall (Cary Institute of 

Ecosystem Studies), and C. Baxter (Idaho State University)

Geographic Scope

Systemwide, from Glen Canyon Dam to Diamond Creek (RM 225)

Project Goals

The aquatic food base project will answer the following fall steady flow related questions:

1. Does flow regime affect rates of primary production or organic and invertebrate drift?

2. Does flow regime affect the residence time of water in backwater habitats?

Need for Project

After habitat, food is the resource that most often limits the distribution or abundance of animal 

populations (Krebs, 1994). Algae and aquatic invertebrates are two of the most common food types 

consumed by native and nonnative fish in the Colorado River (McKinney and Speas, 2001; Valdez and 

Ryel, 1995). Preliminary data indicate rates of algae drift are positively related to discharge, at least in 

Lees Ferry. Further, aquatic invertebrates in the Colorado River actually use filamentous algae as habitat 

(Shannon and others, 1994), so rates of invertebrate drift may also be positively related to discharge. If 

steady flows of low discharge decrease algae and invertebrate drift, then this could lead to an 

accumulation of algae and invertebrates on the river bottom. However, algae and invertebrate biomass 

data are extremely variable (Stevens and others, 1997), so it is unlikely that any observed changes 

would be statistically significant or could be ascribed to the short duration fall steady flows. The food

base project has developed methods for quantifying algae production in the Colorado River using diel 

changes in dissolved oxygen concentration. Further, we have refined the invertebrate drift collection and 

sampling processing methods developed by McKinney and others (1999). Both of these process-based 

metrics (algae production, grams O2·m-2·d-1; invertebrate drift load, g AFDM·s

-1

) should be more 

sensitive to the subtle changes that are likely with fall steady flows compared to static measures of algae 

and invertebrate biomass (g AFDM·m-2).

The degree of nearshore warming appears to be related to the degree of isolation of those habitats from 

the mainstem river. Water temperature data indicate residence time of water in nearshore environments 

is greater when discharge is stable relative to fluctuating. However, the magnitude of this increase in 

residence time is uncertain. Water residence time in backwaters may also influence the productivity of 
26

these habitats because high residence time might allow for a water column food web to develop and 

might also allow for benthic algae and invertebrates to accumulate. 

Strategic Science Questions

Primary SSQ addressed:

SSQ 3-5. How is invertebrate flux affected by water quality (for example, temperature, nutrient 

concentrations, turbidity) and dam operations? 

Information Needs Addressed

CMIN 1.5.1 Determine and track the composition and biomass of drift in the Colorado River in 

conjunction with measurements of flow, nutrients, water temperature, and light regime. 

EIN 1.1.1 How does primary productivity in the reach between Glen Canyon Dam and the Paria 

River change in response to an experiment performed under the Record of Decision, unanticipated 

event, or other management action? 

Methods and Tasks

Primary production is already being measured continuously in Lees Ferry and at Diamond Creek (RM 0 

to 226). Primary production data collected during September and October 2008-2012 will be compared 

with the months before and after to determine whether steady flows affect rates of in-stream primary 

production. Organic and invertebrate drift is measured monthly at Lees Ferry. To determine whether 

steady flows affect drift rates we will compare data collected in September and October 2008-2012 with 

the months before and after. As part of the 1D funding, the food base project began intensive study of 

backwaters on their April 2008 river trip. Data being collected in backwaters includes primary and 

invertebrate production and dye-tracer studies to determine water residence time. Because data 

collection in backwaters began in April 2008, we do not have data on biological parameters from 

previous years to compare with 2008 fall steady flows data. However, water residence time will only be 

affected by the morphology of backwaters and the flow regime, but not season. Thus, we can determine 

whether steady flows affect water residence time in backwaters by comparing data collected during 

other flow regimes (i.e., April and June 2008 and January 2009). The food base project will launch a 

river trip in September 2009 to collect additional samples and water residence time measurements 

during the steady flow experiment.

Links/Relationships to Other Projects

Data from the food base project can be used to inform results of both rainbow trout monitoring and 

nearshore ecology projects. Although food base data collection will be focused on the Lees Ferry reach 

with less intensive data collection at Diamond Creek, our results should still be informative to the 

nearshore ecology project that is focused on the Little Colorado River confluence. Algae production and 

invertebrate drift are much higher in Lees Ferry than downstream reaches. In fact, algae production at 

downstream locations is essentially zero during times of high turbidity, and invertebrate drift 

measurements at Diamond Creek were largely discontinued because of extremely low invertebrate 

loads. Given the effects of the fall steady flows on food base components are likely to be subtle, we feel 

it is prudent to concentrate our efforts on the Lees Ferry reach because the higher food base abundance 

there makes it more likely that we will be able to detect treatment impacts. Even though food web 
27

structure in Lees Ferry is considerably different than around the Little Colorado River confluence, algae 

and invertebrates are important food items consumed by fish at both locations. Therefore, we feel 

conclusions and findings from our work in Lees Ferry can be used to inform results of the nearshore

ecology study. In FY2011 the food base project will be implementing new monitoring protocols. If our 

work in Lees Ferry indicates fall steady flows are having a significant impact on the food base, we 

would expedite the implementation of these monitoring protocols around the Little Colorado River 

confluence.

Logistics 

Logistics will be needed for monthly drift sampling at Lees Ferry and monthly maintenance of water 

quality sondes at Lees Ferry and Diamond Creek, as well as one river trip to study backwaters in 

September 2009. 

Products/Reports

Publications

At least two peer-reviews journal articles that describe whether fall steady flows affected the food base 

will be produced as a result of this project. Tentative subjects for these publications include:

• Longitudinal and seasonal variation in algae production in the Colorado River

• Does flow regime affect rates of invertebrate drift in the Colorado River?

Reports

A brief report summarizing our findings with respect to the fall steady flows experiment will also be 

delivered at the conclusion of the project in September 2010.

Budget

Aquatic Food base (Bio 1.R1) FY10: $440,112

Aquatic Food base (Bio 1.R1) FY11: $207,200

Aquatic Food base Drift (Bio 1.R4) FY10: $56,260

Aquatic Food base Drift (Bio 1.R4) FY11: $0
28

Project 4—Monitoring Lees Ferry Fishes (Bio 4.M1.09)

Start Date

Ongoing

End Date

Ongoing

Principal Investigators

A.S. Makinster (Arizona Game and Fish Department), in cooperation with Josh Korman (Ecometric 

Research, Inc.) and GCMRC

Geographic Scope

Colorado River from Glen Canyon Dam to Lees Ferry

Project Goals

The fall steady flow related goals of this project are:

• Monitor the rainbow trout (RBT) recreational fishery between Glen Canyon Dam and the Paria 

River

• Monitor RBT redds and early life stages to support assessment of experimental flow releases 

from Glen Canyon Dam

This project is designed to monitor the status and population of this RBT fishery in response to 

management actions, and to determine how abundance, reproduction, survival, and growth are 

influenced by operations of Glen Canyon Dam, including fall steady flows. Trend analysis using indices 

of abundance can be used to determine whether changes in dam operations are having population-level 

effects on the fishery. 

The 2009 Protocol Evaluation Panel (PEP) reviewed this project for Grand Canyon Fishes. The panel 

recommended that it was not cost effective or necessary to conduct multiple population monitoring and 

assessment trips each year to assess the Lees Ferry rainbow trout fishery. Rather, the panel 

recommended a single electrofishing trip at the randomized sites each year to physically observe the 

adult population and perhaps to tag fish if that was desired for more data collection. Analysis of this 

long-term dataset will be completed in 2009 to determine impacts of the recommended reduction in 

effort and the ability to meet management objectives.

The 2009 PEP did not recommend maintaining the monitoring of early life stages of rainbow trout that 

has been conducted for 5 of the last 7 years. However, this monitoring technique may be useful for 

studying the response of the fishery to experimental dam releases, and so it should be maintained 

through 2012 in response to the fall steady flow regime. 
29

Need for Project

The Arizona Game and Fish Department (AZGFD) has managed the Lees Ferry recreational fishery 

since 1964. Lees Ferry serves as a popular destination fishery for international and national anglers. As 

such, it provides significant contributions to the Marble Canyon business community. The fishery is 

regulated by biotic and abiotic mechanisms that may in turn be affected by the operations of GCD. The 

monitoring of basic fish population elements, including abundance and distribution of native and 

nonnative fishes, provides the information necessary to assess the status of these resources and inform 

the Glen Canyon Dam Adaptive Management Program (GCDAMP).

Strategic Science Questions

Primary fall steady flow related SSQs addressed:

SSQ 3-6 What GCD operations (ramping rates, daily flow range, etc.) maximize trout fishing 

opportunities and catchability? 

Methods and Tasks

Summary of annual monitoring/sampling:

• Two standardized random sampling surveys

• Two early life history trips (one or both may extend below the Paria River at RM 1)

• Creel surveys, funded by AZGFD

In monitoring, RBT are sampled using electrofishing to estimate biological parameters and to assess the 

status and trends of the fishery. This sampling design was developed to ensure managers have a 

monitoring program with the temporal “power” to detect population trends without biases in site 

selection, as well as a means to precisely estimate status of the rainbow trout population. Electrofishing 

provides information on size composition, relative abundance (catch per minute as an index of 

population size), condition (length-weight relationships), and disease. Electrofishing prior to 2010 

occurred 3 times per year with sampling effort stratified over 27 random and 9 fixed sites. Present 

sampling design can detect a 6–10% linear change in abundance over a 5-year period. Work is currently 

underway to assess the statistical power of intra- and inter-annual comparisons.

