Date:    September 25, 2009

To:     Glen Canyon Dam Adaptive Management  

    Technical Work Group and Other Interested Parties

From:     S. Clayton Palmer

    Western Area Power Administration

    Colorado River Storage Project Management Center  

Subject:  

Final Report:   Annotated Bibliography for the Humpback Chub (Gila cypha) with Emphasis on

the Grand Canyon Population   

    Prepared by Argonne National Laboratory

Western’s representatives on the Glen Canyon AMP committees and others noticed that no

recent compendium existed summarizing the existing literature related to the HBC in the Grand

Canyon. We therefore tasked Argonne National Laboratory to develop the attached annotated

bibliography.  

We hope it will be a helpful resource as we continue to discuss the status of the HBC, work

collaboratively towards improving its status and habitat. We further believe it will assist the

TWG in providing technical advice to the AMWG.  
 
 
 
 

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Humpback Chub Annotated Bibliography September 2009

 iii 

CONTENTS 

NOTATION .............................................................................................................................. v 

1 INTRODUCTION .............................................................................................................. 1

2 BIOLOGY........................................................................................................................... 2 

 2.1 Anatomy and Physiology ............................................................................................. 2 

 2.2 Reproduction ................................................................................................................ 7 

 2.3 Genetics and Systematics ............................................................................................. 9 

 2.4 Supporting Articles ...................................................................................................... 15 

3 ECOLOGY ......................................................................................................................... 20 

 3.1 General Ecology ........................................................................................................... 20 

 3.2 Distribution and Abundance ........................................................................................ 27 

 3.3 Habitat Selection .......................................................................................................... 41 

 3.4 Stream Flow ................................................................................................................. 49 

 3.5 Temperature ................................................................................................................. 54 

 3.6 Foraging and Diet ........................................................................................................ 56 

 3.7 Supporting Articles ...................................................................................................... 58 

4 IMPACTS OF DAM OPERATIONS ................................................................................. 81 

 4.1 Effects on Flow ............................................................................................................ 81 

 4.2 Effects on Sediment and Debris Deposition ................................................................ 107 

 4.3 Effects on Temperature ................................................................................................ 123 

 4.4 Effects on Food Availability ........................................................................................ 124 

 4.5 Supporting Articles ...................................................................................................... 129 

5 OTHER IMPACTS ............................................................................................................. 134 

 5.1 Nonnative Species ........................................................................................................ 134 

 5.2 Parasitism ..................................................................................................................... 139 

 5.3 Climate Change ............................................................................................................ 143 

 5.4 Supporting Articles ...................................................................................................... 145 

6 CONSERVATION AND MANAGEMENT ...................................................................... 149 

 6.1 Habitat and Species Management ................................................................................ 149 

 6.2 Monitoring Techniques ................................................................................................ 196 

 6.3 Computer Modeling ..................................................................................................... 200 

 6.4 Supporting Articles ...................................................................................................... 208 

7 CITATIONS INCLUDED IN BIBLIOGRAPHY .............................................................. 211 
Humpback Chub Annotated Bibliography September 2009

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Humpback Chub Annotated Bibliography September 2009

 v 

NOTATION 

The following is a list of the acronyms, initialisms, and abbreviations (including units of 

measure) used in this document. 

ACRONYMS, INITIALISMS, AND ABBREVIATIONS 

AFDM ash-free dry mass 

AGFD Arizona Game and Fish Department 

AMP Adaptive Management Program 

B-F Baker and Fraser method 

BHBF Beach Habitat-Building Flow 

BNT brown trout 

BO biological opinion 

CFR Code of Federal Regulations

CI confidence interval 

CL confidence limit 

CPE catch per effort 

CPUE catch per unit effort 

CV coefficient of variation 

CY calendar year 

DOI Department of the Interior 

DPS distinct population segment 

EF electrofishing 

EIS Environmental Impact Statement 

FR Federal Register

GCD Glen Canyon Dam 

GCDAMP Glen Canyon Dam Adaptive Management Program 

GCES Glen Canyon Environmental Studies 

GCMRC Grand Canyon Monitoring and Research Center 

GCM General Circulation Model 

GEMSS Generalized Environmental Modeling System for Surface Waters 

GIS geographical information system 

HBC humpback chub 

ICS Intentionally Created Surplus 

ISMP Interagency Standardized Monitoring Program 

Kn relative condition 
Humpback Chub Annotated Bibliography September 2009

 vi 

LCR Little Colorado River 

LSSF low summer steady flow 

mtDNA mitochondrial DNA 

msat microsatellite 

MLFF modified low fluctuating flow 

MSCP Multispecies Conservation Plan 

N sample size 

Nb effective number of breeders per year 

Ne effective population size per generation 

NWR National Wildlife Refuge 

P probability of obtaining a result at least as extreme as that observed, assuming the 

null hypothesis is true. 

PCE primary constituent elements 

PHABSIM physical habitat simulation model 

PIT passive integrated transponder 

PSD proportional stock density 

r correlation coefficient 

R2 coefficient of regression 

RBT rainbow trout 

Reclamation Bureau of Reclamation 

RIP Recovery Implementation Program 

RK river kilometer 

RM river mile 

ROD Record of Decision 

SWS selective withdrawal system 

TL total length 

USC United States Code

USFWS U.S. Fish and Wildlife Service 

USGS U.S. Geological Survey 

VIC Variable Infiltration Capacity 

ww wet weight 

YOY young-of-the-year 
Humpback Chub Annotated Bibliography September 2009

 vii 

UNITS OF MEASURE

μg microgram 

cfs cubic feet per second 

cm centimeter(s) 

d day(s) 

ft foot (feet) 

h hour(s) 

ha hectare(s) 

in. inch(es) 

kg kilogram(s) 

km kilometer(s) 

L liter(s) 

lb pound(s) 

m meter(s) 

maf million acre-feet 

mg milligram(s) 

mL milliliter(s) 

mi mile(s) 

min minute(s) 

mm millimeter(s) 

mo month(s) 

s second(s) 

wk week(s) 

yr year(s) 
Humpback Chub Annotated Bibliography September 2009

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Humpback Chub Annotated Bibliography 1 September 2009

 

ANNOTATED BIBLIOGRAPHY FOR THE HUMPBACK CHUB (GILA CYPHA) 

WITH EMPHASIS ON THE GRAND CANYON POPULATION 

Prepared by 

Celine Goulet and Kirk LaGory 

Environmental Science Division 

Argonne National Laboratory 

September 2009 

1 INTRODUCTION 

Glen Canyon Dam is a hydroelectric facility located on the Colorado River in Arizona 

that is operated by the U.S. Bureau of Reclamation (Reclamation) for multiple purposes 

including water storage, flood control, power generation, recreation, and enhancement of fish 

and wildlife. Glen Canyon Dam operations have been managed for the last several years to 

improve conditions for the humpback chub (Gila cypha) and other ecosystem components. 

An extensive amount of literature has been produced on the humpback chub. We 

developed this annotated bibliography to assist managers and researchers in the Grand Canyon as 

they perform assessments, refine management strategies, and develop new studies to examine the 

factors affecting humpback chub. The U.S. Geological Survey recently created a multispecies 

bibliography (including references on the humpback chub) entitled Bibliography of Native 

Colorado River Big Fishes (available at www.fort.usgs.gov/Products/data/COFishBib). That 

bibliography, while quite extensive and broader in scope than ours, is not annotated, and, 

therefore, does not provide any of the information in the original literature. 

In developing this annotated bibliography, we have attempted to assemble abstracts from 

relevant published literature. We present here abstracts taken unmodified from individual reports 

and articles except where noted. The bibliography spans references from 1976 to 2009 and is 

organized in five broad topical areas, including: (1) biology, (2) ecology, (3) impacts of dam 

operations, (4) other impacts, and (5) conservation and management, and includes twenty 

subcategories. Within each subcategory, we present abstracts alphabetically by author and 

chronologically by year. We present relevant articles not specific to either the humpback chub or 

Glen Canyon Dam, but cited in other included reports, under the Supporting Articles 

subcategory. We provide all citations in alphabetical order in Section 7. 
Humpback Chub Annotated Bibliography 2 September 2009

 

2 BIOLOGY

2.1 ANATOMY AND PHYSIOLOGY 

Berry, C.R. and R. Pimentel. 1985. Swimming performances of three rare Colorado River 

fishes. Transactions of the American Fisheries Society 114:397–402. 

A stamina tunnel was used to determine the prolonged swimming performance of age-0 

humpback chubs Gila cypha, bonytail chubs G. elegans, and Colorado squawfish Ptychocheilus 

lucius and of subadult Colorado squawfish. The “fatigue velocity” in body lengths per second at 

which 50% of the test fish were fatigued (FV50) was determined at 14, 20, and 26°C. The ranges 

of FV50 values for the three fishes (average total length in parentheses) were humpback chubs 

(95 mm), 4.4-5.7; bonytail chubs (99 mm), 4.7-5.8; small Colorado squawfish (104 mm), 4.0-

4.5; large Colorado squawfish (432 mm), 2.0-2.3. Absolute speed of large Colorado squawfish 

was about 2.4 times that of small Colorado squawfish. Swimming ability of the sub-yearlings 

increased with increased water temperature. These rare fish had prolonged-swimming abilities 

similar to other fish species. 

Berry, D.R. 1984. Hematology of four rare Colorado River fishes. Copeia 3:790–793. 

The razorback sucker (Xyrauchen texanus), Colorado squawfish (Ptychocheilus lucius), 

humpback chub (Gila cypha) and bonytail chub (G. elegans) are native to the Colorado River 

system. Fish culture and stocking can be aided by use of clinical tests to determine fish health, 

but hematology of healthy fish must be known. Reported here are hematological characteristics 

for certain life stages of the four Colorado River fishes. 

Didenko, A.V., S.A. Bonar and W.J. Matter. 2004. Standard weight (Ws) equations for 

four rare desert fishes. American Journal of Fisheries Management 24(2):697–703. 

Standard weight (Ws) equations have been used extensively to examine body condition in 

sport fishes. However, development of these equations for nongame fishes has only recently 

been emphasized. We used the regression-line-percentile technique to develop standard weight 

equations for four rare desert fishes: flannelmouth sucker Catostomus latipinnis, razorback 

sucker Xyrauchen texanus, roundtail chub Gila robusta, and humpback chub G. cypha. The Ws

equation for flannelmouth suckers of 100-690 mm total length (TL) was developed from 17 

populations: log10 Ws = –5.180 + 3.068 log10 TL. The Ws equation for razorback suckers of 110-

885 mm TL was developed from 12 populations: log10 Ws = –4.886 + 2.985 log10 TL. The Ws

equation for roundtail chub of 100-525 mm TL was developed from 20 populations: 

log10 Ws = –5.065 + 3.015 log10 TL. The Ws equation for humpback chub of 120-495 mm TL 

was developed from 9 populations: log10 Ws = –5.278 + 3.096 log10 TL. These equations meet 

criteria for acceptable standard weight indexes and can be used to calculate relative weight, an 

index of body condition. 
Humpback Chub Annotated Bibliography 3 September 2009

 

Douglas, M.E. 1993. An analysis of sexual dimorphism in an endangered cyprinid fish 

(Gila cypha Miller) using video image technology. Copeia 1993:334–343. 

Univariate and multivariate techniques were used to evaluate sexual dimporphism in 

53 morphometric measures taken from 63 adult specimens of endangered cyprinid, the 

humpback chub (Gila cypha). Specimens were filmed and released unharmed after their capture 

in the Colorado and Little Colorado rivers of the Grand Canyon (Arizona). Morphometric data 

were later extracted from film using a microcomputer and image analysis software. Because of 

the unique morphology of this fish, analyses emphasized its anterodorsal hump. Only two of 

53 characters (3.8%) revealed significant sexual dimorphism in an analysis of covariance; 

approximately what one would expect from chance alone (i.e., one in 20, or 5%). A discriminant 

analysis correctly classifies specimens by sex only 60% of the time, which is not significantly 

different from random expectations. Multiple group principal components analysis (MGPCA) 

and sheared PCA using all 53 characters also failed to delineate significant sexual dimorphism. 

Morphological shape differences among individuals, regardless of sex, were clearly apparent 

from character loadings onto both principal component 2 and sheared principal component 2. 

These differences were due to extent and development of the nuchal hump and to concomitant 

changes in concavity and length of the head which accompany development. These differences 

appear ontogenetically based and are unrelated to either sexual or seasonal variation. 

Douglas, M.E., M.R. Douglas, J.M. Lynch, and D.M. McElroy. 2001. Use of geometric 

morphometrics to differentiate Gila (Cyprinidae) within the Upper Colorado River basin. 

Copeia 2:389-400. 