Over the last 7 years a contractor, Ecometric Research, Inc., has been conducting surveys of RBT redds 

and early life stages of RBT in the Lees Ferry reach. These studies have been useful, especially in the 

analysis of dam operation impact to RBT. Similar studies may not be incorporated into long-term 

monitoring, but in light of the continued experimental operations of Glen Canyon Dam through 2012 

the work is to be maintained, at least for FY 2010-11. In FY 2010-11 the AZGFD will work 

cooperatively with Ecometric, Inc. to transfer knowledge regarding the techniques and data analysis 

from the contractor to the agency, anticipating that AZGFD will be completely responsible for any early 

life stage monitoring that may be necessary in FY 2012 and beyond.

Links/Relationships to Other Projects

This project will help inform data on fish and habitat collected at downstream locations. Work by 

Korman (Gloss and Coggins, 2005; Korman and Campana, 2009) has provided the most conclusive 

evidence to date of the relationship between dam operations and fish vital rates (i.e., survival). Frequent 
30

and low-cost measurements, and the lack of tributary activity and other complicating factors, makes it 

easier to identify the nature of flow—fish interactions in Lees Ferry relative to downstream work. We 

will continue this work because the rainbow trout response to experimental flows will help inform 

native fish collected at downstream locations, where tributary activity will make it harder to separate the 

effects of flow.

Logistics 

This project will field five trips annually:

• Two standardized random sampling surveys

• Two early life history trips (one or both may extend below the Paria River)

• One nonnative survey (may extend below the Paria River)

All trips are motor supported, launching from and returning to Lees Ferry just upstream of the mouth of 

the Paria River.

Products/Reports

Annual reporting of the results of all monitoring efforts will be delivered to GCMRC by December 15 

of each year. AZGFD and GCMRC will be working together to develop additional peer-reviewed 

products documenting the status and trends of the Lees Ferry RBT fishery in FY 2010-11. These reports 

will include sections describing their findings with respect to impacts of fall steady flows on rainbow 

trout. AZGFD will be responsible for delivering analysis of the data from this project to fish cooperator 

meetings in calendar 2009 and beyond.

Budget

FY 2010: $207,858

FY 2011: $215,500
31

Project 5—Supplemental Water Temperature Data Collection 

Need for Project

There is uncertainty regarding the degree of nearshore warming that will occur during the FSEF.

Korman and others (2006) found that the amount of nearshore warming increased slightly in September 

relative to August, despite cooler air temperatures, because discharge volume and daily fluctuations 

were lower in September. No nearshore warming occurred in October because average daily air 

temperatures were comparable to water temperatures. However, temporal changes in nearshore warming 

may differ during steady flows relative to what Korman and others (2006) observed during fluctuating 

flows. The Physical Sciences and Modeling Program is developing a 2-D model that can be used to 

predict water temperatures in nearshore environments. But this model cannot be parameterized for 

steady flows in the fall because data are lacking. Detailed water temperature data will also be critical for 

interpreting data from the nearshore ecology project.

If steady flows in September and October 2008 through 2012 do not strongly benefit humpback chub, it 

may be because nearshore warming is minimal at this time of year. If this is the case, we suspect 

managers would consider evaluating steady flows during the summer months when there is greater 

potential for nearshore warming (Grand Canyon Monitoring and Research Center, 2008). Thermal infrared imagery collected in June 2000 during the LSSF provide rigorous quantitative data on the degree of 

nearshore warming that can occur in June during steady flows of 8000 cfs. However, because these 

same data have not been collected during fluctuating operations at the same time of year, it is difficult to 

put these data into context. That is, it is unclear whether nearshore habitat with warm water temperature 

is gained during steady flows relative to fluctuating flows and if so, how much?

Scope of Work 1

We propose deploying arrays of water temperature thermistors below the Little Colorado River 

confluence (RM 61) from July 2010 through October 2010 in at least one of each of the different 

shoreline habitat types the nearshore ecology project is evaluating. In addition, we will deploy 

thermistors to monitor mainstem temperature at the upstream and downstream boundaries of the 

nearshore ecology study reach. These data would be used to determine the degree of nearshore warming 

that occurs during steady flows in September and October and also to parameterize and calibrate the 2-

dimensional temperature model that the physical sciences group is developing. Deployment and 

maintenance of thermistors would be done in collaboration with the nearshore ecology project, as they 

will also be a primary user of these data. Thermistors would be deployed on the July 2010 nearshore

ecology trip and retrieved on the October 2010 trip. 

This project will also include analysis and reporting on mainstem and nearshore temperature data that 

were collected at up to 20 different locations from 2007 to 2010. 

Budget

Biological Science Technician (GS-7-temporary): $20,000
32

Justification

Previous experience has demonstrated that maintaining thermistors during diurnal fluctuating flow dam 

operations requires a technician be onsite to visit the thermistor arrays at study sites every day.

Deploying and maintaining thermistor arrays is outside the scope of work for the nearshore ecology 

project. Therefore, we propose hiring a 180-day temporary technician who would go on the nearshore

ecology trips and deploy and maintain thermistors.

Scope of Work 2

We propose collecting thermal infrared imagery in June 2010 during fluctuating operations, so that 

managers can evaluate the increase in nearshore warming that occurs during summer steady flows. We 

also propose collecting these same data in late August during fluctuating operations and again in early 

September during steady operations to evaluate the magnitude of nearshore warming that occurs with 

steady flows in the fall. These data will help inform results of FSEF and also help inform discussions 

about future experiments that might include steady flows in the summer.

Budget

Acquiring thermal infra-red imagery for RM 30 to 72, the same reach that was covered in 2000, would 

cost approximately $35,000 per flight. Two weeks of Phil Davis’ time would be required to process 

imagery from each flight (~$6,000/2-week pay period). 
33

Project 6——Support and Enhancement of Ecosystem Modeling Efforts

(R12.P1.10)

Need for Project

While a variety of experimental management policies have been implemented in recent years, analysis 

and communication of results and responses of indicators to policies have not been completed. More 

complete analysis and subsequent communication of the results of analysis (including modeling) will 

allow more effective selection of further experimental tests. For example, the LSSF flow experiment of 

summer 2000 was not fully evaluated until 2008, and likewise there have not been definitive reviews of 

all high-flow experimental results (1996 to 2008) or the effects of mechanical removal of nonnative fish, 

although the synthesis of flow tests and nonnative control analyses are now forthcoming. Such analyses 

have been hampered by confounding of multiple factors in causing changes (for example, temperature 

changes have made it hard to interpret fish responses to mechanical removal). Modeling tools provided 

by the Senior Ecologist (Walters) can help to at least clarify alternative hypotheses about the possible 

roles and relative importance of the factors.

Additional advancement of the flow and sediment elements of the existing GCEM is also planned as an 

additional element of the new Integrated Flow, Sediment, and Temperature Modeling research project 

(Wright and others in collaboration with Korman and Walters) as a further means of assessing fine 

sediment dynamics associated with various stakeholder planning needs and associated tasks tied to 

developing desired future conditions for GCDAMP goals.

Strategic Science Questions 

The ecological modeling efforts will be directed at addressing priority AMWG questions, SSQs, and 

additional science questions (SAs) - provided by the Science Advisors (SA) in the integrated modeling 

efforts, as follows:

Abundance trends of rainbow trout in the Lees Ferry reach:

SSQ 1-4 Can long-term decreases in abundance of rainbow trout in Marble and eastern Grand 

Canyons be sustained with a reduced level of effort of mechanical removal or will recolonization 

from tributaries and from downstream and upstream of the removal reach require that mechanical 

removal be an ongoing management action? 

This question also applies to future removal programs targeting other nonnative species. 

SSQ 1-8 How can native and nonnative fishes best be monitored while minimizing impacts from 

capture and handling or sampling?

Abundance trends in native fish below the Lees Ferry reach: 

SSQ 1-1 To what extent are adult populations of native fish controlled by production of young fish 

from tributaries, spawning and incubation in the mainstem, survival of young-of-year and juvenile 

stages in the mainstem, or by changes in growth and maturation in the adult population as influenced 

by mainstem conditions? 
34

SA 1 What are the most limiting factors to successful humpback chub adult recruitment in the 

mainstem: spawning success, predation on young of year and juveniles, habitat (water, temperature), 

pathogens, adult maturation, food availability, competition? 

SA 2 What are the most probably positive and negative impacts of warming the Colorado River on 

humpback chub adults and juveniles?]

Linkages between (productivity) food web changes and fish population changes:

SSQ 3-5 How is invertebrate flux affected by water quality (for example, temperature, nutrient 

concentrations, turbidity) and dam operations? 

SA 1 What are the most limiting factors to successful HBC adult recruitment in the mainstem: 

spawning success, predation on YoY and juveniles, habitat (water, temperature), pathogens, adult 

maturation, food availability, competition?

Responses of native fish to mechanical removal of nonnative fish, fall steady flows, and backwaters

created by experimental high flows: 

SSQ 1-2 Does a decrease in the abundance of rainbow trout and other cold- and warmwater 

nonnatives in Marble and eastern Grand Canyons result in an improvement in the recruitment rate of 

juvenile HBC to the adult population? 

SSQ 5-1 How do dam release temperatures, flows (average and fluctuating component), 

meteorology, canyon orientation and geometry, and reach morphology interact to determine 

mainstem and nearshore water temperatures throughout the CRE?

Using the new shifting rating curve method for routing suspended sand through the CRE, the project 

will produced advanced simulations for flow operations at Glen Canyon Dam and fate of tributary 

supplied sand inputs:

SSQ 4-1 Is there a “Flow Only” operation (that is, a strategy for dam releases, including managing 

tributary inputs with BHBFs, without sediment augmentation) that will rebuild and maintain sandbar 

habitats over decadal timescales?

Note: Results from element 5, will integrate suspended-sediment simulations with aquatic/fish

simulations within the Ecopath with Ecosim (EwE) modeling being developed by Walters and others.

Links/Relationships to Other Projects

This project will uses data from all studies that collect information on the aquatic biota of Glen, Marble, 

and Grand Canyons, including the aquatic food web, HBC monitoring, Lees Ferry trout monitoring, 

mechanical removal, nonnative fish monitoring, and the nearshore ecology project. The main benefits to 

the projects listed will be to provide novel analyses of data and methods for linking project results into 

overall conceptual and quantitative models for response of the Colorado River aquatic ecosystem to 

management changes. The flow and sediment modeling elements of this project are linked most closely 

to the Integrated Flow, Sediment, and Temperature Modeling project.
35

Products/Reports 

FY2010

• ChubIBM.exe computer program, narrative review for GCMRC fish scientists on probable 

biases and precision of future population estimates (Walters and others).

• Spreadsheets for use by GCMRC scientists in checking ASMR results from existing assessment 

programs, stock assessment report providing abundance trend estimates for sucker species 

(Walters and others).

• Revised flow and suspended-sediment submodel of the GCEM, including the recently innovated 

“shifting rating curve” for sand transport that will be reported by Wright and others (manuscript 

currently in preparation). This work is being integrated with ongoing modeling research funded 

in FY2010 (Wright and Korman).

• Ecopath with Ecosim Access database (mdb) with improved models and historical forcing data, 

including forcing time series data from updated GCEM, narrative report sections for use by 

GCMRC scientists in preparation of peer-reviewed papers on findings from the EwE models and 

GCEM/EwE model linkage (Walters and others).

• Senior Ecologist (Walters) will lead a science workshop for GCMRC scientists and cooperators 

in February/March 2010 to evaluate ecosystem model performance and produce a consensus 

scientific report on role of trophic interactions (food base changes, predator-prey interactions) in 

causing recent changes in native and nonnative fish abundances. 

• Oral presentation (Walters) of the consensus ecosystem response report in a workshop/retreat for 

GCDAMP stakeholders (TWG, AMWG) in April 2010 (proposed venue - Saguaro Lake Ranch, 

Ariz.).

• Oral presentation (Wright and Korman) to TWG on progress of physical submodel upgrade 

(shifting sand rating curve model), along with simulations of suspended-sediment concentrations 

between Lees Ferry and Diamond Creek (output delivered to Walters for use in EwE model) 

during fall/winter 2009–10.

• Results of isotopic analyses of flannelmouth sucker otoliths from State University of New York

laboratory.

FY2011

• Submission of refereed journal article with Josh Korman on “Surprise and opportunity in Grand 

Canyon ecosystem management”

• Contributions by Senior Ecologist and co-investigators to the high-flow experimental synthesis 

(proposed as report by Schmidt and others) relating to the sediment and biological responses 

associated with the 1996, 2004 and 2008 experimental releases.

• Multi-attribute tradeoff analysis (MATA) workshop deferred in FY2011

Budget

FY2010: $239,986

FY2011: $148,945
36

References Cited

Coggins, L.G., Jr., and C.J. Walters, 2009, Abundance trends and status of the Little Colorado River 

population of humpback chub; an update considering data from 1989-2008: U.S. Geological Survey 

Open-File Report 2009-1075, 18 p.

Blinn, D.W., J.P. Shannon, L.E. Stevens, and J.P. Carder, 1995, Consequences of fluctuating discharge 

for lotic communities: Journal of the North American Benthological Society, v. 14, p. 233-248.

Gloss, S.P., and Coggins, L.G., Jr, 2005, Fishes of Grand Canyon, in Gloss, S.P., Lovich, J.E., and 

Melis, T.S., eds, The state of the Colorado River ecosystem in Grand Canyon: U.S. Geological Survey 

Circular 1282, p. 33-56.

Grams, P.E., Schmidt, J.C., and Andersen, M.E., 2010, 2008 high-flow experiment at Glen Canyon 

Dam—morphologic response of eddy-deposited sandbars and associated aquatic backwater habitats 

along the Colorado River in Grand Canyon National Park: U.S. Geological Survey Open-File Report 

2010-1032, 73 p.

Grand Canyon Monitoring and Research Center, 2008, USGS workshop on scientific aspects of a longterm experimental plan for Glen Canyon Dam, April 10–11, 2007, Flagstaff, Arizona: U.S. Geological 

Survey Open-File Report 2008-1153, 79 p.

Krebs, C.J., 1994, Ecology (4th ed.): N.Y., Harper Collins College Publishers. 801 p.

Korman, J., Kaplinski, M., and Buszowski, J., 2006, Effects of air and mainstem water temperatures, 

hydraulic isolation, and fluctuating flows from Glen Canyon Dam on water temperatures in shoreline 

environments of the Colorado River in Grand Canyon: Final Report for Cooperative Agreement No. 

04WRAG00006, Modification 1. 

Korman, J., and Campana, S., 2009, Effects of hydropeaking on near-shore habitat use and growth of 

age-0 rainbow trout of a large river: Transactions of the American Fisheries Society, v. 138, p. 76-87.

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

density on capture probabilities of age-0 rainbow trout estimated from electrofishing at discrete sites 

in a large river: Transactions of the American Fisheries Society, v. 128, p. 58-75.

MacKenzie, D.I., Nichols, J.D., Royle, J.A., Pollock, K.H., Bailey, L.L., and Hines, J.E., 2005,

Occupancy estimation and modeling—inferring patterns and dynamics of species occurrence: San 

Diego, Elsevier.

McKinney, T., Ayers, A.D., and Rogers, R.S., 1999, Macroinvertebrate drift in the tailwater of a 

regulated river below Glen Canyon Dam, Arizona: Southwestern Naturalist, v. 44, p. 205-210. 

McKinney, T., and Speas, D.W., 2001, Observations of size-related asymmetries in diet and energy 

intake of rainbow trout in a regulated river: Environmental Biology of Fishes, v. 61, p. 435-444. 

Ralston, B.E., Lauretta, M.V., and Kennedy, T.A., 2007, Comparisons of water quality and biological 

variables from Colorado River shoreline habitats in Grand Canyon, Arizona, under steady and 

fluctuating discharges from Glen Canyon Dam: U.S. Geological Survey Open File Report 2007-1195, 

29 p. 

Shannon, J.P., Blinn, D.W., and Stevens, L.E., 1994, Trophic interactions and benthic animal 

community structure in the Colorado River, Arizona, USA: Freshwater Biology, v. 31, p. 213-220. 

Stevens, L.E., Shannon, J.P., and Blinn, D.W., 1997, Colorado River benthic ecology in Grand Canyon, 

Arizona, USA—dam, tributary and geomorphological influences: Regulated Rivers—Research and 

Management, v. 13, p. 129-149. 

Stone, D.M., and Gorman, O.T., 2006, Ontogenesis of endangered humpback chub (Gila cypha) in the 

Little Colorado River, Arizona: American Midland Naturalist, v. 155, p. 123-135.
37

Souchon, Y., Sabaton, C., Deibel, R., Reiser, D., Kershner, J., Gard, M., Katopodis, C., Leonard, P., 

Poff, N.L., Miller, W.J., and Lamb, B.L., 2008, Detecting biological responses to flow management—

missed opportunities; future directions: River Research and Applications, v. 24, p. 506-518.

Topping, D.J., Schmidt, J.C., and Vierra, L.E., Jr., 2003, Computation and analysis of the instantaneousdischarge for the Colorado River at Lees Ferry, Arizona: May 8, 1921, through September 30, 2000: 

U.S. Geological Survey Professional Paper 1677, 118 p.

U.S. Department of the Interior, 1995, Operation of Glen Canyon Dam, Final Environmental Impact 

Statement: Salt Lake City, Utah, Bureau of Reclamation, Upper Colorado Regional Office, 337 p.

U.S. Department of the Interior, 2008, Final Environmental Assessment: Experimental Releases from 

Glen Canyon Dam, Arizona, 2008 through 2012: Salt Lake City, Utah, Bureau of Reclamation, Upper 

Colorado Regional Office, 60 p.

U.S. Fish and Wildlife Service, 2008, Final Biological Opinion for the Operation of Glen Canyon Dam 

(22410-1993-F-167R1): Albuquerque, N. Mex., U.S. Fish and Wildlife Service, 88 p.

Valdez, R.A., and Ryel, R.J., 1995, Life history and ecology of humpback chub (Gila cypha) in the 

Colorado River, Grand Canyon, Arizona: Final report (TR-250-08) to the Bureau of Reclamation, Salt 

Lake City, Utah, BIO/WEST, Inc.

Vernieu, W.S., Hueftle, S.J., and Gloss, S.P., 2005, Water quality in Lake Powell and the Colorado 

River, in Gloss, S.P., Lovich, J.E., Melis, T.S., The State of the Colorado River ecosystem in Grand 

Canyon: U.S. Geological Survey Circular 1282, p. 69-85.

Voichick, N., and Wright, S.A., 2007, Water-temperature data for the Colorado River and tributaries 

between Glen Canyon Dam and Spencer Canyon, Northeastern Arizona, 1988-2005: U.S. Geological 

Survey Data Series Report 251, 24 p.

Walters, C., Korman, J., Stevens, L.E., and Gold, B., 2000, Ecosystem modeling for evaluation of 

adaptive management policies in the Grand Canyon: Journal of Conservation Ecology, v. 4, no. 2, 

[http://www.consecol.org/vol4/iss2/art1, last accessed January 5, 2010].

Wright, S.A., Anderson, C.R., and Voichick, N., 2008, A simplified water temperature model for the 

Colorado River below Glen Canyon Dam: River Research Applications, v. 25, p. 675-686. 

Williams, B.K., Szaro, R.C., and Shapiro, C.D., 2007, Adaptive management—the U.S. Department of 

the Interior technical guide: Washington, D.C., Adaptive Management Working Group, U.S. 

Department of the Interior, 72 p. 

Yard, M.D., Coggins, L.G., and Baxter, C.V., in press, Predator prey interactions—nonnative trout 

predation on native fishes in the Colorado River, Grand Canyon, in Melis, T.S., Hamill, J.F., Coggins, 

L.C., Jr., Grams, P.E., Kennedy, T.A., Kubly, D.M., and Ralston, B.E., eds., Proceedings of the 

Colorado River Basin Science and Resource Management Symposium, November 18-20, 2008: U.S. 