Video images of 215 adult Gila robusta and 148 endangered Gila cypha were collected 

from May 1991–October 1992 at eight Colorado River basin localities (seven upper basins and 

one lower basin). The two species were sympatric at five of these locations; G. robusta was 

absent at one site, whereas G. cypha was missing at two others. Saggital views of each individual 

were videotaped and 25 morphological points (15 anatomical landmarks and 10 helping points) 

identified. Bookstein shape coordinates were calculated from Cartesian coordinates of these 

landmarks and points, whereas centroid size was used as a measure of body size. Shape 

differences were evaluated among populations of each species using MANOVA and canonical 

variates analysis. In G. cypha, variation encompassed three aspects: nuchal hump (most 

pronounced in Grand Canyon forms), relative head size (larger in Cataract Canyon forms), and 

caudal peduncle dimensions (shorter with a tapering depth in Cataract Canyon forms but longer 

and uniformly deeper in those from Desolation Canyon). Nuchal development in G. robusta is 

slight, hence only head and peduncle dimensions distinguished populations. Those individuals 

from Cataract Canyon had relatively shorter peduncles that (again) tapered in depth from anterior 

to posterior, whereas G. robusta from Desolation Canyon possessed peduncles that were much 

longer and of uniform depth. Specimens from Debeque and Rifle Canyons had proportionally 

smaller heads. Variation among all 13 populations (i.e., both species together) was evaluated 

using relative warp analysis, with G. cypha and G. robusta clearly separated at all sympatric 

locations except those from Desolation and Caratact Canyons. Here, body shapes of the two 

species converged. Overall, shape variation in both species is clinal. Although results from our 

geometric morphometric analysis were statistically similar to those based on distances derived 
Humpback Chub Annotated Bibliography 4 September 2009

 

from a truss analysis, the geometric approach visually demonstrated phenotypic differences 

among populations and species and this, in turn, has management implications. 

Hendrickson, D.A. and E.B. Brothers. 1994. Utility of otoliths of Grand Canyon 

humpback chub Gila cypha for age determinations and as indicators of ecological history of 

individuals. Proceedings of the Desert Fishes Council 25:30-31. 

Otoliths of teleosts are crystalline structures of the inner ear, the micro- structure and 

chemistry of which have been found in other species to contain detailed growth and temperature 

histories of individuals. We have verified the daily periodicity of increment formation in 

hatchery populations of the surrogate bonytail chub Gila elegans, and have used daily increments 

in one of the three otoliths (lapillus) to age young of the year humpback chubs taken in 1990 and 

1991 from both the mainstream Colorado River and the Little Colorado River (LCR). Spawning 

in the LCR appears to correlate with decreasing discharge in that river in spring or early summer. 

Growth is rapid in the LCR, whereas, all fish taken from the mainstream Colorado (a cold, nearconstant temperature river comprised almost entirely of hypolimnetic releases from Glen Canyon 

dam) are much smaller than individuals of equal age captured in the LCR. Growth in the 

mainstream is extremely slow, but otoliths indicate that young-of-the-year (YOY) occasionally 

encounter warmer, diurnally cycling, temperature regimes, perhaps tributary mouths or 

backwaters, where they remain for periods of up to a week and grow at much higher rates. In 

some individuals taken from the mainstream Colorado, abrupt transitions from periods of rapid 

to very slow growth are interpreted to equate to movement from the LCR to the much colder 

mainstream. Ages, otolith structure, and locations of some YOY taken from the mainstream 

almost certainly preclude an origin in the LCR. At least limited spawning and recruitment to at 

one or two months of age does appear to have occurred in the mainstream or closely associated 

habitats outside of the LCR, both up- and downstream of the LCR. 

 

Lorenzen, K. 1996. The relationship between body weight and natural mortality in fish: a 

comparison of natural ecosystems and aquaculture. Journal of Fish Biology 49:627-647. 

The relationship between body weight and natural mortality in juvenile and adult fish was 

analysed for different aquatic ecosystems: lakes, rivers, the ocean, and pond, cage and tank 

aquaculture systems. Mortality was modelled as a power function of weight, and the parameters 

b (exponent) and Mu (mortality at the unit weight of 1 g) estimated for fish in the six ecosystems, 

as well as within selected populations, species and families. At the ecosystem level, no 

significant differences in parameters were found between lakes, rivers and the ocean and a joint 

mortality-weight relationship for all natural ecosystems was estimated with parameters b = 

-0.288 (90% confidence limit [CL; -0.315, -0.261]) and Mu = 3.00 (90% CL[2.70, 3.30]) per 

year. Among the culture systems, mortality-weight relationships in ponds and cages were not 

significantly different and a joint relationship was estimated. The weight exponents of mortality 

in ponds/cages and tanks were very similar at about b = −0.43, and significantly more negative 

than in natural ecosystems. Mortalities at unit weight were significantly lower in tanks (0.91/yr) 

than in ponds/cages (2.24/yr), and both were significantly lower than in natural ecosystems. No 

systematic differences were found between the mortality-weight relationships determined for 

individual populations, species or families, and fish in the respective ecosystems. It is 

hypothesized that aquaculture mortality-weight relationships indicate the allometric scaling of 

non-predation mortality, which is therefore more strongly size dependent than predation 
Humpback Chub Annotated Bibliography 5 September 2009

 

mortality. If non predation mortality in natural ecosystems shows a similar scaling with body 

weight, then the allometric exponent of predation mortality must be less negative than that 

observed for total natural mortality. Implications of the established mortality-weight 

relationships for aquaculture and culture-based fisheries are discussed. 

Meretsky, V.J., R.A. Valdez, M.E. Douglas, M.J. Brouder, O.T. Gorman, and P.C. Marsh. 

2000. Spatiotemporal variation in length-weight relationships of endangered humpback 

chub: implications for conservation and management. Transactions of the American 

Fisheries Society 129:419–428. 

The largest population of endangered humpback chub Gila cypha inhabits the lower LCR 

and the main-stem Colorado River near its confluence with the LCR in Grand Canyon, Arizona. 

At present, fish in both rivers spawn almost exclusively in the LCR. Flows in the main-stem 

Colorado River are regulated by Glen Canyon Dam, and water temperature approximates predam winter temperatures year-round. The LCR continues to provide a relatively natural 

hydrograph and seasonal warming patterns. Length–weight relationships among adult humpback 

chub from the lower Colorado River basin showed a seasonal pattern of declining condition 

during spring spawning season followed by recovery of condition during summer through early 

winter. Fish from the main stem recovered condition more rapidly after reproduction than did 

fish from the LCR and may have benefited from dam-mediated environmental changes. Grand 

Canyon Colorado River fish had the greatest weight at length of eight locations sampled in the 

upper and lower basins. Records since 1978 indicate a decline in condition of lower basin 

humpback chub coincident with a reported decline in population size in Grand Canyon. We 

recommend increased monitoring of all populations, including mark–recapture studies to provide 

population estimates during the spawning season and condition monitoring during October–

November to determine more subtle changes in fish health. 

Portz, D. and H. Tyus 2004. Fish humps in two Colorado River fishes: a morphological 

response to cyprinid predation? Environmental Biology of Fishes 71(3):233–245. 

Extant fishes endemic to the upper Colorado River of the American southwest include 

only cyprinids and catostomids. A curious attribute in species of both groups is the presence of a 

large nuchal hump. Largest cyprinid humps occur in humpback chub, Gila cypha, and largest 

catostomid humps occur in razorback sucker, Xyrauchen texanus. Several authors have 

suggested the humps confer a hydrodynamic advantage to life in fast flow, but this premise has 

not been confirmed with experimental work. To test the role of humps in Colorado River fishes, 

the authors subjected whole-body casts of preserved specimens with humps and with humps 

removed to controlled flows in an experimental tank. These tests confirmed that humps increased 

drag coefficients for X. texanus and G. cypha with no additional lift component. High energetic 

costs of locomotion and position-holding with a large hump, and the additional metabolic 

expense of forming large humps, suggest that the humps are not relict structures. Instead, the 

authors argue that these large humps represent convergent evolution prompted by predation from 

a cyprinid piscivore. Colorado pikeminnow, Ptychocheilus lucius, top piscivore in the Colorado 

River system, is the only native fish capable of consuming large X. texanus and G. cypha, and it 

also is sympatric with them. However, lack of jaw teeth and a relatively small jaw gape limit the 

maximum prey size that P. lucius can consume. Based on gape size, about 55% of X. texanus and 
Humpback Chub Annotated Bibliography 6 September 2009

 

71% of G. cypha could be consumed by even the largest P. lucius. However, vulnerability would 

increase to 73 and 83% respectively if these species did not have humps. Co-evolution tends to 

favor predator defense mechanisms in prey most vulnerable to such a voracious predator. 

Development of a large nuchal hump provides a deep body that is difficult or impossible for P. 

lucius to ingest. 

Robinson, A.T. and M.R. Childs. 2001. Juvenile growth of native fishes in the Little 

Colorado River and in a thermally modified portion of the Colorado River. North 

American Journal of Fisheries Management 21:809–815. 

We estimated juvenile growth rates of four native fish species using the von Bertalanffy 

growth equation and length data from fish captured in 1991-1994 in the Little Colorado River, a 

tributary to the Colorado River in Arizona in the Grand Canyon. We compared growth rates to 

water temperatures for all four species and modeled the effects of warming the Colorado River 

(through proposed retrofit of the Glen Canyon Dam) on the growth of age-0 emigrants from the 

tributary. Juvenile growth rates in the Little Colorado River were faster for flannelmouth sucker 

Catostomus latipinnis, slowest for speckled dace Rhinichthys osculus, and intermediate for 

humpback chub Gila cypha and bluehead sucker Catostomus discobolus. Our model indicates 

that native fish immigrating into the cold Colorado River (8-12°C) from the relatively warm 

Little Colorado River during their first 3 months of life will grow very little by the end of their 

first year. According to other studies, older, larger fish that disperse into the Colorado River are 

more likely to survive than those that migrate as larvae. Growth, and possibly survival, of native 

fish larvae that drift from tributaries into the Colorado River could be increase if water released 

from Glen Canyon Dam is warmed during the period of larval drift. 

Snyder, D.E. 1976. Terminologies for intervals of larval fish development. Pages 41–60 in 

J. Boreman, editor. Great Lakes fish egg and larvae identification, proceedings of a 

workshop. U.S. Fish and Wildlife Service FWS/OBS–76/23. 

Several terminology systems for larval fish phases are reviewed, and a new standardized 

system is recommended, based on four phases: (1) larva, (2) protolarva, (3) mesolarva, and (4) 

metalarva. The phases are based on the morphogenesis of the median finfold and fin elements 

(spines, and rays); paired fins are included in the definition of the last phase. The larval phase is 

characterized by obvious fin morphogenesis following hatching or parturition, ending 

immediately before: (1) the last finfold and atrophying fins are adsorbed beyond recognition; (2) 

the full complement of distinct fin elements (spines and rays) become apparent in all fins; and (3) 

principal ray segmentation becomes apparent in all fins. This phase may be absent in some fish. 

In the protolarval phase distinct median fin elements (dorsal, anal, or caudal spines or rays) are 

not yet apparent. In the mesolarval phase at least one but not the full complement is present and 

the adult possesses pelvic fins, the pelvic buds or fins are not yet apparent. The metalarval phase 

is characterized by the presence of the full complement of distict principal rays in the median 

fins and, if the adult possesses pelvic fins, the pelvic buds or fins are apparent. Thirteen 

terminology systems are reviewed in this paper, and a term frequency table is given.
Humpback Chub Annotated Bibliography 7 September 2009

 

2.2 REPRODUCTION 

Gorman, O.T. and D.M. Stone. 1999. Ecology of spawning humpback chub, Gila cypha, in 

the Little Colorado River near Grand Canyon, Arizona. Environmental Biology of Fishes 

55:115–133. 

The morphologically unique and endangered humpback chub, Gila cypha, is found in 

canyon-bound reaches of the Colorado River and its tributaries. Now limited to six isolated 

reproducing populations, this species is believed to have been once distributed over a large 

portion of the mainstem river. Because the species inhabits remote canyon areas, little is known 

about its spawning ecology. The largest remaining population occurs in the lower Little 

Colorado River (LCR) near Grand Canyon, where we conducted a three-year study of spawning 

ecology during spring (March-June) 1993-1995. We analyzed seasonal patterns of movement, 

population density, relative condition, spawning scores, and frequency of ripe condition and fin 

abrasions and compared these data with seasonal discharge and water temperature to determine 

spawning phenology and ecology. Spawning commenced in late March, peaked in mid-April, 

and waned in mid-May. A high proportion of males remained ripe over this period, whereas ripe 

females were relatively abundant only in April. Increased densities of adult fish in March-April 

and rapid declines in May-June coupled with recaptures of 18.4% of these adults in the Colorado 

River suggest that portion of the population migrated from the Colorado River into the LCR to 

spawn and then returned. Ripe males aggregated in areas of complex habitat structure with high 

angular variation in bottom profiles (matrix of large boulders, travertine masses combined with 

chutes, runs, and eddies, 0.5-2.0 m deep) and were associated with deposits of clean gravel. Ripe 

females appeared to move to these male aggregations to spawn. Near-spawning (including 

gravid) females and non-spawning fish used similar habitats and were segregated but close (<50 

m) to habitats occupied by aggregations of ripe males. Abrasions on anal and lower caudal fins 

of males and females suggest that spawning involves contact with gravel substrates, where semiadhesive eggs are deposited and females fertilized. The findings of this study should aid 

recovery efforts for humpback chub by identifying spawning habitat within the historic 

distributional range where additional spawning stocks could be established. 