Geological Survey Circular.
38
39

Appendix A

Nearshore Ecology Proposal
40

Funding Opportunity Number: 09WRPA0001

Principal Investigators: Drs. William E. Pine1,4,5, III, J. Korman2, Karin E. Limburg3, Mike S. 

Allen5, and Thomas K. Frazer5

Date of Proposed Research: February 1, 2009 – September 20, 2012

1

 Department of Wildlife Ecology and Conservation, 110 Newins-Ziegler Hall, University 

of Florida, Gainesville, Florida 32611

2

 Ecometric Research Inc. 3560 W 22nd Avenue, Vancouver, BC V6S1J3

3

 Environmental and Forest Biology, State University of New York, 249 Illick Hall, 1 

Forestry Drive, Syracuse, NY 13210

4

School of Forest Resources and Conservation, University of Florida, 7922 NW 71st

Street, Gainesville, Florida 32653

5

 PI to whom correspondence should be addressed Bill Pine, email: billpine@ufl.edu

Telephone: 352 225 1643.

Section 1 Study motivation - The primary goal of this project is to understand how river flow, 

through its interaction with physical habitat structure, influences the survival rates of juvenile native and 

non-native fishes in the Colorado River in Grand Canyon. Nine research questions related to this goal 

have been identified in the RFP (RFP pages 27-28). These questions have a hierarchical structure and 

vary in scope. Some questions are fundamental and process oriented in nature (e.g., does river flow 

conditions alter juvenile native fish survival rates?) while others are focused on methodology (e.g., how 

to measure juvenile fish abundance, can small fish be marked?). Some questions, though related to the 

broader goals of the RFP, are quite specific (e.g., what is the Colorado River mainstem survival rate for 

humpback chub emigrating from the Little Colorado River (LCR) during freshets?). Some questions 

will be very difficult to answer within the time-frame of this project (e.g., how do biotic and abiotic 

factors influence individual fish growth and survival by habitat type?), or may be quite easy to answer 

with existing data (e.g., what is the feasibility of marking small humpback chub?). 

We propose two key fundamental research questions (RQ) should guide the design of this 

project: 

(RQ1) Do steadier flows during summer and/or fall increase survival rates of juvenile native 

and non-native fish? 

(RQ2) To what extent does physical habitat structure (e.g., sand bars and backwaters), in 

conjunction with flows during these periods, influence survival rate? 
41

We propose to address these research questions and link results to a proposed conceptual model for 

humpback chub Gila cypha (HBC) and other native and non-native fish (below) by first describing an 

approach to assess shifts in fish density by tracking habitat specific abundance and survival of native 

and non-native fish in response to changing near-shore habitat availability related to and created by the 

fall steady flow experiment. We then detail an approach to determine the source populations of juvenile 

native fish that populate near-shore habitats created by the proposed Fall Steady Experimental Flow 

(FSEF). Our intent is to link this new insight into juvenile fish ecology, with a focus on humpback 

chub, with the flow and habitat management capabilities of the Glen Canyon Dam (GCD) Adaptive 

Management Program (AMP), to create a better understanding of how flow and habitat management can 

be used to cultivate and enhance survival of juvenile native fish and, with time, adult native fish 

populations in Grand Canyon.

Section 1.1 Conceptual Model – The questions developed in the RFP (RFP pages 27-28) and RQ1 and 

RQ2 are part of a broader conceptual model of native and non-native fish population dynamics 

developed over the last 10-15 years in Grand Canyon. Such models have a long history of development 

in the Glen Canyon Dam Adaptive Management Program (e.g., Walters et al. 2000), and we summarize 

essential elements for juvenile humpback chub as they relate to this proposal:

A. Humpback chub juveniles recruit to the mainstem juvenile population from the Little Colorado 

River as very small juveniles during the spring, and larger juveniles recruit to the mainstem 

during monsoon-driven flood events in late-summer and fall, or from mainstem spawning events.

B. The quantity and quality of juvenile habitat in the mainstem is driven by variation in flow and 

temperature regimes and also channel morphology. Habitat characteristics are determined by 

the monthly average discharge and hourly variation in discharge from Glen Canyon Dam, as 

well as sediment supply in the mainstem, and the frequency and timing of flows from Glen 

Canyon Dam designed to create habitat believed to be important for native fish (e.g., 

backwaters).

C. Survival rates of HBC juveniles in the mainstem depend on the quantity and quality of physical 

habitat, food availability, and the intensity of competition and predation from both native and 

non-native fishes.

D. Abundance of HBC juveniles will increase with improvements in the quality and quantity of 

habitat because survival rates will be higher. Over the long-term, greater juvenile production 

will increase the abundance of the adult population.

Section 2 Experimental Design - To resolve uncertainties in the conceptual model above, survival rates, 

growth, and abundance of native and non-native juvenile fish must be quantified under contrasting 

conditions of flow, which, in turn, drives variation in habitat availability and quality. The experimental 

design for this project, which determines the extent and timing of contrasts, has already been defined, in 

large part, by the GCD AMP. Over the next five years, there will be hourly variation in flow rates 

(related to diel variations in energy demand) during summer months (Mean Low Fluctuating Flows, 

MLFF, June-August), and lower, steady experimental flows during the fall (Fall Steady Experimental 

Flows, FSEF, September and October). We will quantify abundance, survival, habitat use, growth, and 

natal source of selected native and non-native juvenile fish over three flow periods (summer MLFF, 

MLFF-FSEF transition, FSEF) based on four sampling trips (trip launch month July, August, 
42

September, October, Table 1) given this experimental flow regime. Due to costs, natal source would be 

determined for only a sub-set of species (likely HBC only) after discussions with partner agencies.

Section 2.1 Sampling methods to estimate fish habitat use, growth, and survival –

Estimation of juvenile abundance, survival rate, growth rate, and habitat use is fundamental to resolving 

uncertainties in the conceptual model and the two key research questions outlined and identified above. 

We propose sampling trips in late July and late August to characterize abundance, habitat use, growth, 

and survival rate of juvenile fish over the summer under MLFF flow fluctuations. These trips would be 

followed by sampling trips in early September and late October to characterize juvenile fish responses 

during the MLFF-FSEF transition, and FSEF period. Differences in abundance in each habitat type, 

between each sampling trips would be used to estimate habitat specific, reach-wide survival rates across 

flow events.

We propose two basic sampling approaches for estimating these characteristics: (1) reach-wide 

abundance estimation (RWAE); and (2) robust-design mark-recapture (RDMR) at replicate sites. The 

RWAE approach follows the two-stage design developed by Korman (2009) to track abundance, habitat 

use, growth and survival of age-0 rainbow trout in the Lee’s Ferry reach of the Colorado River. 

Applying this approach to native and non-native juvenile fish in the lower Colorado River, we would: 

(1) Select a relatively large study reach that contains multiple habitat types (e.g., Kwagunt rapid 

[River Mile 56] to Lava Chuar rapid [River Mile 65.5]) and stratify this reach into sites by 

habitat type (informed by, and integrated with, ongoing GCMRC project 2, Table 2); 

(2) Sample fish at a large number of randomly selected sites within the reach using methods 

established in previous GCMRC efforts and Korman 2009 (e.g., single-pass electrofishing and 

mini-hoop nets) to quantify catch per effort. Site selection would be stratified by habitat type 

which, in turn, would likely require use of multiple gear types. Gear types and number of 

samples required will be informed by, and integrated with GCMRC ongoing projects 1, 3, 5, 6, 

7, 11 and Trip 1 of this proposal, Table 2 ; 

(3) Quantify capture probabilities by habitat/gear type, species, and fish size using short-term, 

closed, mark-recapture experiments (number of sampling events per trip ≥ 2 depending on 

recapture rate and number of sites from 2 above, e.g., Korman et al. 2009 [see Appendix]) at a 

smaller number of sites; 

(4) Convert catch-rates at index sites (from 1 above) to population estimates based on capture 

probabilities estimated from (3 above); and 

(5) Scale up site-specific estimates of population size to a reach-wide estimate based on the 

amount of habitat of each type in the reach. 

Population size by sampling trip would be estimated for each habitat type and will be used to 

examine seasonal and flow-driven changes in habitat use. Fish would most likely be marked with a 

gear, habitat, and sampling pass specific mark using unique location and color combinations of VisualImplant-Elastomer (VIE) (Brennan et al. 2005; GCMRC NSE pilot sampling, fall 2008). Ideally, 

unique marks would be applied to each animal (Bailey et al. 2004 for an example with VIE marks). 

Growth during summer-unsteady and fall-steady periods could be quantified based on differences in 
43

length-frequency distributions over time, as well as by measurements of otolith increments on a small 

sub-sample of fish (as in Korman and Campana 2009 [see Appendix]; see also section 2.2.3 and 2.2.4 of 

this proposal). As in Korman (2009), we would integrate most information from the proposed program 

in a stock synthesis model to jointly estimate parameters of interest (including abundance and survival 

rate by habitat type, growth, recruitment to the juvenile population over the growing season) and to 

identify shifts in habitat use. This approach is based on standard closed population mark-recapture 

approaches to estimate abundance and capture probability (analogous to those outlined in Otis et al. 

(1978)) and allows for incorporation of size dependence in capture probability (to account for 

heterogeneity in capture probability by size). The critical assumption of the RWAE approach (and all 

closed population models) is that the population can be treated as effectively closed within trips and that 

differences in abundance across trips are caused by recruitment (LCR and mainstem) and mortality 

only. The approach is unable to separate emigration from mortality. Radio telemetry data, and 

movement rates of marked fish within sites across trips would help evaluate the extent of potential 

emigration from study sites (see section 2.3.2 of methods). Immigration would be estimated. 

Differences in abundance and distribution among habitat types across trips would be used to estimate 

survival and changes in habitat use during changing flow conditions from summer MLFF, the MLFFFSEF transition period, and FSEF conditions. If significant changes in abundance are observed, an 

additional sampling trip, if supplemental funds were available, following the return to normal flow 

operations in November could be added to assess fish population responses to the transition from 

experimental steady flows to winter operation flows. Modal shifts in length-frequency and direct ageing 

would be used to evaluate growth.

The second approach to estimating growth, survival, and abundance by habitat type is based on a 

robust design mark-recapture approach (RDMR) that would estimate habitat specific abundance for 

each trip using closed models (RWAE), and relax the assumption of population closure between 

sampling trips (Pollock et al. 1982). Essentially, the RDMR provides a finer-scale assessment of 

abundance and survival, and is generally similar to RWAE with the following differences: 

(1) Select a series of study sites within a broader reach (e.g., three to four 500-m sites between 

Kwagunt and Lava Chuar rapids). These sites would likely each contain a mix of all or most of 

the habitat types within the broader reach. 

(2) Conduct multi-pass (3-5 pass events) mark-recapture assays in each of the study sites during 

each of the four trips. 

(3) Estimate abundance at each study site on each trip. 

As with the RWAE approach, we would employ a marking strategy to estimate abundance 

within habitat types at each site for each trip. Multiple gear types would likely be needed to sample the 

full range of habitat types and water depths. Under the RDMR approach, we would assume that 

populations within each site are effectively closed within trips, but not among trips. We would also 

assume that changes in abundance at the sites across trips represent changes at a reach-wide scale. 

Differences in abundance and distribution in each habitat type across trips will be assessed during 

summer-MLFF, MLFF-FSEF flow transition, and FSEF periods. Survival estimates for each habitat 

between sampling trips could be estimated using open population models (Pollock et al. 1990) following 

the robust design framework. If the recaptures between trips are too low to estimate survival, then the 

RDMR approach basically collapses to the RWAE approach for estimating survival – i.e., these 
44

approaches are not mutually exclusive in design or analyses employed. Shifts in length-frequency and 

direct ageing using otoliths will be used to evaluate growth (see section 2.2.3). 

Section 2.2 Site Selection - We propose to use existing data and models from the GCMRC physical 

science program (Projects 1, 2, and 10, Table 2 to quantify habitat availability over the study reach that 

contains the RDMR sites, habitat availability within the sites, and how habitat changes with flow. Such 

an approach has already been used to quantify juvenile chub habitat use in the Colorado River near the 

LCR (Korman et al. 2003). The existing GCMRC shoreline GIS database and other surveys can be used 

to stratify habitat into classes such as talus slopes, open sand bars, vegetated sand bars, cobble bars, and 

backwaters. Existing bathymetry and hydrodynamic two-dimensional models that cover the entire study 

reach can be used to predict water temperature, depth and velocity in shoreline habitats at daily 

minimum and maximum flows during the summer-unsteady period, and at the average flow during the 

steady-fall period (Korman 2003; Projects 1 and 10, Table 2). Velocity and temperature criteria will be 

used to further classify habitat for various species and life stages (e.g., into usable and unusable 

categories, or some finer scale). Additionally, shoreline stability during the summer can be quantified 

based on daily flow variation. For example, in summer, backwaters that are barely flooded at the daily 

maximum flow may be far more stable, warmer environments than those subject to complete inundation 

on each diel flow cycle. Similarly, steeper shorelines with cover (e.g., vegetated cut banks) may be more 

stable than low angle, open sand bars or cobble bars, where low velocity littoral areas vary more. These 

characteristics of stability can be related to patterns of fish habitat use (density or occupancy) to help 

evaluate effects of fluctuating flows. A strong relationship between fluctuating flows, near-shore

habitat use, and otolith growth has been observed for age-0 rainbow trout in the Lee’s Ferry reach of 

the Colorado River (Korman and Campana, 2009). Similar relationships are expected for juvenile 

native and nonnative fish in the Grand Canyon and, in fact, is part of the motivation for the current fall 

steady flow test. We hypothesize that unstable habitat types will be used only minimally during the 

summer-unsteady flow period, but that use of these habitats will increase during the fall-steady period 

when flows are stabilized. If this difference in habitat use is ecologically important, we would also 

predict increase in growth and survival during the fall-steady flow period relative to the summer. 

Information we collect as part of Sections 2.1 and 2.3 can be used to test these ideas directly.

Section 2.3 Assumption evaluation and alternative approaches to assess native fish habitat use and 

response to FSEF - Any mark-recapture approach to estimating abundance and density depends on 

recapturing sufficient numbers of marked individuals to draw inferences on the parameters of interest. 

In many fisheries mark-recapture studies, capture probabilities are low (often < 10%, Pine et al. 2003) 

and heterogeneity in capture probability across fish size is often observed (Pine et al. 2003; Korman et 

al. 2009; Coggins 2008). Closed population models generally have fewer parameters (and assumptions) 

than open models and are thus better able to estimate parameters of interest (capture probability and 

abundance) when recaptures are low. By design, some closed models can account for heterogeneity in 

capture probability directly (i.e., Mh type models, Otis et al. 1978) or captures and recaptures can be 

stratified by length group and capture probability estimated for each length stratum. These are two key 

reasons why closed population models have been recommended for use in fisheries studies to estimate 

abundance (Pine et al. 2003). One concern is the closed model assumption of no emigration from the 

sites of interest (i.e., habitat specific sites) both for the RDMR and RWAE approaches to estimate site 

specific abundance. Korman et al. 2009 successfully used closed model techniques in the Lee’s Ferry 

reach of the Colorado River to estimate capture probabilities of juvenile rainbow trout across spatially 

discrete sites. These authors evaluated closure assumptions by employing a site specific marking 
45

technique and then sampling up and down-stream of their study reach to estimate emigration from each 

site. Emigration rates were low, ranging from 2.2-2.6%, leading these investigators to conclude that 

rainbow trout populations within discrete sites effectively can be considered closed. We would evaluate 

the closure assumption in our mark-recapture experiments using methods similar to Korman et al. 2009. 

Additionally, recaptures of fish marked on previous trips will provide useful information on growth and 

movement (e.g., movement into backwaters during periods of steady flow) between sampling trips and 

associated flow conditions. The NSE pilot sampling data from 2008 should provide some information 

on closure and also provide information on capture probability which is necessary to fully assess how 

violation of the closure assumption biases abundance estimates. Zehfuss et al. (1999) demonstrate 

declining bias in abundance estimates with increasing capture probability and emigration from the study 

site for Jolly-Seber and robust design models. 

Section 2.3.1 Estimating site occupancy - If catches and recapture rates within trips are low, abundance 

estimates within sites will be highly uncertain. However, as pointed out in the RFP, in this case it will 

be possible to retreat from estimating abundance to estimating the probability of site occupancy (by 

habitat type and over time; MacKenzie et al. 2006). Site occupancy, although not as useful as direct 

estimates of abundance, can be used to index habitat use and changes in habitat use over time and with 

associated changes in flow. In all likelihood, the mark-recapture program will be able to estimate 

habitat-specific abundances for some species and size classes, and occupancy would be estimated for 

species and sizes with lower abundance and/or capture probability. Total number of site visits required 

would be based on trip 1 and information from ongoing GCMRC projects 3, 6, 7, 11 (Table 2).

Section 2.3.2 Incorporating telemetry information - The potential exists for radical changes in capture 

probability or behavioral shifts by fishes across sampling events within a season (~July-October) due to 

fish growth and possible ontogenetic habitat shifts such as fish moving into deeper, less accessible 

portions of the river. These behavioral shifts could also be caused by the designed flow experiments 

and associated changes in available habitat, or biotic interactions (changes in food availability or 

predation risk). To examine these behavioral responses, directly assess habitat use, and test capturerecapture model assumptions such as closure, a small sub-set of native and non-native fish (5-10 

individuals of 3-4 key species, including humpback chubs, > 150-mm TL) will be tagged with telemetry 

tags and their movements, habitat use, and fates assessed directly. 

Implantable, compact telemetry tags coupled with autonomous receivers (which monitor a given 

area continuously for extended time periods for the presence of tagged animals) and deployed as a fine 

scale array within a sample reach could allow the telemetered animals to be “virtually” captured by 

detecting their tags as they move through the environment via either the autonomous receiver array, or 

from boat-based receiver units when field crews were onsite. This technology is mature, and thousands 

of telemetered fish and autonomous receivers are currently deployed globally (Simpfendorfer et al. 

2008; Hedger et al. 2008). However, the use of telemetry techniques in Grand Canyon is 

technologically challenging, given the large amount of ambient noise from rapids, moving rocks, and 

coarse sediments, all of which greatly impair the ability to detect acoustic tags. Radio tags have been 

used successfully in Grand Canyon to track movements of adult humpback chubs (Valdez and 

Hoffnagle 1999) in response to flood events, but the attenuation distance of radio tags is greatly 

impaired by high conductivity in areas of Grand Canyon near the Little Colorado River. Current 

GCMRC projects 3 and 7 have been involved in several pilot projects exploring the utility of these 

techniques with non-native fishes to assess movement and capture probability. Industry cooperator 

Marlin Gregor, President of Sonotronics Inc. (http://sonotronics.com) has been involved in the above 
46

projects and has developed specific tag and receiver design combinations to maximize the potential of 

this technology in the challenging conditions presented by the Colorado River in Grand Canyon. Marlin 

Gregor has also agreed to accompany on our first sampling trip as we test a variety of receiver and tag 

types. If this pilot sampling during trip 1 reveals poor performance of telemetry equipment due to high 

levels of ambient noise in Grand Canyon, we will abandon the telemetry component of this project. We 

will work with cooperators to then identify alternative research efforts such as experiments to assess 

DNR:RNA ratios as a measure of short-term growth as recommended by NSE review panel.