Hamman, R.L. 1982. Spawning and culture of humpback chub. Progressive FishCulturist 44:213–216. 

 During 1981, humpback chub (Gila cypha) were spawned and cultured at Willow Beach 

(Arizona) National Fish Hatchery. This species is listed as endangered by the U.S. Fish and 

Wildlife Service. Seventeen wild females ovulated after injection with 4 mg acetone-dried carp 

pituitary per kilogram of body weight. Eight females were stripped manually, whereas the 

remaining nine injected females spawned naturally in a trout raceway. Mean fecundity of eight 

females was 2,523. Incubation periods ranged from 102 to 146 h at water temperatures of 21-

22°C, 115 to 160 h at 19-20°C, 167 to 266 h at 16-17°C, and 340 to 475 h at 12-13°C. Survival 

of eggs was 79% at 21-22°C, 84% at 19-20°C, 62% at 16-17°C, and 12% at 12-13°C. At 

hatching, total length and weight of fry ranged from 6.7 to 7.4 mm and 2.8 to 4.2 mg. The 

survival of swim-up fry was 99% at 21-22°C, 95% at 19-20°C, 91% at 16-17°C, and 15% at 12-

13°C. The length of fry placed in raceways had doubled by 21 to 28 days, and fingerlings 

attained a range of 36.9 to 47.5 mm and 586.5 to 887.4 mg by day 56 after hatching. 
Humpback Chub Annotated Bibliography 8 September 2009

 

Kaeding, L.R., B.D. Burdick, P.A. Schrader and C.W. McAda. 1990. Temporal and 

spatial relations between the spawning of humpback chub and roundtail chub in the upper 

Colorado River. Transactions of the American Fisheries Society 119:135–144. 

Gonadosomatic indices (100  gonad weight/whole-body weight) and the occurrence of 

expressible gametes indicated a temporal overlap in the spawning of humpback chub Gila cypha 

and roundtail chub G. robusta at Black Rocks, a turbulent, deepwater reach of the upper 

Colorado River, Colorado (39°N, 109°W). Radiotelemetry showed that roundtail chub moved 

throughout the upper Colorado River during the spawning season, whereas humpback chub were 

restricted almost entirely to the 1.8-km Black Rocks reach; however, spatial isolation of the 

species during spawning was not demonstrated. A principal component analysis of morphologic 

measurements taken from live fish supported taxonomic assignments made in the field and 

suggested that most of the few specimens considered hybrids or intergrades by field personnel 

were actually humpback chub; however, an analysis based on fin ray counts indicated that this 

group included roundtail chub, hybrids, or backcross individuals. The strong affinity of 

humpback chub for the unique habitat conditions created by water flowing rapidly among large, 

angular boulders and shoreline rock outcrops at Black Rocks and elsewhere suggests that the 

unusual morphology of this species is an adaptation to life in such habitats. The limited 

availability of such habitats might be an important factor controlling the distribution and relative 

abundance of the humpback chub, a species now listed as endangered. 

Stone, D.M. and O.T. Gorman. 2005. Ontogenesis of endangered humpback chub (Gila 

cypha) in the Little Colorado River, Arizona. The American Midland Naturalist 155:123–

135. 

 

The largest population of endangered humpback chub Gila cypha inhabits the Colorado 

River below Glen Canyon Dam and the lower 14 km of the Little Colorado River (LCR), 

Arizona. Currently, adults from both rivers spawn and their progenies grow and recruit to 

adulthood primarily within the LCR, where we studied G. cypha’s life history using hoop net 

capture data. Humpback chub undergo an ontogenesis from diurnally active, vulnerable, 

nearshore-reliant YOY (30–90 mm total length) into nocturnally active, large-bodied adults 

(≥180 mm TL). During the day, adults primarily resided in deep midchannel pools; however, at 

night they dispersed inshore amongst the higher densities of YOY conspecifics. Many YOY G. 

cypha shifted to nocturnal habitats that provided greater cover, possibly, to avoid inshore 

invading adults. These findings mirror predator-prey scenarios described in other freshwater 

assemblages, but do not refute other plausible hypotheses. Gila cypha piscivorous activity may 

escalate in hoop nets, which can confine fish of disparate sizes together; adults were significantly 

associated with YOY conspecifics and small dead fish in hoop nets at night and eight G. cypha

(156–372 mm TL) regurgitated and/or defecated other fish body parts during handling following 

capture. Gila cypha can definitely be piscivorous given the opportunity, but the magnitude of 

their piscivorous activity in the wild is debatable. 
Humpback Chub Annotated Bibliography 9 September 2009

 

2.3 GENETICS AND SYSTEMATICS 

DeMarais, B.D. and T.E. Dowling. 1993. Introgressive hybridization and evolution of 

Colorado River basin Gila (Teleostei: Cyprinidae). Proceedings of the Desert Fishes 

Council 24:67. 

Allozymes and mitochondrial DNA (mtDNA) were used to assess population and 

phylogenetic relationships among Gila elegans, Gila cypha, and stocks of Gila robusta from the 

Colorado River basin. Admixture of molecular markers diagnostic for these three species in 

stocks of G. robusta and discordance of phylogenetic topologies for allozymes and mtDNA 

resulted from introgressive hybridization. Examples of relatively recent as well as evolutionary 

old hybridization have been identified; therefore, interspecific gene flow have been an important 

evolutionary force that has contributed to morphological diversity in these fishes. 

Douglas, M.E., W.L. Minckley and H.M. Tyus. 1989. Qualitative characters, chubs of the 

genus Gila (Pisces: Cyprinidae) and the "art of seeing well". Copeia 3:653-662. 

Qualitative scoring is frequently overlooked in preference to counts or measurements of 

individual characters, particularly for species whose overlap in morphology makes clear 

separation difficult. Quantitative measurements and counts of single characters were compared to 

qualitative rankings of selected morphological features of chubs from the Yampa River, 

Colorado. Data were collected by technicians with no specialized training in systematics. A high 

degree of morphological variability confounded identification using the quantitative data set, 

while principal components analysis of qualitative data clearly separated Gila cypha (humpback 

chub) and G. robusta (roundtail chub). Totals of 32 G. cypha and 336 G. robusta were identified; 

no intermediates were indicated. We thus demonstrate that scoring of complex characteristics is 

useful for endangered fishes that must be minimally handled to insure uninjured release. The 

clean separation of syntopic G. cypha and G. robusta supports protection of the lower Yampa 

River, the only location in the upper Colorado River basin in which apparent hybridization.

Douglas, M.E., W.L. Minckley and H.M. Tyus. 1998. Multivariate discrimination of 

Colorado Plateau Gila spp.: the art of seeing well revisited. Transactions of the American 

Fisheries Society 127:163–173. 

Fishery managers have long been troubled by phenotypic variation within and among 

Colorado Plateau Gila. The problem is twofold. From an historical perspective, there was 

reticence to investigate fishes long considered as “undesirable.” In a taxonomic sense, there is 

confusion over within- and among-species variability. We document the former, then clarify the 

latter by applying discriminant analysis to meristic and morphometric data collected from 

museum specimens. We test three hypotheses: roundtail chub G. robusta, humpback chub G. 

cypha, and bonytail G. elegans are morphologically indistinguishable; juveniles are assignable to 

species based upon adult characters; and putative hybrids are morphologically intermediate 

between parental forms. Through the use of meristic characters in nonparametric discriminate 

analysis, over 95% of all adults were segregated to species. By using morphometric characters, 

97% could be allocated to species. Gila robusta was easily separated from G. cypha and G. 

elegans. The latter were most difficult of all species-pairs to discriminate, yet field characters 
Humpback Chub Annotated Bibliography 10 September 2009

 

still segregated them at better than 95%. A discriminant function, based upon five morphometric 

characters, will allocate unknowns to species. Juvenile G. elegans were often misidentified as G. 

robusta. Putative hybrids were generally assigned to one or the other parental form; thus, hybrid 

intermediacy could not be rejected. However, paucity of hybrids weakened the test. We 

conclude that factors most important in segregating these species are character selection, 

adequate analyses, and the “art of seeing well.” 

Douglas, M.R. and M.E. Douglas. 2007. Genetic structure of humpback chub Gila cypha

and roundtail chub G. robusta in the Colorado River ecosystem. Final report, Department 

of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, 

Colorado. 

Humpback chub, Gila cypha, and roundtail chub, G. robusta, are found in the Upper 

Colorado River drainage (Green and Colorado rivers and their tributaries, in the states of 

Colorado, New Mexico, Utah, Wyoming). The former species is also found in Marble and Grand 

Canyons (Arizona) of the lower basin Colorado River. Natural populations of a third species, 

Bonytail, G. elegans have been mostly extirpated from the wild. All three species have been 

affected by anthropogenic modifications of the Colorado River ecosystem, with two (G. cypha 

and G. elegans) listed as federally endangered, and the third considered for listing, as well as 

state-designated ‘of concern’ throughout its range. We evaluated molecular genetic diversity 

across four mtDNA regions (total 1,869 base pairs) for 336 specimens representing four upper 

basin populations of G. cypha, seven upper basin populations of G. robusta, and nine lower basin 

Marble/ Grand canyon “aggregates” of G. cypha. In addition, using larger sample sizes, we also 

surveyed these same populations and species at 16 microsatellite (msat) DNA loci for a total of 

643 specimens. 

Neither G. cypha nor G. robusta could be discriminated using mtDNA, although this 

marker was successful in separating both from G. elegans at 4.7—4.8% sequence divergence 

(± 0.0—0.1%). The recent coalescence of lineages in G. cypha / G. robusta is unusual, especially 

given (a) fossil history, (b) the broad geographic sampling conducted in this study, and (c) the 

number (and evolutionary rate) of the mtDNA regions examined. 

The most parsimonious explanation for these data is that both species were reduced to 

very small populations by an end-of-Pleistocene warming event and were subsequently forced 

together into refugial (and shrinking) riverine habitat, thus becoming syntopic with one another. 

They then hybridized, possibly backcrossing (progeny to parental forms) over an extended 

temporal span. Eventually, pluvial conditions returned, the aquatic environment subsequently 

expanded, and both species returned to familiar and exclusive niches within the river where they 

reproduced with like kind. Nevertheless, the large-scale population reduction would have re-set 

their mtDNA evolutionary clocks, and hybridization event(s) would have provided both species 

with the same mtDNA haplotype(s). 

These data are also congruent with shallow mtDNA diversity uncovered in a basinwide 

study of Flannelmouth sucker (Catostomus latipinnis), giving credence to the fact that the 

aforementioned perturbation at end-of-Pleistocene was ecosystem-wide and thus affected more 

than a single species of fish. Two interesting points emerged from the G. cypha / G. robusta 
Humpback Chub Annotated Bibliography 11 September 2009

 

mtDNA data analysis. One is a lack of haplotype differentiation in Desolation Canyon, a location 

previously identified in a morphological analysis as exhibiting a ‘locality effect’ for G. cypha 

and G. robusta, where individuals of both species resembled one another more closely than 

either resembled conspecific populations elsewhere in the basin. Desolation Canyon specimens 

also reflected the lowest mtDNA k-value (i.e., an estimate of how much on average two random 

haplotypes differ), thus indicating that G. cypha and G. robusta are more similar to one another 

on the mtDNA level at this site than they are at other sites. These mtDNA results mirror the 

morphological results at Desolation Canyon. 

Haplotype trees generated for all specimens graphically display the admixture of 

individuals with regard to mtDNA haplotype. This confusion extends not only across populations 

in each basin, but across upper and lower basins, and most importantly, across species as well. 

Although mtDNA is not well suited for hybrid analysis, our data nevertheless uncovered seven 

G. cypha with a G. elegans haplotype (with six of these in Marble and Grand canyons, the other 

in Desolation Canyon), whereas but a single G. robusta was found to possess a G. elegans 

haplotype (also from Desolation Canyon). 

Analysis of nuclear DNA offered additional perspectives. Microsatellite DNA provided 

sufficient resolution to discriminate among populations and basins when G. cypha and G. 

robusta were evaluated. However, one difficulty with our msat analysis is that upper basin G. 

cypha and G. robusta are too similar to one another to adequately differentiate them. This 

problem is particularly manifest in upper basin G. cypha. Different software algorithms provide 

separate perspectives on the number of discrete populations within the upper basin and lower 

basin, and across both species. 

We elect to take a conservative approach to delineating subgroups based on our msat data and 

select the analyses that recognize six groups. These six-clusters are: (1) G. elegans; (2) all Grand 

Canyon G. cypha ‘aggregates’; (3) Desolation Canyon G. cypha and G. robusta; (4) upper basin 

G. cypha (excluding G. cypha from Desolation Canyon); (5) upper basin G. robusta (excluding 

G. robusta from Desolation Canyon and Yampa River); and (6) upper basin G. robusta from the 

Yampa River. 

Within Marble and Grand canyons, the northern and southern extremities of the 

distribution of G. cypha represent populations with greatest admixture overall. All other Grand 

Canyon aggregates (from HLCR through HHAV) are linked via gene flow, and this has kept 

them relatively homogeneous amongst themselves. It has also contributed to the high scores they 

reflect in our admixture evaluations. Marble and Grand canyon aggregates of G. cypha are 

relatively homogeneous amongst themselves (save for the populations at the upper and lower end 

of the canyon), yet as a group they are differentiated from upper basin G. cypha. However, the 

two extrema populations (30- mile and Western Grand Canyon) reflect very small sample sizes 

(eleven and ten, respectively). Given this, there is little statistical basis for making any claims 

with regard to supposed uniqueness. 

Conclusions 1: Our data support the recognition of six ‘Management Units’ (MUs). The 

Marble/ Grand Canyon aggregates of G. cypha would represent a distinct MU, as would 

Desolation Canyon G. cypha and G. robusta (as a group). Another MU would consist of 
Humpback Chub Annotated Bibliography 12 September 2009

 

G. robusta from the Yampa River. In addition, G. robusta from upper basin locations (save 

Desolation Canyon and Yampa River) could be recognized as an MU, as could G. cypha from 

upper basin locations (save Desolation Canyon). In addition, bonytail would represent the sixth 

MU. 

Conclusions 2: Marble and Grand canyon ‘aggregates’ of G. cypha were not overly 

distinct at the msat level. Aggregates appeared to be connected by gene flow, suggesting 

downstream drift of larvae and juveniles as a likely scenario. The Little Colorado River 

population would be the primary source, but contribution from occasional local reproduction by 

mainstem aggregates cannot be excluded. 

Conclusions 3: The G. cypha population at 30-mile in Marble Canyon was recorded as 

having two individuals with G. elegans haplotypes, and the msat profile for this population is 

intermediate between genotypes found in Desolation Canyon (a hypothesized hybrid population) 

and Grand Canyon. Although reproduction has been documented for the 30-mile population, it 

suffers from chronic low numbers (at least chronic low numbers of catchable fish). However, this 

is the only population in Grand Canyon that is upstream from the Little Colorado River and is 

least likely to receive migrants from downstream locations. Due to its potential distinctiveness it 

should be further studied. 

Conclusions 4: Upper basin G. robusta are seemingly more distinct than are upper basin 

G. cypha, and G. robusta from the Yampa River fall out as distinct in the five- and six-cluster 

models. Only the four-cluster model groups upper basin G. robusta with upper basin G. cypha. 

While G. robusta in the Yampa River certainly appears distinct and potentially unique, our data 

are inconclusive about status of Yampa River G. cypha. Additional studies must be conducted on 

G. cypha from the Yampa River, in that only seven individuals were available to us. Such 

chronic low numbers preclude any statistically valid conclusions. Management decision should 

not be based on the assumption of Yampa River G. cypha being distinct, simply because this is 

neither supported nor rejected by our data. 

Conclusions 5: Our last conclusion centers on G. elegans. The individuals we evaluated 

in this study were hatchery-derived, but in some analyses, they were grouped with the unique 

G. cypha/ G. robusta populations of Desolation Canyon. We identified a single individual from 

this population that retained both a mtDNA haplotpye and a msat DNA genotype of G. elegans. 

Given the propensity for Colorado River native fishes to hybridize throughout their long history, 

it is not surprising that alleles characteristic for G. elegans apparently persist in wild populations 

of G. cypha and G. robusta. Similarly, alleles considered characteristic for the latter two species 

were occasionally detected in G. elegans we examined. Albeit historic, admixture among the 

Colorado River Gila species should be taken into account when G. elegans are reintroduced into 

the wild, particularly in locations where the other two species still persist. 

Dowling, T.E. and B.D. DeMarais. 1993. Evolutionary significance of introgressive 

hybridization in cyprinid fishes. Nature 362:444–446. 

Botanists have long recognized introgressive hybridization as important in the evolution 

of plants1, 2. Hybridization among animals is also common3, yet few zoologists have considered 

it evolutionarily important4–6. We report here that in the genus Gila, a morphologically diverse 
Humpback Chub Annotated Bibliography 13 September 2009

 

group of minnows from western North America7, we have discovered a pervasive influence of 

hybridization throughout their evolutionary histories. Gene exchange among distinctive forms 

has contributed to existing diversity, supporting the hypothesis that introgressive hybridization 

can play a significant role in evolution of vertebrates. 

Garrigan, D., P.C. Marsh and T.E Dowling. 2002. Long-term effective population size of 

three endangered Colorado River fishes. Animal Conservation 5(2):95-102. 

The extant genetic variation of a population is the legacy of both long-term and recent 

population dynamics. Most practical methods for estimating effective population size are only 

able to detect recent effects on genetic variation and do not account for long-term fluctuations in 

species abundance. The utility of a maximum likelihood estimator of long-term effective 

population size based upon the coalescent theory of gene genealogies is examined for three 

endangered Colorado River fishes: humpback chub (Gila cypha), bonytail chub (Gila elegans) 

and razorback sucker (Xyrauchen texanus). Extant mtDNA variation in humpback chub suggests 

this species has retained its historical equilibrium genetic variation despite recent declines in 

abundance. The mtDNA variation in razorback suckers indicates the population was quite large 

and expanding prior to recent declines and that rare alleles still survive in the remnant 

populations. The remaining mtDNA variation in bonytail chub indicates that dramatic, recent 

declines may have already obliterated a substantial portion of any historical variation. The results 

from long-term effective population size analyses are consistent with known natural history and 

illustrate the utility of the analysis for endangered species management. 

Hamman, R.L. 1981. Hybridization of three species of chub in a hatchery. Progressive 

Fish Culturist 43(3):140–141. 

A study was undertaken to determine whether the bonytail chub (Gila elegans ) could 

hybridize with the roundtail chub (G. robusta ) and the humpback chub (G. cypha). Of 12,000 

bonytail x roundtail hybrids and 8000 bonytail x humpback hybrids obtained, 7 months after 

hatching, some 500-1000 from each cross survived. Embryos in eggs of both crosses died after 

110 hours in low temperatures, indicating a possible reason for the decline of this endangered 

species in the upper Colorado River Basin. Both hybrids failed to spawn naturally, but it is 

suggested that alterations in the upper basin of the river may increase the potential hybridization 

and the decline of genetically pure stock. 

 

Holden, P.B. and C.B. Stalnaker. 1970. Systematic studies of the cyprinid genus Gila in 

the Upper Colorado River Basin. Copeia 1970:409–420. 

Three hundred and nine specimens of Gila from the Colorado River basin were studied 

by taximetrics analysis. Results of the study indicate that the concept of ecosubspecies or 

ecological subspecies does not fit Colorado basin Gila. The roundtail and bonytail chubs, G. 

robusta and G. elegans respectively, currently treated as subspecies, are well separated 

morphologically, ecologically, and apparently reproductively, and therefore, are better 

considered two species. The relationship between G. cypha, the humpback chub, and G. elegans

is clouded by the presence of intergrade forms. Future investigations are needed to resolve this 

problem. Insufficient material was available to make any conclusions on taxonomic status of the 
Humpback Chub Annotated Bibliography 14 September 2009

 

Virgin River population. However, the subspecies name seminude Cope and Yarrow should be 

restricted to Gila of Virgin River. 

Hurt, C. and P. Hedrick. 2004. Conservation genetics in aquatic species: general 

approaches and case studies in fishes and springsnails of arid lands. Aquatic Sciences 

66(4):402–413. 

 Many aquatic species have become endangered because of the elimination and 

fragmentation of their habitat, human alteration of the environment, and introduced species. New 

applications and insights from genetic studies of endangered species are being used to 

formulate management plans to prevent extinction of endangered taxa. Here we discuss three 

applications of genetic techniques to the conservation of endangered aquatic species in the desert 

Southwest, USA. First, we discuss estimation of long-term effective population size in 

three endangered big-river fishes, bonytail chub (Gila elegans), humpback chub (G. cypha) and 

razorback suckers (Xyrauchen texanus), of the lower Colorado River. For all three species, the 

current census number is much smaller than the estimated effective population size in 

which these species evolved. Second, we discuss the determination of species, ESUs, and MUs 

in the endangered Sonoran topminnow. Molecular genetic data show that the Gila and Yaqui 

topminnows are different species. Experimental examination of pre-mating and postmating reproductive isolation demonstrates that some reproductive isolation has already 

developed between these two species. Finally, springsnails (Pyrgulopsis) of the lower Colorado 

River basin exist only in remote and isolated springs. Examination of molecular variation 

generally supports the morphological designation of 16 different species, although a few species 

have several ESUs. There does not appear to be a correlation of genetic and geographic distance 

between species, suggesting that they are quite old. These genetic studies provide insight into the 

conservation of these rare aquatic species. Although mitigating ecological factors may be most 

significant in preventing extinction, genetic studies can provide the evolutionary context 

for endangered species and identify what units are most in need of conservation. 

Keeler-Foster, C.L., I.B. Spies, V. Bondu-Hawkins and P. Bentzen. 2004. Development of 

microsatellite markers in bonytail (Gila elegans) with cross-species amplification in 

humpback chub (Gila cypha). Molecular Notes 4(1):23–25. 

Bonytail, Gila elegans, is an endangered species of fish native to the Colorado River. 

Primers are presented for 17 microsatellites cloned from bonytail as well as the results of test 

amplifications in bonytail and humpback chub, G. cypha. Bonytail exhibited three to 18 alleles 

per locus across the 17 microsatellites and a mean expected heterozygosity of 0.58 among 10 loci 

used to screen 160 broodstock. Humpback chub exhibited one to six alleles and a mean 

expected heterozygosity of 0.69 among 10 loci that were successfully amplified in that species. 

Minckley, W.L. and B.D. DeMarais. 2000. Taxonomy of chubs (Teleostei, Cyprinidae, 

genus Gila) in the American Southwest with comments on conservation. Copeia (1):251-

256. 

Chubs of the Gila River basin have been variously classified as nominal species, 

subspecies of Gila robusta, or a “complex.” Three full species, robusta, intermedia, and nigra
Humpback Chub Annotated Bibliography 15 September 2009

 

are here recognized, the last possibly arising through more than one hybridization event between 

robusta and intermedia. Following resolution of a nomenclatural problem, G. nigra is 

characterized in a key for species identification. Listing under the Endangered Species Act is 

suggested for all species of Gila in the Colorado River basin. 

Rosenfeld, M.J. and J.A. Wilkinson. 1989. Biochemical genetics of the Colorado River 

Gila complex (Pisces: Cyprinidae). Southwestern Naturalist 34:232–244. 

Protein variation in members of the cyprinid genus Gila endemic to the Colorado River 

drainage (Gila cypha, Gila elegans, Gila robusta robusta, and G. r. seminuda) was examined 

through electrophoresis of 23 presumptive loci. Fixation of loci for different alleles between 

morphologically recognized taxa was not found. Allelic differentiation was incomplete, with 

some variation distributed in a specific or subspecific fashion. Although now extremely reduced 

in numbers, G. elegans may have retained a significant fraction of its original variability. In 

contrast, G. cypha in the Upper Colorado River Basin may have experienced substantial allelic 

loss in recent years. Considerable hybridization may have occurred between G. cypha and 

G. r. robusta in the Upper Basin. The origin of G. r. seminuda may have included hybridization 

between G. elegans and G. r. robusta or their progenitors. Sample sizes were sometimes small, 

and tissues were obtained over a 4-year period from localities often hundreds of kilometers apart; 

consequently, sampling error, temporal shifts in allele frequencies, and isolation by distance as 

well as local differentiation remain unresolved factors. 

2.4 SUPPORTING ARTICLES 

Berry, C.R. 1988. Effects of cold shock on Colorado River squawfish larvae. Southwestern 

Naturalist 33(2):193–197. 