The incorporation of telemetry information with the mark-recapture sampling is experimentally 

risky, but has huge potential to boost our ability to draw inferences about juvenile fish abundance and 

habitat use. Pollock et al. (2004) showed an example of using both tag types to improve estimation of 

fishing and natural mortality rates using a complementary, multinomial approach to the tagging 

component of the stock synthesis model used in Korman et al. in-press and this proposal. We have 

extensive previous experience with these types of telemetry systems and similar applications (Bennett 

2005; Marcinkiewicz 2007; Tetzlaff 2008; Burgess 2008). Coupled with ongoing GCMRC projects 3 

and 7, and industry cooperator commitment, it is likely that technological hurdles could be overcome. 

Exact tag types, receiver deployment strategies, numbers of tags and receivers required would be 

determined based on in-situ range testing of tag and receiver combinations. An array network would 

not guarantee perfect, continuous detection because behaviors of individual animals such as occupying 

habitat types similar to interstitial spaces between rocks, would attenuate the signal from the sonic tags. 

Conceptually, an autonomous receiver array could be deployed during a July sampling trip (first trip of 

sampling season) and a small batch of fish tagged and released with telemetry tags. The receivers 

would then remain deployed, monitoring these fish until the next sampling trip, at which time the data 

would be retrieved and an additional batch of fish tagged. Similar procedures would be followed for 

each additional trip, until the last trip of the year when no additional fish would be tagged and the 

receivers would be removed from the study site. Multiple batches of fish would be used (a “staggered 

entry” design, Pollock et al. 1989) because of limitations in tag battery life. The staggered entry design 

would allow specific size cohorts of fish to be tracked from the first through the fourth study period 

coincident with the same flow transition periods discussed in Section 2.0. 

Section 2.3.3 Determining origin of recruits – The FSFE will likely almost immediately create 

thermally favorable microhabitats for juvenile HBC and other native fish (RFP, page 27) which 

motivates Question 6 of the RFP (page 27), “Are replicated flows September-October steady flows 

(2008 through 2012) likely to improve the survival and recruitment of young humpback chub in the 

Colorado River ecosystem?” Additionally, while management actions such as FSFE are certainly likely 

to modify and create habitat types, some of which may be favorable to juvenile HBC, where do the 

juvenile HBC come from to colonize these habitats and if they colonize these habitats, how well do they 

survive? As outlined in Sections 2-2.2, we describe approaches to assess survival of young HBC (and 

other species) in response to the FSFE. However, recruitment of young HBC and other juvenile fish 

from the LCR to the mainstem study site during July-September (Conceptual Model point A) could 

confound information on patterns in juvenile fish density in different habitats and their survival, 

unrelated to flow events. For example, in the absence of any direct measure of age-0 fish recruitment 

from the LCR to the mainstem population, observed patterns in density, growth, and survival of juvenile 

fish from our mark-recapture study could be attributed to the flow experiment, when, in fact, these 

density changes were actually independent of the experiment, and instead related to natural emigration 

from the LCR to the mainstem. Without an understanding of this recruitment from the LCR to the 
47

mainstem, the estimated growth, survival, and movement among habitat types in the mainstem from the 

tagging data (Sections 2-2.2) could be confounded with new recruits. 

We propose to use otolith microchemistry to determine the origin of juvenile fish (mainstem vs. 

LCR), most likely only HBC because of cost concerns, utilizing available habitats across the different 

flow regimes from July-October. As pointed out in the RFP (page 27) there are at least two potential 

sources of juvenile HBC that use habitats available during MLFF and migrate to habitats created by 

FSFE: (1) LCR spawned juveniles that enter the mainstem river in May-June outmigration and (2) LCR 

spawned juveniles that remain in the LCR until they enter the mainstem following July-September 

freshets. A third possible source of HBC juveniles would be mainstem spawned individuals who could 

also be identified through otolith microchemistry. This information will be used to compliment and 

strengthen inference from estimates of habitat specific patterns in abundance, movement patterns of 

telemetered fish, and fish size distributions (Sections 2.1-2.3). 

Otoliths are paired structures that form part of the inner ear of teleost fish and are commonly 

used by fisheries researchers to estimate fish age, and increasingly, their chemical constituents are used 

to determine fish movements (Campana 2005). Otoliths are composed of biogenic calcium carbonate 

that accretes new crystalline and protein material daily. Within these accumulating layers, trace 

elements are incorporated into the otolith from the fishes environment, creating a temporal sequence of 

accumulated elements. This represents a chronology of the environment the fish has occupied over its 

life (Elsdon et al. 2008). Within the otolith, the different accumulated elements and chemical signatures 

can be used as a natural tag. These tags can then be linked to groups of fish that have similar chemical 

signatures to show associations of fish with their environment in both time and space (reviewed in 

Elsdon et al. 2008). Chemical signatures in an otolith can be examined, for example across a transect, to 

assess patterns in chemical profiles at different ages of the fish. When these chemical signatures are 

paired with information on the chemical profiles of the water in the spatial locations where the fish 

could have lived, movement patterns of individuals and groups of fish can be determined. A key 

assumption is that the chemical signatures from the different environments are separable, and that these 

signatures can be matched on the correct temporal scale. To test these assumptions, during 2009 we 

will test our proposed methods on flannelmouth sucker (Catostomus latipinnis) a more common native 

species thought to have similar life history characteristics as humpback chub. Samples of flannel mouth 

sucker are also available from the 2008 NSE pilot sampling (M. Yard, USGS-GCMRC, personal 

communication). We will attempt to analyze at least a sample of these otoliths from 2008 to inform 

2009 field collection efforts. Additionally, we will also examine a sample of previously collected adult 

humpback chubs used in earlier analyses (Hendrickson 1997). 

Recent advances in otolith microchemistry will enable us to assay for a suite of major, minor, 

and trace elements through the use of laser ablation inductively coupled plasma mass spectrometry (LAICPMS; Figure 1). SUNY-ESF has just acquired a state-of-the-art laser ablation system (New Wave 

Research UP-193 nm solid state) and has connected it to an also new Perkin-Elmer DRC-e ICPMS. 

This setup, with analytical resolution to low ppb and spatial resolution to approx. 10 microns, will be 

used to collect the bulk elemental data, using one of each pair of lapillar otoliths. Other data, potentially 

including strontium and other stable isotopic ratios will be taken on the corresponding otolith at a 

partner institution such as University of Arizona Lunar and Planetary Science Laboratory or the 

Department of Nuclear Physics at Lund University in Sweden (where KL has ongoing collaborations 

since 1997). In addition, we will explore the utility of trace elemental mapping by means of 

synchrotron-based X-ray fluorescence (S-XRF) at the Cornell High Energy Synchrotron Source 

(CHESS). The S-XRF will allow us to explore which elements might be of interest to trace using the 

LA-ICPMS. This approach of using the S-XRF to first map multiple trace elements in otoliths and the 
48

coupling of this information with high-resolution LA-ICPMS work has provided new insights into the 

environmental history of a variety of fish (marine and freshwater) and their lifetime movement patterns 

(see Limburg et al. 2007). Given that run times per otolith are long with S-XRF, and time available is 

limited at the CHESS facility, we anticipate that bulk of the work will be accomplished using LAICPMS once multiple otoliths have been mapped at CHESS. In addition to addressing questions related 

to the near-shore ecology of Grand Canyon fishes proposed here, there are obviously additional research 

questions that these approaches could be applied to using otoliths from existing collections. For 

example, older fish from archival collections (HBC otoliths used in Hendrickson 1997) are prime 

candidates for S-XRF mapping coupled with LA-ICPMS analysis to assess movement patterns and 

provide alternative age assessments of larger, older, fish collected at earlier time periods during different 

river conditions. If suitable archived samples were available, such as from HBC spawned prior to the 

Glen Canyon Dam, it would be very interesting to assess the life time movement patterns (spawning, 

rearing, and migratory) or pre- vs. post-dam HBC or other native fish.

As an example of this approach Limburg (1995, 1998, 2001) used ratios of strontium (Sr) 

relative to calcium (Ca) from American shad (Alosa sapidissima) otoliths along a transect in the Hudson 

River, linked with otolith derived age estimates to identify the age and size when American shad were 

transitioning from the Hudson River to the Atlantic ocean. Limburg (2001) compared Sr:Ca ratios and 

size and age structure in young-of-year American shad with the Sr:Ca ratios of adult fish from these 

same cohorts migrating back to spawn in the Hudson River in subsequent years. From these 

comparisons Limburg (2001) found that in three of the four year classes analyzed, differential mortality 

had occurred in juveniles, and was related to time of emigration from the Hudson River. A similar 

approach with humpback chubs over multiple years, coupled with Sections 2-2.2 of this proposal, could 

help us to identify the linkages between the timing of out migrating juveniles from the LCR, available 

rearing habitat in the mainstem as determined by flow conditions, and the interaction between available 

habitat and juvenile fish survival. 

Section 2.3.4 Determining growth and survival using otoliths - Measurements of fish growth integrates 

information from a variety of environmental (e.g., temperature) and biotic (e.g., food availability) 

sources into a useful single metric. Growth can be used, for example, as a response metric to a variety 

of management options (DeVries and Frie 1996) and also used to provide insight into survival patterns 

(Lorenzen 1996). For larval and juvenile fish, growth information is commonly measured by analyzing 

size frequency distributions or using fish hard parts such as otoliths (DeVries and Frie 1996). The use 

of otoliths to determine juvenile fish growth has been used to address a variety of questions for 

Colorado River native (Bestgen et al. 2006) and nonnative fish (Korman and Campana 2009). For 

example, Korman and Campana (2009) documented a strong relationship between fluctuating flows, 

near-shore habitat use, and rainbow trout otolith growth rates in the Lee’s Ferry reach of the Colorado 

River. As proposed in section 2.2, we hypothesize that fish growth may change as a function of shifts in 

habitat utilization driven by flow related changes in habitat availability – thus differences in growth may 

be evident between MLFF, MLFF-FESF transition, and FESF period. 