 Larvae of Colorado squawfish (Ptychocheilus lucius) acclimated to 22°C were subjected 

to water temperature decreases of 5, 10, or 15°C within 5 min or within 240 to 300 min. Most 

mortality due to shock occurred in the first 48 h. The 15°C shock in 5 min caused significant 

mortality of 14-day old larvae but did not affect 40-day olds. In addition to causing this direct 

mortality, shocks of 10 or 15°C min caused behavioral changes in 14-day olds that could result 

in indirect mortality of wild fish. 

Bozek, M.A., L.J. Paulson and G.R. Wilde. 1990. Effects of ambient Lake Mohave 

temperatures on development, oxygen consumption and hatching success of the razorback 

sucker. Environmental Biology of Fishes 27:255–263. 

Spawning of razorback suckers, Xyrauchen texanus, in Lake Mohave occurred from 10–

22°C and larvae were collected at water temperatures from 10–15°C in 1982 and 1983. In the 

laboratory, hatching success was similar from 12–20°C, but reduced hatching success was found 

at 10°C while none hatched a 8°C. Development rate and oxygen consumption were positively 

related to incubation temperature. Direct effects of ambient Lake Mohave water temperatures on 

hatching success of razorback sucker embryos are considered minimal. Historical spawning 

temperatures for the species are hypothesized based upon successful incubation temperatures and 

comparison to the white sucker, Catostomus commersoni. 
Humpback Chub Annotated Bibliography 16 September 2009

 

Chart, T. E., D. P. Svendson and L. D. Lentsch. 1999. Investigation of potential razorback 

sucker (Xyrauchen texanus) and Colorado pikeminnow (Ptychocheilus lucius) spawning in 

the lower Green River, 1994 and 1995. Final report of Utah Division of Wildlife Resources 

to Upper Colorado River Endangered Fish Recovery Program, Lakewood, Colorado. 

Colorado pikeminnow spawn in the lower 210 km of the Green River. Based on the 

infrequent collections of adults in the past ten years, sampling efforts for razorback sucker were 

focused around the mouth of the San Rafael River at Green River kilometer (RK) 156. 

Investigations of Colorado pikeminnow spawning were centered on a cobble bar at the mouth of 

Millard Canyon (RK 53.9). Electrofishing and trammel nets were used to sample adults; larval 

light traps and seines were used to sample the early life stages. One adult razorback sucker was 

collected while conducting Interagency Standardized Monitoring Program (ISMP) electrofishing 

in 1995 near Mineral Bottom RK 83.7). This fish (TL = 559 mm, Wt = 2150 g, PIT # = 

lF74374E68) was caught 69 km below the San Rafael River at RK 86; on 16 May, 1995. No 

adult razorback suckers were collected as result of specific project efforts near the mouth of the 

San Rafael River. A total of 48 larval razorback suckers were collected during this study, with 

the majority (91.7%; N=44) of those collected in 1994 near the mouth of the San Rafael River. 

Twenty-eight larvae were collected in the mouth of the San Rafael River and the remaining 

larvae were collected in habitats immediately downstream. No larvae were collected in habitats 

upstream of the San Rafael River/Green River confluence. Incorporating the results of this study 

with those of concurrent efforts in the middle Green River, Muth et al. (1998) determined that 

larval razorback suckers collected in the lower Green River were likely spawned there. Water 

temperatures warm earlier each spring in the lower Green River than the middle Green River. 

The thermal regimes of the Green River at Jensen, Utah, and at Green River, Utah, are discussed 

in light of razorback sucker spawning time. Further investigation into the timing, magnitude, and 

specific location of razorback sucker spawning in the lower Green River is recommended. No 

evidence was found of Colorado pikeminnow spawning in the lower 60 km of the Green River. 

Based on the results of other project efforts it was determined that the timing of sampling for 

adults at the Millard Canyon bar was likely better in June, 1994, than in June, 1995. 

Pikeminnow spawning was delayed throughout the upper Colorado River basin until the latter 

part of July in 1995. Further investigations into pikeminnow spawning in the lower Green should 

be more intensive than this effort and should occur within the next five years. 

Converse, Y.K., L.D. Lentsch and R.A. Valdez. 1999. Evaluation of size-dependent 

overwinter growth and mortality of age-0 Colorado squawfish. Final report of Utah 

Division of Wildlife Resources to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

This report encompasses two important aspects of age-0 Colorado pikeminnow life 

history. First, we investigated usefulness of scale analysis and length-frequency distributions for 

evaluating overwinter mortality and growth of age-0 Colorado pikeminnow. Second, we 

examined associations of age-0 fish length and relative abundance in fall and spring with spatial 

and temporal degree-day accumulation and flow regimes in the Green River system. 
Humpback Chub Annotated Bibliography 17 September 2009

 

Using the relationship between total number of circuli and total length of young Colorado 

pikeminnow, we estimated maximum number of circuli formed in the first year for 1) fish that 

formed a first year growth check and 2) for those that did not. We found that most age-0 

Colorado pikeminnow (49%) collected in fall of 1991 (only year scales were collected from age0 fish) were too small (<40 mm TL) to form a first year growth check but that a first year growth 

check was present on scales of most adults (75%) collected between 1978–1989. 

We then examined length frequency information collected over eight winter seasons 

(1987 to 1994). In the middle Green River, 45 to 75% of age-0 fish were less than 40 min in fall 

for years examined (1989 to 1993); in the lower Green River, 50 to 90% of fish were less than 40 

min TL in fall for years examined (1987 to 1993). This information suggests that some size 

dependent mechanism, such as mortality or growth, favored larger Colorado pikeminnow. 

 

To assess size-selective mechanisms (growth or mortality) affecting survival of age-0 

Colorado pikeminnow, we examined shifts in length-frequency data, plotted as quantiles, from 

fall to spring over the 8 year period. In the middle Green River, all years showing a significant 

effect of a size-selective overwinter mechanism indicated mortality was dominant. In the lower 

Green River, mortality was dominant in five years, but two years showed dominant size-selective 

growth. We were not able to discern the interaction between growth and mortality. The relative 

importance of these size-dependent mechanisms most likely varies from year to year depending 

on biological and environmental factors like nonnative predation, competition, and degree day 

accumulation in the first growing season. 

These results lead us to explore relationships between physical variables of temperature 

and flow with size of age-0 Colorado pikeminnow in fall. If degree-day accumulation influenced 

size of fish in fall, we would have expected to see differences among middle and lower river 

reaches for both size of age-0 fish entering winter and consequently, their overwinter survival 

assuming they were hatched during the same period. We calculated degree-day accumulation for 

pre- and post-dam periods to determine large-scale changes due to Flaming Gorge Dam and then 

for individual winter and summer seasons that corresponded with fall and spring age-0 fish 

sampling (1987 to 1994). We found that mean daily water temperatures of the Green River near 

Jensen, Utah, and near Green River, Utah, were higher on average at the downstream Green 

River station than the upstream Jensen station, and total degree day accumulation was 37% 

greater at the downstream station during the period of record. However, no change was found to 

be associated with dam operations. We also found that degree day accumulation for summer and 

winter periods was consistently and substantially greater in the lower Green River during the 

study period. Despite the differences in degree-day accumulation between sites, age-0 Colorado 

pikeminnow were not larger in the lower Green River in fall. 

Furthermore, analysis showed that overwinter degree-day accumulation did not appear to 

be associated with different size-selective overwinter mechanisms between the middle and lower 

reaches or among years. One exception to this was a dominant mechanism of size-selective 

growth occurring only in the lower Green River where temperatures were warmer (1987-88 and 

1990-91). Fish growth did not appear to be related to mainstem degree-day accumulation which 

suggests limitations of age-0 Colorado pikeminnow growth may have been due to differences in 

specific habitat type quantity or quality between the two areas or possibly differential food, 
Humpback Chub Annotated Bibliography 18 September 2009

 

predation or competition pressure. This contention is further supported by a lack of a detectable 

association between age-0 year class size and length in fall and physical flow attributes, such as 

timing and magnitude of peak flows, average summer flows, and summer degree-day 

accumulation. A notable but insignificant association between degree-day accumulation and size 

of age-0 fish in fall in the lower Green river (which did not show up in the middle Green River) 

suggests limiting factors of early life-stage survival may be different at different sites. In fact, 

age-1 year class size and length in spring was best predicted by age-0 year class size and length 

in the fall and was not related to average winter flows or winter degree-day accumulation. The 

largest and most abundant fall year classes were also the largest and most abundant spring year 

classes. Such a finding lead us to the conclusion that limiting factors on age-0 Colorado 

pikeminnow recruitment to age-1 generally occurs before fall of their first year, not overwinter 

as has been previously hypothesized. 

 

We recommend further investigations between size-dependent overwinter growth and 

mortality to quantify limitations on age-0 Colorado pikeminnow survival and more information 

on factors limiting pre-winter recruitment of age-0 Colorado pikeminnow. 

Haines, G.B. 1995. Effects of temperature on hatching success and growth of razorback 

sucker and flannelmouth sucker. Final report of U.S. Fish and Wildlife, Vernal, Utah, to 

Upper Colorado River Endangered Fish Recovery Program, Lakewood, Colorado. 

Laboratory experiments were conducted to assess the effects of water temperature on the 

developmental rate and hatching success of embryos and growth of larvae of the endangered 

razorback sucker (Xyrauchen texanus) and the sympatric and common flannelmouth sucker 

(Catostomus latipinnis). Embryos and larvae were reared at 12, 16, or 20o

C for 45 d postfertilization. Mean number of days between fertilization and peak hatching of embryos decreased 

as water temperature increased for both species; 6.5 d (20oC) to 12.5 d (12oC) for razorback 

sucker and 6.0 d (20o

C) to 16.5 d (12oC) for flannelmouth sucker. The period from first to last 

hatch averaged 2.0 d longer for razorback sucker than flannelmouth sucker over all temperatures. 

Percent hatch of flannelmouth sucker embryos was independent of water temperature and, at 

each water temperature, was higher for flannelmouth sucker (83–91%) than for razorback sucker 

(48–67%); hatching success of razorback sucker embryos increased as water temperature 

increased. At 20oC on each sampling day, embryos and larvae of flannelmouth sucker were 

substantially larger than those of razorback sucker. 

Waples, R.S. 1990. Conservation genetics of Pacific salmon. II. Effective population size 

and the rate of loss of genetic variability. Journal of Heredity 81:267–276. 

A simulation model for genetic change in Pacific salmon (Oncorhynchus spp.) 

populations is extended to examine the loss of genetic variability. The study was designed to 

address three major questions: 1) What is the rate of loss of genetic variability from Pacific 

salmon populations as a consequence of finite population size? 2) How can existing population 

genetics theory be used to predict patterns of genetic change in Pacific salmon? and 3) What do 

the concepts "effective population size" and "generation length" mean with respect to Pacific 

salmon? Results indicate that effective population size per generation (Ne) is equivalent to the 

effective number of breeders per year (Nb) times the average age at spawning, or generation 
Humpback Chub Annotated Bibliography 19 September 2009

 

length (g), and that the use of Ne= g Nb in standard equations for the variance of allele 

frequencies, loss of heterozygosity, and loss of alleles over time accurately predicts the rate of 

genetic change in the population as a whole. With Pacific salmon, however, genetic data are 

seldom gathered for a population as a whole; instead, data are typically taken from individual 

brood years, which represent only a portion of the individuals comprising a generation. The 

magnitude of genetic change among brood years is larger than predicted using standard 

equations. In addition, uniting of progeny from different brood years in each year’s spawning 

population creates a Wahlund effect that slightly reduces the observed proportion of 

heterozygotes. Formulas are provided to adjust standard population genetics equations for the 

effects of measuring change among subsets of the population. It is shown that low frequency 

alleles are subject to rapid extinction in Pacific salmon populations with Nb less than about 100 

per year, and the implications of this result for the conservation genetics of wild and cultured 

populations is discussed. 

Waples, R.S., G.A. Winans, F.M. Utter and C. Mahnken. 1990. Genetic approaches to the 

management of Pacific salmon. Fisheries 15(5):19–25. 

 The complex problems involved in managing Pacific salmon (Oncorhynchus spp.) are 

largely a consequence of the unusual life history features of these species. The strong homing 

instinct leads to the formation of discrete, locally-adapted spawning populations, each of which 

has the potential to evolve as an independent evolutionary unit. It is important, therefore, that the 

genetic consequences of different management policies be carefully evaluated. If current 

management goals (e.g., doubling the abundance of anadromous salmonids in the Columbia 

River basin through increased hatchery production and supplementation of natural populations) 

are realized, genetic issues will assume even greater importance in the future. To date, however, 

genetic concerns have not been adequately incorporated into the management process. We 

identify three genetic approaches, primarily based on easily obtained electrophoretic data, that 

can provide valuable information on which to base management decisions: (1) Using the Genetic 

Stock Identification method for identifying stocks contributing to oceanic, mixed-stock fisheries. 