We propose to assess growth in three ways: (1) by tracking modal progression of native and 

non-native fish size in during each sampling trip, (2) if unique VIE marks are possible through 

recaptures of marked fish, and (3) direct estimation using otoliths collected for the microchemistry 

analyses of HBC described above. The first approach is straight forward and simply requires plotting 

the size frequency of individuals from each species and sample trip as a function of length and 

identifying distinct peaks in the distribution. These peaks are then followed in subsequent trips and 

growth estimated by tracking the progression in the modal peaks of each size frequency distribution. 
49

This approach generally works best if sample sizes for each cohort are large and growth is fairly 

uniform among cohorts such that the size modes for each cohort can be distinguished. If sample sizes 

are small or growth within a cohort is inconsistent, then cohort modes become indistinguishable in the 

length frequency distribution and estimating growth is not possible. This approach is low cost, nonlethal, and would be used to estimate growth for all possible fish species.

The second approach is dependent on being able to mark fish for the capture-recapture 

experiment using unique marks. The VIE marks we propose to use come are available in a variety of 

colors and there are numerous body locations in which fish can potentially be marked. However, it is 

not until live fish are examined and the color patterns and marking locations assessed to determine 

whether VIE colors can contrast sufficiently with natural fish color patterns to offer reliable marking 

locations. We acknowledge the difficulty in creating a unique marking scheme and the potential bias 

induced in the analyses from mistakes made in the marking program thus necessitating careful 

consideration to the design of the fish marking program.

The third approach is based on the standard technique of visually counting daily growth rings on 

otoliths to estimate age (Pannella 1971; Stevenson and Campana 1992; Pine and Allen 2001). 

Following this approach, the second HBC otolith from whichever otolith pair is used for the 

microchemistry analyses (most likely the lapillar pair; Hendrickson 1997) would be mounted 

individually on microscope slide, polished to the mid-plane following standard otolith preparation 

procedures, examined at 400-1250x using a compound microscope, and then the daily increment marks 

on the otoliths from the origin to the edge counted 2-4 times. Daily otolith increments have not been 

validated in humpback chubs, but preliminary work by Hendrickson (1997) provides strong 

circumstantial evidence to suggest that the lapillar increments do form with daily periodicity. If 

recapture rates between trips are sufficiently high as evident from trips 1 and 2 in field season 1, a 

validation study could be designed by immersing juvenile HBC in an alizarin solution to “mark” the 

otolith, then releasing the fish with the expectation to recapture that fish on a future trip. Recaptured 

fish would then be sacrificed, otoliths removed and prepared as described in section 2.3.4, and the 

otolith rings since the immersion in alizarin counted and compared to the actual days elapsed (Devries 

and Frie 1996). Average daily growth rates can then be determined from dividing the fish TL when 

captured by the age. 

Recent juvenile HBC growth over short time periods, such as just prior to and during the 

transition from MLFF to FSFE and during the FSFE, could be estimated by measuring otolith growth 

increments from the nucleus to a distance along the growth axis that would correspond to a point in time 

(and the fish’s life) during MLFF, and then measure from this point to a second point that would 

represent the time period including the MLFF-FSEF transition, and then a third measurement from the 

MLFF period to a time period near the end of the FSEF. The approach outlined would obviously be 

dependent on collecting juvenile HBC near the end of the FSEF such that the growth transition could be 

measured across each of the three flow periods described. Obviously these candidate fish would have to 

survive any changes created by the flow events – and it would be impossible to collect growth 

information on any fish that died during the flow events. Alternatively, juvenile HBC could be sampled 

on each of the four sampling events and incremental growth measured from these fish using methods 

described above. However, given the short time period between the flow treatment and the timing of 

the sampling trip, contrasting growth information may be not detectable along the post-rostral edge of 

the otolith because not enough time may have elapsed for sufficient otolith deposition along the edge to 

see or measure. This growth information would be linked to the otolith microchemistry results related 

to natal origin of HBC. For example, this linkage could be useful in assessing growth patterns of HBC 
50

that were early vs. late season emigrants from the LCR to mainstem Colorado River or growth patterns 

of mainstem origin juvenile fish.

A major drawback of using otoliths to estimate age and growth is that the fish must be sacrificed 

to extract the otoliths. Given the listing status of most native fish in Grand Canyon, including HBC, we 

share concerns that any research associated mortality could be deleterious to the population overall, and 

we acknowledge that permits to collect and sacrifice these fish may be difficult to receive. Recruitment 

trends for humpback chubs and other native fish have been increasing over the last 4-5 years (ongoing 

GCMRC projects 5, 6, Table 2; Coggins 2008) reducing the potential for population impact from 

removing a small number of native fish from the population for research needs. Exact numbers of fish 

required would be determined by examining otoliths from juvenile humpback chubs incidentally taken 

as part of routine sampling in prior research efforts (i.e., Near-shore Ecology pilot sampling in August 

and September 2008 and backwater sampling efforts in summer 2005). We propose to collect a small 

number of juvenile fish, most likely 5-10 age-0, age-1, age-2, and age-3 humpback chubs and also 

flannel mouth suckers each trip (no more than 50 fish per age class and species per year). In addition to 

providing information from the microchemistry and age-growth analyses in response to the FSEF, there 

are at least two other major areas that could be assessed by using tissues from these animals. First, age 

information on these small fish would be very useful in informing the age-length key used to assign ageat-first capture in the standard age-structured mark-recapture program (ASMR, Coggins et al. 2006a; 

GCMRC projects 4 and 6, Table 2) used to assess trends in HBC growth, recruitment, and survival 

(Coggins et al. 2006b; Coggins 2008). This age-length key is currently based on a limited set of 

approximately 60 estimates of HBC length-age (Coggins 2008) and this small growth sample, 

particularly for very small and young fish, could be improved with additional growth information 

possibly leading to reduced bias in the recruitment estimates from the ASMR model. Additionally, the 

previous growth data were not collected during the recent time period of warmer water temperatures, 

which may have led to increased HBC growth. Thus, the currently used growth information may be 

negatively biased due to slow growth of humpback chubs in cold-water conditions vs. the current 

warmer-water conditions. 

Fin rays also offer an alternative approach for aging fish to otoliths with the major advantage of

not having to sacrifice the fish (DeVries and Frie 1996). Using a sub-set of fish sacrificed for otolith 

analyses, we will conduct an exploratory analysis to assess the feasibility of the same age and 

microchemistry assessment on the fin ray sections as on the otoliths. This will provide information on 

the possibly utility of using fin rays as a non-lethal technique to determine age of young fish to help 

inform the HBC stock assessment and monitoring program (ongoing GCMRC projects 3 and 4). If 

successful, and necessary, this approach could provide information useful to assessing recruitment 

responses of HBC to planned and unplanned experiments at younger ages (and less time lag) than the 

current 3-4 year response time required before fish recruit to the tagging program and recruitment trends 

assessed as part of ASMR.

A final alternative for both the microchemistry and otolith based age and growth estimation 

would be to use a surrogate species for humpback chubs that was thought to have a similar life history. 

Alternative species to humpback chubs could include native fish such as bluehead suckers Catostomus 

discobolus, flannelmouth Catostomus latipinnis suckers, speckled dace Rhinichthys osculus or 

nonnative species such as fathead minnows Pimephales promelas.

Section 3.1 Contingency plans to alternate flow scenarios, expanded spatial replication, or inability to 

secure variance during no-motor season – The proposed sampling framework and experimental design 

(i.e., timing of trips) can easily be modified to address alternate flow-related hypotheses. For example, 
51

question (9) in the RFP (page 28), “What happens to juveniles that used the warmed areas when 

fluctuating flows are resumed?”, could be addressed by adding one or two trips (and additional costs) to 

the proposed four-trip schedule. In this case, a trip following the resumption of fluctuating flows, (midNovember) and an additional trip one month later, would quantify immediate changes in habitat use as 

well as survival rates under fluctuating flows during early winter. A similar strategy, where sampling is 

conducted before and after a beach habitat building flow, could be used to evaluate the effects of flows 

above power plant capacity or normal daily maxima (item 6, RFP page 31). Additional spatial 

sampling, at other known HBC aggregation sites (“Randy’s Rock”, RM 126; “30-mile”, RM 29-32) 

could also be implemented based on results from Section 2 above. The key point is that our approach 

will provide estimates of habitat use, survival, growth, and origin of juvenile fish during summer and 

fall, and that it is relatively easy to expand sampling into other times of year to look at other flowrelated hypotheses. That said, the objectives and research questions that are the focus of the RFP are 

very challenging. Our philosophy is to do a few things well, rather than many things poorly. Given 

available resources, we will focus on population dynamics during summer and fall only as outlined 

above. 

We expect that some elements of the proposed sampling framework would become part of the 

GCD AMP’s long-term monitoring protocol. For example, methods developed in this project could be 

used to estimate juvenile HBC abundance in the mainstem during late summer and late fall. Over many 

years, these estimates could be related to recruitment estimated from the Age-Structure Mark-Recapture 

(ASMR) model (Coggins et al. 2006 a, b). Ultimately, a stock-recruitment relationship between age-0 

chub in the mainstem during both fall and summer, and recruitment determined from the ASMR model, 

would be very helpful in the interpretation of the juvenile data. For example, if there is strong density 

dependence in survival between summer and fall, and little density dependence for later life stages, we 

would expect an asymptotic relationship (e.g., Beverton-Holt shaped relationship) between summer and 

fall juvenile abundance, and between summer juvenile abundance and ASMR-based recruitment 

estimates. In this case, there would also be a strong linear relationship between fall juvenile abundance 

and ASMR recruitment. Such analyses are very relevant to current policy debates. For example, strong 

density dependence between summer and fall would indicate that it is unlikely that improving habitat 

conditions during the summer will result in substantive changes in juvenile abundance during the fall, 

and consequently to improvements in recruitment to the adult population. It will take many years to 

establish reliable relationships (which will likely be noisy), but we see no alternative for the GCD AMP. 