Genetic Stock Identification has several advantages over traditional tagging methods, including 

cost-effectiveness and easy access to wild as well as hatchery stocks. (2) Monitoring genetic 

changes in hatchery stocks. Analysis of the nature and magnitude of such changes is the best 

means of identifying stocks in which potentially dangerous levels of inbreeding may be 

occurring. (3) Detecting mixtures of gene pools. The ability to detect hybridization and 

introgression is necessary for an evaluation of the genetic consequences of releasing artificially 

propagated fish into the wild. 
Humpback Chub Annotated Bibliography 20 September 2009

 

3 ECOLOGY 

3.1 GENERAL ECOLOGY 

Kaeding, L.R. and M.A. Zimmerman. 1983. Life history and ecology of the humpback 

chub in the Little Colorado and Colorado Rivers of the Grand Canyon. Transactions of 

the American Fisheries Society 112:577–594. 

The loss of habitat for some native fishes of the Colorado River drainage coincided with 

the closure of Flaming Gorge Dam on the Green River. Humpback chubs in the Little Colorado 

River grew rapidly to about 250-300 mm in length at 3 yr of age, the onset of reproductive 

maturity for the female. Annual reproductive success was greatest when spawning coincided 

with seasonal river runoff. Use of the physical habitat by age-0 and juvenile humpback chubs 

was affected by light intensity. Shallow littoral areas were used during darkness, but during 

daylight only when the water was turbid. Year-round low temperatures in the Colorado River did 

not inhibit seasonal gonadal maturation of humpback chubs. However, lab studies indicate that 

such low temperatures result in nearly complete mortality of embryonic and larval humpback 

chubs. Persistence of the fish in the Little Colorado River could be attributable, in part, to the 

unsuitability of that environment, and that of the Colorado River, for potential competitor or 

predator species in the drainage. 

Karp, C.A. and H.M. Tyus. 1990. Humpback chub (Gila cypha) in the Yampa and Green 

Rivers, Dinosaur National Monument, with observations on roundtail chub (G. robusta) 

and other sympatric fishes. Great Basin Naturalist 50:257–264. 

We evaluated distribution, habitat use, spawning, and species associations of the 

endangered humpback chub (Gila cypha) in the Yampa and Green rivers, Dinosaur National 

Monument, from 1986 to 1989. Adult and juvenile humpback chub were captured in highgradient reaches of Yampa and Whirlpool canyons where they were rare (N=133, <1% of all fish 

captured). The fish was primarily captured in eddy habitats in association with 7 native and 12 

nonnative fish species. Roundtail chub (G. robusta) were widely distributed in eddies, pools, 

runs, and riffles. Humpback chub (N=39) and roundtail chub (N=242) in reproductive condition 

were sympatric in eddy habitats during the 5-6-week period following highest spring runoff. 

River temperatures at this time averaged about 20 degree C. Nonnative channel catfish (Ictalurus 

punctatus) were abundant in eddies yielding humpback and roundtail chubs, suggesting a 

potential for negative interactions between the native and introduced fishes. 

Kubly, D.M. 1990. The endangered humpback chub (Gila cypha) in Arizona: a review of 

past studies and suggestions for future research. Arizona Game and Fish Department, 

Phoenix, Arizona. Abstract excerpted from report objectives. 

 Much of the available information on the endangered humpback chub (Gila cypha) 

population in the Grand Canyon region of Arizona lies in the confines of fisheries biologists’ 

field notes or government agency and contract reports. This body of “grey literature” is difficult 

to access for even the most persistent investigator, and it has seldom been subjected to critical 
Humpback Chub Annotated Bibliography 21 September 2009

 

evaluation as part of the peer review process involved in publishing in scientific journals. During 

the course of the ongoing Section 7 Consultation on the Operation of Glen Canyon Dam (2-ZL57-F-23), a decision was made to gather together the available data and literature on humpback 

chub in the Grand Canyon, including data gathered by the Arizona Game and Fish Department 

(Department) during 1987-1989. The objectives of this effort were threefold: 

(1) Review the literature, both published and unpublished on the ecology of the species in the 

study area; 

(2) Compile in a computerized relational database the existing data and, where necessary, 

sample (or resample) and interpret these data; and 

(3) Determine what areas of our knowledge are lacking and needful of further research to 

help ensure the sustained presence of Gila cypha in the Colorado River and its tributaries 

below Glen Canyon Dam. 

 Although this report is limited in scope to consideration of the endangered humpback 

chub, this limitation does not indicate a lack of concern by the Department for other threatened 

and endangered species of wildlife in the Colorado River and its tributaries below Glen Canyon 

Dam. Department concerns for these species in Grand Canyon are being addressed through 

provisions of the Fish and Wildlife Coordination Act and the National Environmental Policy Act 

as they pertain to compliance with the October 27, 1989, directive by the Secretary of the Interior 

to evaluate the effects of the operation of Glen Canyon Dam. 

Minckley, C.O. 1996. Observations on the biology of the humpback chub in the Colorado 

River Basin, 1908–1990. Doctoral Dissertation. Northern Arizona University, Flagstaff, 

Arizona. 

The humpback chub is listed as a federally endangered species primarily as the result of 

the impacts of hydroelectric dam operations and the introduction of nonnative fishes. 

 Geographic distribution of the humpback chub in the Colorado River basin is well 

documented, occurring in the major tributaries of the upper basin including the Green, White, 

Yampa, and Little Snake Rivers. Currently there are five upper basin populations to include: the 

Green, Yampa, and Colorado River (at Black Rocks, Westwater Canyon and Cataract Canyon). 

In the lower basin distribution is from Glen Canyon Dam into Lake Mead. In Grand Canyon, the 

largest population occurs in the Little Colorado River although fish occur consistently at five 

other areas along the river. 

 The habitats used by the humpback chubs are similar throughout the basin, varying with 

the life stage. Generally, larvae and fry occupy shoreline backwater habitats in slowly moving 

eddies and adjacent backwaters. Juveniles live in deeper water such as low-velocity eddies and 

backwaters <10 m deep. Adults are in deep eddies and backwaters, presumably including depths 

> 10 m. 

 Adult humpback chubs are considered sedentary, occurring in canyon-bound reaches of 

the Colorado River Basin. However, there are exceptions when some individuals move further. 
Humpback Chub Annotated Bibliography 22 September 2009

 

 The diet of this species consists of a variety of aquatic and terrestrial invertebrates, and 

occasionally fish. Reproduction has been confirmed throughout the basin but spawning has not 

been observed. Humpback chub host several parasites but only two present potential threats, the 

anchorworm and Asian tapeworm. These parasites have been found in the lower basin and may 

have negative impacts n the future. 

 A recovery plan is in place for this species addressing the upper basin population. No 

specific plan is extant for the lower basin. 

Stone, D.M. 1999. Ecology of humpback chub (Gila cypha) in the Little Colorado River, 

near Grand Canyon, Arizona. Master's thesis, Northern Arizona University, Flagstaff. 

 Within the Colorado River and its major tributaries, a unique assemblage of fish species 

began to evolve during the Miocene that were morphologically and physiologically capable of 

surviving periods of drought intermingled with stochastic flood events, high sediment loads, and 

fluctuations in the types and quantity of food resources. Within the last century, anthropogenic 

disturbances have decimated much of this original ichthyofauna. The lower 141 km of the LCR 

is the last holdout where humpback chub (Gila cypha) numerically dominate over other piscine 

species. Moreover, the other most common fishes are native species and include speckled dace 

(Rhinichthys osculus), bluehead sucker (Catostomus discobolus) , and flannelmouth sucker (C. 

latipinnis) . We found evidence that adult humpback chub, which are considered opportunistic 

feeders, can be highly piscivorous and may structure the life history of smaller fish in the LCR. 

Regardless of water clarity, all small native fish in this system were diurnally active including 

dace and all YOY fish; whether this was a result of undeveloped sensory abilities or a behavioral 

response is unknown. In contrast, adult humpback chubs (>180 mm TL) were predominately 

nocturnally active. During nighttime, adult chubs shifted habitat use to nearshore areas where

they could forage on small fish. Piscivory by adult chubs is supported by observations of dead 

small fish being found in miniature hoopnets during the nighttime and cases where adults 

regurgitated or defecated undigested fish while being handled. Also, in clear water conditions 

(<30 NTUs), when adults moved inshore at night, YOY chubs (<90 mm TL) shifted to areas of 

greater cover, while juvenile chubs (110-160 mm TL) and dace shifted to midchannel habitats. 

At night in turbid water conditions (>30 NTUs), the two smaller size classes of chubs and dace 

appeared to avoid habitats occupied by adult chub spawning aggregations. During daytime 

irrespective of water clarity, habitats used by chubs were delineated by fish size, such that 

increasingly larger chubs were captured progressively further midchannel, at greater depths, and 

in faster currents. Patterns of diel activity and habitat use documented in this study are consistent 

with predator-prey interactions found in other freshwater fish assemblages. 

Suttkus, R.D. and G.H. Clemmer. 1977. The humpback chub, Gila cypha, in the Grand 

Canyon area of the Colorado River. Occasional Papers of the Tulane University Museum 

of Natural History, New Orleans, Louisiana 1:1–30. 

The humpback chub, Gila cypha, is redefined from specimens taken in the Colorado 

River in the Grand Canyon. Specimens from 24'6 ' 320 mm are depicted, and notes on growth 
Humpback Chub Annotated Bibliography 23 September 2009

 

and development, sexual dimorphism, breeding tubercles and coloration, and reproduction are 

presented with standard meristic and morphometric data. 

Valdez, R.A. and R.J. Ryel. 1995. Life history and ecology of the humpback chub (Gila 

cypha) in the Colorado River, Grand Canyon, Arizona. Final report of Bio/West, Inc., 

Logan, Utah, to U.S. Bureau of Reclamation, Salt Lake City, Utah. Abstract was excerpted 

from report. 

The life history and ecology of the humpback chub (Gila cypha) in the Colorado River in 

the Grand Canyon was studied from October 1990 through November 1993, as part of the Glen 

Canyon Environmental Studies (GCES). The purpose of the investigation was to describe the 

ecological requirements of the species and evaluate the effects of Glen Canyon Dam operations 

on the various life stages. The objectives of the study were to describe and identify limiting 

factors to distribution, abundance, survivorship, movement, habitats, food habits, and 

reproductive capacity. Important biotic interactions and the life history schedule for the species 

were also described. This life history information was used to identify management options and 

recommendations for core research and monitoring with respect to dam operations. The 

investigation was designed to integrate with other companion studies and provide the framework 

for an integrated scientific report by GCES. 

 The physical, chemical, and biological nature of the Colorado River in the Grand Canyon 

was changed dramatically after it was impounded by Glen Canyon Dam in March 1963. Since 

impoundment, water has been released through the dam under six operational scenarios, each 

with unique characteristics, but all with common features. The dam eliminated spring floods and 

increased low base flows in later summer, fall, and winter. Daily fluctuations for hydropower 

generation became a normal feature of the hydrograph, and flows of over 31,500 cfs and below 

1,000 cfs were eliminated. 

 Key findings of each objective were as follows: 

 The present distribution of humpback chub in the Grand Canyon is related to mainstem 

temperature, locations of warm tributaries and springs, occurrence of suitable adult 

habitat, and food availability; 

 The largest and only self-sustaining population of humpback chub in the canyon was 

located in the lower reaches of the LCR and adjacent mainstem Colorado River; 

 The present distribution of the humpback chub in the Grand Canyon is believed to be the 

remnant of a more dispersed historic distribution. Pre-dam humpback chub in the Grand 

Canyon probably spawned in the mainstem, and likely occurred in higher concentrations 

in areas of more suitable habitat or greater food supplies; 

 Fish populations of the Colorado River have been affected in numerous ways by land use 

practices, water diversions, and non-native fishes starting in the late 1800s. 
Humpback Chub Annotated Bibliography 24 September 2009

 

 The combined estimates for the nine mainstem aggregations were about 3,300 to 3,800 

adults; 

 Survival of humpback chub in the mainstem is probably limited by cold temperatures, 

suitable habitat, food availability, and predation. Parasites are not believed to be a 

significant factor to survival in the mainstem, although an increased incidence of Asian 

tapeworms could affect the health of individual fish under stress; 

 Adult humpback chub in Grand Canyon exhibited strong spatial fidelity for specific river 

sites, which was similar to the behavior observed in other populations; 

 Adults in the mainstem moved very little during non-spawning periods, in summer, fall, 

and winter, when local movement was primarily influenced by time of day, turbidity, 

flow magnitude, and ramping rate; 

 Sub-adult humpback chub used primarily shallow sheltered shorelines, while adults used 

primarily large recirculating eddies; 

 Adult humpback chub in the Colorado River in the Grand Canyon ate primarily simuliids, 

introduced freshwater amphipods, chironomids, other aquatic invertebrates, and 

terrestrial insects. The algae, Cladophora glomerata, also made up a significant portion 

of the gut volume, but it was not determined if this was consumed incidentally or selected 

by the fish; 

 Cold releases from the Glen Canyon Dam have disrupted life cycles of aquatic 

invertebrates and greatly affected fish food diversity and availability; 

 Average lengths of sub-adult humpback chub at the first three scale annuli formations 

were 96, 144, and 186 mm TL; 

 The only self-sustaining population of humpback chub in the Grand Canyon was found in 

the lower 14.9 km of the LCR and the adjacent 13.5 km of the mainstem Colorado River; 

and 

 Fourteen species of fish were sympatric with humpback chub, including 3 native species 

and 11 non-natives. These interacted with humpback chub as known or potential 

predators, competitors, and vectors for parasites and diseases. 