Ultimately, life-stage specific stock-recruitment functions need to be established to fully interpret results 

from the proposed study in the context of GCD AMP management objective for adult HBC.

Depending on the start of the FSFE, it is likely that one or two of our proposed sampling trips 

would launch after the start of the no-motor season (September 15). In this case, we would require a 

variance from the Park Service for operating motorized equipment (boat motors and generators) 

required for our electrofishing sampling. While we intend to use multiple gear types (most likely 

electrofishing and hoopnets) during each of our sampling events, we have high expectations for 

successful electrofishing sampling for use in mark-recapture (Section 2.1) based on results from 

Korman et al. (2009) and fall 2008 Near-shore Ecology pilot sampling. Failure to secure a variance 

allowing us to use electrofishing would increase our dependence on hoopnet sampling to track patterns 

in habitat specific abundances, estimate survival, and track growth via changes in length frequency. 

Gear selectivity patterns between electrofishing and hoopnets likely differ, and by deploying both gears 

on each sampling trip we intend to minimize the confounding that can occur in the data due to changes 

in gear between trips and associated selectivity patterns (i.e., responses could be due to the flow 

experiment or simply to changes in the gear type). Compromises to help meet the Park Service’s no-
52

motor requirements are possible. One option would be to create a stash of 1-2 electrofishing boats in 

the study reach just prior to the end of no-motor season. Any trips that occurred during the no-motor 

season would then be supported by rowing trips out to the sampling sites, where electrofishing boats 

would be used to complete the required sampling effort. At the end of sampling, these boats would be 

floated or flown out of Grand Canyon in cooperation with other sampling efforts with USFWS and 

AZGF. Additional options would be to increase the reliance on telemetered fish and to follow the 

movements and habitat use of telemetered fish using rafts and kayaks during no motor season. A final 

option would be to not grant the variance; thus, electrofishing would not be possible. Our proposed 

closed population models (both mark-recapture and occupancy) estimates capture probability with each 

sampling trip, so if hoopnets were the only sampling gear available during the last trip, then our capture 

probabilities would be based on marks and recaptures from hoopnet gear only. Hoopnet catches alone 

would likely result in very low capture probabilities, limiting the use of some mark-recapture models. 

However, habitat occupancy using methods outlined in section 2.3.1 may be used to estimate occupancy 

even with low capture probabilities. If no variance is granted, extensive comparisons between 

electrofishing and hoopnet catches based on pilot sampling during motor season and previous fish 

sampling efforts in Grand Canyon would be done to develop a better understanding of the selective 

properties of each gear. The style of electrofishing developed and used by Korman et al. (2009) was 

first used in the Lee’s Ferry reach, but was also used as part of the pilot NSE sampling during fall 2008 

thus limiting the number of comparisons that can be made between gear types using historical data. 

Section 4 Conclusions - Certain aspects of the proposed experimental design are beyond our control, and 

will limit the inferences from the resulting data. We propose to compare juvenile habitat use, survival, 

and growth during summer-unsteady and fall-steady flow periods to evaluate the potential benefits of 

steady flows. However, such an assessment assumes there is no seasonality in the parameters of interest, 

which we know is not likely to be the case. For example, growth rates will likely decline as fish increase 

in size, and as water temperature declines due to reduced solar irradiance. Habitat use may also have a 

flow-independent component that depends on fish size. Ultimately, the proposed work, or key elements 

of the proposed work, will need to be repeated under an alternate flow regime. The two logical 

alternatives are to extend the period of steady flows (e.g. July-Oct), or to revert to unsteady flows 

(MLFFA or greater fluctuations) during the fall. Results from the proposed work will be helpful in 

choosing among these alternatives because: (a) we will have a much better sense of our ability to detect 

changes in juvenile survival rates and other life history characteristics; and (b) expected and 

serendipitous insights from the proposed work will provide for more refined hypotheses and a more 

fully articulated conceptual model. 

Section 5 Budget narrative - The proposed project budget (~$300,000 per year, for four years) is 

provided in the attached spreadsheet. The travel budget category (Part A) includes travel for University 

of Florida supported personnel to assist with field trips, meet with cooperators (including members of 

the GC AMP as specified in the RFP) including airfare, car rental, per diem, and lodging charges for 

trips to Flagstaff. Mileage charges are for local mileage in Gainesville for acquiring supplies and other 

project related activities on University of Florida vehicles. This category also includes a Flagstaff based 

lodging and utility expenses for field crews (a rental house or apartment) and other project personnel fur 

use during the field season, and also for approximately one month prior and after the field sampling 

events. Our intent is for several project staff to spend several months of the year working with GCMRC 

cooperators on this project to maximize interaction amongst cooperators and facilitate project planning, 

logistics, and analyses. The supplies category (Part B) includes items such as telemetry tags and 
53

receivers, surgery supplies for telemetry gear, and disposable field items such as batteries, vials, 

preservative etc. Charges for preparing the otolith samples for microchemical analyses are also 

included in this section. We have also included an Osprey boat for use during this project, but to meet 

budget requirements have spread these charges over several years. While GCMRC has two Ospreys 

available, these boats are in high demand by cooperating projects and we do not want field activities to 

be limited by a limitation of a specialized boat. The supplies section also includes charges from 

Ecometric consulting for development of specialized analytical software. Humphrey summit logistics is 

also included in the supply category to provide assistance with field activities related to the telemetry 

efforts including modifying Osprey boat for deploying and retrieving hydrophones and towable 

hydrophones for tracking. Part C is the wages, benefits and tuition section that covers University of 

Florida of Florida project personnel. This includes recruiting a PhD student to assist with all aspects of 

design, field sampling, and data analyses. This student will be paid a stipend, health insurance will be 

provided, and tuition to the University of Florida will also be paid by project funds. A portion of a 

technician/biological scientist employed by the University of Florida is also included on this grant as 

well as benefits for this person. Section D of the project is a subcontract to SUNY-ESF and includes 

tuition, stipend, and salary charges for a PhD student at SUNY-ESF. This student will assist with all 

aspects of the design, field sampling, and data analyses with particular emphasis on the otolith 

microchemistry work. Section D also includes a small travel budget for SUNY-ESF travel costs to meet 

with other project cooperators at GCMRC in Flagstaff. Costs associated with the LAICPMS analyses 

are also included in Section D. Section E includes indirect cost figures for the total award, for the subcontract to SUNY-ESF and also transfer between USGS GCMRC and USGS CRU program. These 

indirect costs represent ~20% of the total costs of the contract. It should be noted that this contract 

includes support for two graduate students who could potentially be recruited by USGS GCMRC as 

fulltime employees to continue this type of work. 
54

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57

Table 1. Proposed sampling schedule and key tasks for Near-shore Ecology of Grand Canyon Fish project. MLFF = Mean

Low Fluctuating Flows, FSEF = Fall Steady Experimental Flows.

Year Activity Month Trip 

Number

Likely 

river flow

Key tasks or project milestones

2009-

2011

Field sampling Late July 1 MLFF Mark-recapture, deploy receiver array, implant 

telemetry tags, manual tracking of telemetered fish, 

collect fish for otolith analyses

2009-

2011

Field sampling Late August 2 MLFF Mark-recapture, implant telemetry tags, manual 

tracking of telemetered fish, collect fish for otolith 

analyses

2009-

2011

Field sampling Early 

September

3 MLFFFSEFMark-recapture, implant telemetry tags, manual 

tracking of telemetered fish, collect fish for otolith 

analyses, possible otolith validation experiment

2009-

2011

Field sampling Late October 4 FSEF Mark-recapture, retrieve receiver array, implant 

telemetry tags, manual tracking of telemetered fish, 

collect fish for otolith analyses, possible otolith 

validation experiment

2009-

2011

Sample 

processing

October -

March

Estimate growth from size distributions, estimate 

abundance and survival from mark recapture, assess 

movement and habitat use from telemetry 

information, and conduct otolith analyses

2009-

2011

Annual Report April Present annual project updates, submit reports, meet 

with all cooperators to revise sampling plans for 

upcoming field season

2011-

2012

Analyze data and 

write report

May 2011-

Aug 2012

2012 will include additional isotopic analyses of 

otoliths and funds for mapping chemical signature 

of water

2012 Final Report September Submit final report and presentation to GCMRC 

staff
58

Table 2. Existing monitoring and research studies in Grand Canyon as listed in the RFP. Numbers in this table correspond 

to referenced cooperative and complimentary research described in this proposal.

Project Number Project title

1 Monitoring of biological and physical aspects of backwater habitats

2 Integrated analyses and modeling: mapping shoreline habitat changes

3 Monitoring mainstem fishes

4 Stock assessment of native fish in Grand Canyon

5 Investigate factors affecting the survival rate of juvenile native fishes in the mainstem 

Colorado River

6 Native fishes habitat data analysis

7 Nonnative control planning and pilot testing

8 Status and trends of Lees Ferry trout

9 Monitoring rainbow trout redds and larvae

10 Thermal modeling of near-shore habitat

11 Aquatic food base program
59

Fig. 1. Fish otoliths are located in the semi-circular canals underneath the brain (top left); daily growth 

increments seen in 0.5 mm otolith of young fish (top right); annual rings (bottom left) can be used to 

age adult fish, and elements such as strontium are deposited in proportion to ambient concentrations 

(bottom, middle) whereas zinc (bottom right), in this case, is deposited in a seasonal pattern. The 

analyses shown in the bottom two panels were conducted with a nuclear microprobe. This kind of 

analysis will continue to complement the work we are proposing to do with LA-ICPMS.