Valdez, R.A. and R.J. Ryel. 1997. Life history and ecology of the humpback chub in the 

Colorado River in Grand Canyon, Arizona. Final report TR-250-08. BIO/WEST, Inc., 

Logan, Utah. 

 The endangered humpback chub (Gila cypha) is found as six populations in the Colorado 

River Basin. The largest is in Grand Canyon, Arizona, where in 1990-1993, fish were 

distributed as nine aggregations in 307 km of the Colorado River, as well as in the lower 14.9 km 

of the LCR, a seasonally warmed tributary. An estimated 3,700 adults inhabited the mainstem in 
Humpback Chub Annotated Bibliography 25 September 2009

 

1993, with 3,480 adults in the largest aggregation near the LCR. The LCR was the only area 

with significant spawning and recruitment of fish to the mainstem, but it was used only by the 

mainstem aggregation and a resident LCR population. Year-round release of 8-10°C water from 

Glen Canyon Dam precluded successful mainstem reproduction and limited growth of young 

chubs. Adults exhibited a high degree of spatial fidelity for specific river locales, mean net 

movement was 1.49 km (range = 0–6.11; SD = 1.50) for 69 radiotagged fish and 1.64 km 

(range = 0–9.8; SD = 1.72) for 238 passive integrated transponders (PIT)-tagged fish. Annual 

survival of chubs during the first 3 years of life was estimated at 0.10, while estimated annual 

survival of adults (age3+) was 0.93. A major source of subadult mortality was predation by 

brown trout (Salmo trutta) and channel catfish (Ictalurus punctatus), which together potentially 

consumed about 228,850 chubs annually. Adult chubs inhabited primarily large recirculating 

eddies (88% captures, 74% radio contacts), whereas subadults used shorelines with vegetation, 

talus, and debris fans as well as eddy return channels (i.e., backwaters). Diet by volume of 

mainstem adults neat the LCR consisted of Gammarus lacustris (freshwater amphipods, 45%). 

Simuliidae (blackflies, 40%) terrestrial invertebrates (9%), Chironomidae (midges, 5%), and 

other aquatic invertebrates(1%). Adults from more downstream aggregations consumed a lower 

proportion of G. lacustris and a higher proportion of terrestrial invertebrates. External parasitic 

copepods (Lernaea cyprinacea) were on 8 of 6,294 (<1%) chubs examined and Asian tapeworms 

(Bothriocephalus acheilognathi) were in guts of 6 of 168 (4%) adults flushed with a stomach 

pump. 

Valdez, R.A. and T.L. Hoffnagle. 1999. Movement, habitat use and diet of adult 

humpback chub. Pages 297–307 in R.H. Webb, J.C. Schmidt, G.R. Marzolf and R.A. 

Valdez (eds.). The controlled flood in Grand Canyon. Geophysical Monograph 110. 

American Geophysical Union, San Francisco, California. 

 The humpback chub (Gila cypha) is a big-river cyprinid fish endemic to the Colorado 

River, where river regulation has contributed to its endangerment. Flooding is essential to 

reshaping its habitat, redistributing nutrients, flushing terrestrial insects for food, and, in the postdam river, controlling non-native competitors and predators. Effects of the 1996 controlled flood 

on movement and habitat use of adults were monitored with radiotelemetry, and diet was 

evaluated with a non-lethal stomach pump. Movement of 9 radio-tagged adults during the flood 

(mean, 0.40 km; range, 0-1.24 km) was not significantly different (P≤0.05) from movement in 

the month preceding the flood (mean, 1.26 km; range, 0.1-2.95 km), indicating no unusual 

movement or displacement of fish by the flood. Habitat used during the flood, as a percentage of 

radio-contacts (i.e., 73% eddies, 19% runs, 8% tributary inflows), was similar to that used under 

normal operations by 69 fish tracked during 1990-1992 (i.e., 74% eddies, 12% runs, 7% 

backwaters, 6% tributary inflows, 1% pools, <1% riffles). Diet of 43 adults showed dramatic 

shifts to items scoured by the flood. Simuliidae (68% ash-free dry weight) and Chironomidae 

(15%) dominated pre-flood diets; Amphipoda (31%), Simuliidae (25%), and terrestrial insects 

(i.e., beetles, ants, grasshoppers, 20%) were ingested during the flood; and Simuliidae (62%) and 

Amphipoda (18%) were eaten post-flood. While composition of the diet changed, biomass 

consumed was not significantly affected by the flood (P=0.9157). The controlled flood had no 

detrimental effects on movement, habitat use, or diet of adult humpback chub. Effects of habitat 

reshaping and nutrient redistribution can only be evaluated through long-term monitoring. Floods 

of higher magnitude or at a different time of year may have different effects on this endangered 
Humpback Chub Annotated Bibliography 26 September 2009

 

species and should be investigated before implementing controlled floods as an element of dam 

operations. 

Valdez, R.A., W.J. Masslich, W. Leibfried, A. Wasowicz, B. Cowdell, R. VanHaverbeke, M. 

Yard, T.M. Trinca and L.I. Brown. 1992. Characterization of the life history and ecology 

of the humpback chub in the Grand Canyon. Annual report TR 250-05 of BIO/WEST, Inc. 

to U.S. Bureau of Reclamation, Salt Lake City, Utah. 

Investigations of the endangered humpback chub were initiated in the mainstem Colorado 

River of the Grand Canyon on September 1. 1990 by BIO/WEST, Inc, of Logan, Utah. The first 

month of the project was dedicated to training personnel, assimilating field equipment, defining 

standard sampling methods, and developing standardized data collection procedures and forms. 

Five Achilles sport boats were outfitted as research boats including two for electrofishing and 

three for netting and radiotracking. Equipment for fish sampling radiotelemetry, water quality, 

and habitat mapping was also assembled. A Data Collection Plan was developed together with a 

Fish Sampling Protocol, Fish Handling Protocol, and Database Management Protocol. These 

documents detail the methodologies to be employed by BIO/WEST in this investigation and 

were made available to agencies and individuals involved in the Glen Canyon Environmental 

Studies (GCES). 

 

 The study area was defined as 170 miles of river from Kwagunt rapid (river mile [RM] 

56) to Diamond Creek (RM 226). The region was divided into three sample reaches designated 

as the Little Colorado (LCR) Reach, Granite Gorge Reach, and Havasu Creek Reach. Sampling 

was conducted monthly in October, November, and December with field trips of 10, 20, and 10-

days durations, respectively. The 10-day field trips were designed for one team of 6 people to 

sample the LCR Reach only, while the 20-day trips were designed for two similar teams to 

sample with approximately equal effort in all three sample reaches. 

 Six gear types were used to sample humpback chub in 1990, including 1 and 1.5 in. mesh 

trammel nets, 1.5 in. and 2 in. gill nets, experimental gill nets, and electrofishing. The 1 in. and 

1.5 in. mesh trammel nets and the 1.5 in. gill nets produced the greatest numbers of chubs (26, 

30, and 28, respectively) with approximately equal catch rates of 1.49, 1.57, and 1.45 fish/100 

feet/10 hours respectively. Electrofishing yielded 6 fish with a catch rate of 4.03 fish/10 hours. 

Gear efficiency will continue to be evaluated in 1991. 

 

Ten species of fish representing five families were captured during the three field trips in 

1990. The most abundant species were rainbow trout and carp. A total of 94 humpback chub 

were captured and released alive; 83 were PIT tagged and 17 were radiotagged (16 with PIT 

tags). Of the 94 fish captured, 10 had been previously tagged with Floy or Carlin tags by other 

investigators, 2 were previously PIT tagged by other investigators, and 3 were fish previously 

PIT tagged during the investigation. Morphometric measurements and meristics were recorded 

on 46 humpback chub. 

 BIO/WEST initiated a radiotelemetry study to evaluate its use in the Grand Canyon for 

assessing habitat use and movement of humpback chub. Preliminary results show that 

radiotelemetry will be a useful tool in monitoring movement and habitat use of fish in the Grand 
Humpback Chub Annotated Bibliography 27 September 2009

 

Canyon and for evaluating the impacts of Glen Canyon Dam operations. Use of radiotelemetry 

will be further evaluated in a 5-mile section of the LCR Reach; 10 fish were Radiotagged in 

October and 7 I November. In November, 8 of the 10 October fish were recontacted, and in 

December 11 of the 17 fish were recontacted for a recontact rate of 80% and 65%, respectively. 

The position of each fish was determined several times daily to monitor both horizontal and 

vertical movement (radiosignals are extinguished at about 4 m depth). Radiotagged fish were 

monitored for 24-hour periods and for 2-hour periods. Movement and habitat was recorded on 

standard data sheets and maps, and relative changes in river stage were recorded during these 

monitoring modes. Eight temporary bench marks established in the LCR Reach that will 

eventually be surveyed to permanent U.S. Geological Survey (USGS) bench marks so that all 

relative stage readings can be tied to absolute stage changes and to the operation of Glen Canyon 

Dam. 

 Movement and change in macrohabitat use were noted for Radiotagged fish relative to 

changes in flow, turbidity, and time of day. These variables will continue to be measured and 

closely monitored during this investigation in order to describe their relationships to fish 

movement and habitat use. Macrohabitat mapping of area occupied by humpback chub as well 

as areas not used by the fish will also continue in order to evaluate the availability of habitat and 

changes in flow. 

 A food habits pilot study using non-lethal stomach pumping will be initiated in January 

1991 to evaluate the diet of the humpback chub in the mainstem Colorado River. Drift samples 

will be collected and data gathered from other investigators on benthic invertebrate communities 

in order to assess the availability of food resources. 

 Plans were developed for the 1991 investigation including establishing remote 

radiotelemetry stations to monitor fish movement into the LCR, establishing temporary bench 

marks to monitor river stage change during radiotelemetry observations, identifying relationships 

for measuring river turbidity, procuring appropriate maps for macrohabitat mapping, interfacing 

macrohabitat mapping with development of depth and velocity isopleths to stage relationships 

being developed by other investigators, and coordinating efforts near tributary inflows and in 

backwaters with other investigators. 

3.2 DISTRIBUTION AND ABUNDANCE 

 

Ackerman, M.W., D. Ward, T. Hunt, R.S. Rogers, D.R. Van Haverbeke, A. Morgan and C. 

Cannon. 2006. 2006 Grand Canyon long-term fish monitoring in the Colorado River, 

Diamond Creek to Lake Mead. Annual report to the U.S. Geological Survey, Grand 

Canyon Monitoring and Research Center, Flagstaff, Arizona. Abstract excerpted from 

report. 

The 2006 Trip Report for Trip ID:GC20060523 provides a summary of methods and 

preliminary observations from the 2006 Diamond Creek to Lake Mead monitoring. May 2006 

was the third long-term monitoring trip for fish downriver of Diamond Creek since 1996. These 

trips are part of an ongoing, long-term monitoring program designed to determine trends in 
Humpback Chub Annotated Bibliography 28 September 2009

 

relative density and distribution of fish within the Colorado River between Lake Powell and 

Lake Mead. Monitoring below Diamond Creek was initiated in 2004 as an extension to the 

current monitoring program for Grand Canyon fishes. With recent higher river temperatures in 

the Colorado River, it has become increasingly important to understand the distribution and 

potential sources of warm-water non-native fish species within the Colorado River ecosystem 

including the area from Diamond Creek to Lake Mead. In 2006, catch by trammel netting and 

electrofishing saw an observed increase in comparison to 2005. It is important that flow and 

season remain similar among sampling periods as these factors are known to influence catch 

rates, and catchability can have significant effects on catch rates used for index monitoring. The 

ability to compare data between 2005 and 2006 due to similar sampling conditions seems to be 

an important tool that will be useful during long-term monitoring. 

Badame, P.V. 2008. Population estimates for humpback chub (Gila cypha) in Cataract 

Canyon, Colorado River, Utah, 2003–2005. Final report of Utah Division of Wildlife 

Resources to Upper Colorado River Endangered Fish Recovery Program, Lakewood, 

Colorado. 

 Humpback chub (Gila cypha) are listed under the Endangered Species Act of 1973, as 

amended. In accordance with recovery goals finalized in 2002, population estimates were 

completed for adult humpback chub in Cataract Canyon on the Colorado River. The sampling 

was conducted from 2003 to 2005 with the objective of obtaining annual point estimates for 

humpback in the canyon. Sampling occurred between mid September and early November each 

of the three years of the study. Three sites were sampled for two nights on three occasions each 

year with approximately one week between sampling occasion. Approximately 28% (1.9 river 

miles) of the available habitat in Cataract Canyon was sampled on each occasion. The primary 

method of capture was trammel netting with supplemental electrofishing on one pass per year. 

 Population estimates were generated from mark-recapture data using closed population 

models calculated with program CAPTURE. Separate estimates were generated for each year of 

the study. Results indicated a non-significant decline in the adult humpback chub population 

during the 2003 – 2005 sampling period. The adult point estimates were 126 (2003), 91 (2004), 

and 70 (2005). The interpretation of these estimates relative to the amount of available habitat in 

Cataract Canyon depends on how movement, or lack thereof, effects the assumptions of the 

estimator. Every annual and intra-annual recapture of a humpback occurred in the individuals 

original capture site. No movement implies that mixing between the sample areas does not occur 

and that fall point estimates would relate only to the area sampled (2 river miles); therefore, the 

density estimates for the sampling period would be 63-35 fish/mile (no mixing model). If the 

density estimates are applied to the total available habitat in the canyon (approximately 7 river 

miles) the total population size would have varied between 468-262 adult humpbacks during the 

sampling period. Relative to other upper basin humpback chub populations; the density is similar 

to that of Desolation/Gray Canyons, and significantly less than found in Westwater Canyon. 

 Growth of humpback chub in Cataract Canyon was slow relative to other upper basin 

populations. In addition, the relative size structure of this population is small and is within a 

narrow range. In three years of sampling, the smallest humpback captured was 195 mm. Results 

from Desolation and Westwater trammel netting suggest our inability to capture smaller 
Humpback Chub Annotated Bibliography 29 September 2009

 

juveniles in Cataract is likely a limitation of net size used. Electrofishing has been the preferred 

method for finding juvenile chubs in other canyons; however, none were captured using this 

technique in Cataract Canyon. It is unclear if they are not present or if they are utilizing habitats 

which are unreachable with electrofishing. 

 Analysis of catch per unit effort (CPUE) totals for the period of 2003 to 2005 has shown 

no statistically significant changes for humpback chub. The average trammel net CPUE for 

humpback chubs in Cataract Canyon was lower than both Desolation Canyon and Westwater 

Canyon. Mean CPUE for bonytail chub declined quickly from 2003 to 2004 and 2005. 

 The small size of this population suggests a need to reassess how it is monitored. 

Although there are not enough adult individuals to consider this a core population, it is still 

considered an integral part of the overall upper basin population recovery. The persistence of 

stocked adult bonytail within Cataract Canyon also warrants continued monitoring. 

Chart, T. E., and L. D. Lentsch. 2000. Reproduction and recruitment of Gila spp. and 

Colorado pikeminnow (Ptychocheilus lucius) in the middle Green River 1992–1996. Report 

C in Flaming Gorge Studies: Reproduction and recruitment of Gila spp. and Colorado 

pikeminnow (Ptychocheilus lucius) in the middle Green River. Final report of Utah 

Division of Wildlife Resources to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

This report presents data collected from five annual monitoring trips in Desolation and 

Gray (Deso/Gray) canyons of the Green River, Utah; 1992–1996. Pre-project data, in some cases 

as early as 1985, is incorporated in long term comparisons of catch data. Low velocity habitats 

were sampled throughout the canyon (two habitats/8 km) with seines. Main channel habitats 

were sampled with trammel nets, hoop nets, and electrofishing. Main channel sampling occurred 

at four trend sites (Cedar Ridge, RK 295.7; Surprise Canyon/Rock Creek area, RK 280.5; Joe 

Hutch, RK 256; and Coal Creek, RK 232.8) each year. Additional sites were sampled each year 

to determine if Colorado pikeminnow spawned there. Nonnative cyprinids, most importantly 

Cyprinella lutrensis, dominated the catch in low velocity habitats. Low velocity habitat sampling 

during August, 1993, resulted in the greatest catch (N=162) of YOY chubs (approximately 

0.1 fish/m2). YOY chubs were collected in relatively low numbers every other year of the study. 

Annual YOY chub CPE was weakly correlated with Green River peak flow (R2 = 0.1). Back 

calculated spawning dates indicate chubs spawned in Deso/Gray under a wide range of flows 

(1,650–25,800 cfs). Adult and juvenile Gila spp. net catch rates at the four monitoring sites 

remained below 0.2 fish/23 m net-hour throughout this five year period and dropped below 

0.1 the final year of study, 1996. Considering pre-project data, adult Gila spp. catch rates have 

been declining since 1989. The 1993 chub cohort was sampled in 1994 as Age 1+ fish and offers 

the strongest evidence of recruitment since pre-project monitoring in 1989. Juvenile chubs 

(likely the 1993 and 1994 cohorts) were collected again in 1995. Kolmogorov-Smirnov tests for 

differing distributions indicated population structure (as characterized in length frequency 

analysis) of Deso/Gray chubs are dynamic and recently (incorporating 1997 data) were 

comprised of smaller (younger) individuals. Colorado pikeminnow trammel net CPE remained 

low at the four trend sites, with the greatest catch (0.065 and 0.08) collected at RK 280.5 in 1994 

and 1995. Concentrations of ripe male pikeminnow were found at Rabbit Valley RK 238) in 
Humpback Chub Annotated Bibliography 30 September 2009

 

1994 and 1995. Concentrations of spawning pikeminnow were also found at Joe Hutch RK 256) 

in 1997. The Three Fords spawning area was determined to be an 18 km stretch of river between 

RK 256 and 238, with the focus of spawning shifting within that stretch through time. 

Netting catch rates for native catostomids have been in general decline since 1989, however 

rebounded in recent years. Electrofishing has provided a relatively strong sample of both 

Catostomus latipinnis and C. discobolus since 1994 including some strong evidence of recent 

recruitment. Native catastomid recruitment appears to be more successful since 1993 than was 

observed in 1992 and during pre-project monitoring years. Channel catfish (Ictalurus punctatus) 

was the most abundant species collected in main channel habitat each year of study. The only 

apparent lapse in channel catfish recruitment was observed in 1994 after the higher flows of 

1993. We recommend incorporating Deso/Gray fish community monitoring into the Interagency 

Monitoring Program and targeting flows of 7,000–8,000 cfs to maximize sampling efficiency. 

Population estimates at the four trend sampling sites would help validate CPE values collected in 

this canyon since 1986. If a more intensive study to estimate chub population size is initiated, 

incorporation of a catfish control component at the trend sites should be considered. This 

monitoring data set does not lend itself to developing flow recommendations. However, the 1993 

cohort of chubs appeared to overwinter better than the 1994 cohort. Overwinter flows averaged 

3,250 cfs from Oct 1993–Feb 1994 opposed to 2,250 cfs the next winter. 

Coggins, L.G. 2007. Abundance trends and status of the Little Colorado River population 

of humpback chub: an update considering 1989-2006 data. United States Geological 

Survey open file report 2007–1402. 

The abundance of the LCR population of federally listed humpback chub Gila cypha in 

Grand Canyon has been monitored since the late 1980s by means of catch rate indices and 

capture–recapture-based abundance estimators. Analyses of data from all sources using various 

methods are consistent and indicate that the adult population has declined since monitoring 

began. Intensive tagging led to a high proportion (>80%) of the adult population being marked 

by the mid-1990s. Analysis of these data using both closed and open abundance estimation 

models yields results that agree with catch rate indices about the extent of the decline. Survival 

rates for age-2 and older fish are age dependent but apparently not time dependent. Backcalculation of recruitment using the apparent 1990s population age structure implies periods of 

higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate 

that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met 

for this population. Also, there is a critical need to develop new abundance indexing and tagging 

methods so that early, reliable, and rapid estimates of humpback chub recruitment can be 

obtained to evaluate population responses to management actions designed to facilitate the 

restoration of Colorado River native fish communities. 

Coggins, L., C. Walters, C. Paukert and S. Gloss. 2003. An overview of status and trend 

information for the Grand Canyon population of the humpback chub, Gila cypha. U.S. 

Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona. 

Abstract excerpted from report. 

Recent analyses of historical data on humpback chub in Grand Canyon have caused 

considerable consternation, because of uncertainties about the current size of the population and 
Humpback Chub Annotated Bibliography 31 September 2009

 

because of the strong probability that the population has been declining steadily for at least a 

decade. Our most recent assessment models indicate that the current spawning population is 

probably somewhere between 2,000 and 4,000 age 4 and older fish, We remain quite uncertain 

about the absolute population size because of uncertainties about whether field procedures have 

met some assumptions of the main method used to estimate absolute abundance (mark-recapture 

sampling) and because of limited sample sizes, but all the assessment methods are in clear 

agreement about the population being in decline. One assessment model (called “Supertag”) 

resulted in a considerably lower estimate for recent adult abundance (1,100-1,200 fish in 2001), 

but we now believe that estimate was biased downward because of using two inappropriate 

assumptions in the calculations: the population was assumed to have a stable age structure in the 

early 1990s, and older chubs were assumed to be equally vulnerable to sampling programs. 

There are two strategic options for monitoring and population assessment in Grand Canyon: 

(1) make independent population (and/or trend index) estimates each year using multiple-trip 

mark-recapture experiments (mark fish on successive trips and measure the proportion of the 

population made up by these “known” marked numbers) along with index catch-per-effort 

sampling; and/or (2) use more elaborate stock assessment models to integrate current and past 

information into more complex estimators of current abundance. In Grand Canyon adaptive 

management, a really key issue is whether various management policies can improve humpback 

chub juvenile survival and recruitment. Integrated stock assessment methods are particularly 

critical for recruitment assessments. 

 

Converse, Y.K. 1995. Use of geomorphology to predict subadult humpback chub 

distribution in the Colorado River. Proceedings of the Desert Fishes Council. 

Subadult (less than 200 mm TL) humpback chub (Gila cypha) densities were examined 

for 16 miles of the Colorado River below the confluence of the Little Colorado River. Geology 

and surficial hydraulic criteria were used to describe geomorphic reaches. Geomorphic processes 

were used to describe shoreline types within geomorphic reaches. Narrow reaches with greater 

total eddy area had higher densities than wider reaches with greater total riffle area. Vegetation, 

talus and debris fan shorelines with greater fish densities, had lower velocities, were deeper and 

offered more cover than bedrock, cobble and sand shorelines. Stability of these conditions for the 

range of Interim Flow Operations of Glen Canyon Dam was also examined. 

Douglas, M.E. and P.C. Marsh. 1993. Monthly population estimates of endangered 

humpback chub (Gila cypha) in the Little Colorado River of Arizona. Proceedings of the 

Desert Fishes Council 24:65-66. 

Gila cypha (the humpback chub) is restricted in distribution to tight, canyon-bound 

reaches of the Colorado River and its tributaries. This fish achieves greatest abundance in the 

lower basin where it utilizes the LCR (a tributary of the Colorado River in the northern Grand 

Canyon) for spring reproduction and summer residence. However, the onset of its reproductive 

movements within this important river and its seasonal variance in population density remain 

unquantified and anecdotal. An understanding of these factors is clearly imperative for proper 

management of this endangered species. To remedy this, humpback chub were captured by hoop 

and trammel nets at monthly intervals from July 1991 to present in three study reaches of the 

LCR: the Confluence (from 0.0 to 1.4 km upriver); Powell Canyon (1.5 to 7.0 km above 
Humpback Chub Annotated Bibliography 32 September 2009

 

confluence on the Navajo Indian Reservation); and Salt Canyon (8.0 to 15.0 km above 

confluence on the Navajo Indian Reservation). Fish were PIT-tagged and standard monitoring 

data collected. Monthly population estimates were derived from tag/recapture data applying the 

best-fitting of 7 different models, using the computer program CAPTURE. For computational 

purposes, fish collected within each reach were considered to be from closed populations (i.e., 

with no immigration or emigration). This assumption is valid given the brevity of monthly 

sampling periods (i.e., from 6-8 days). During 1992, chub density peaked at the confluence 

during early March when adults staged for movement upriver but declined by May. Density at 

Powell Canyon peaked in late March and gradually declined into July, while density at Salt 

Canyon peaked in April and remained high through summer months. These data indicate that 

chubs migrate into the LCR during spring and remain in residence within upper reaches 

throughout summer. 

 Douglas, M.E. and P.C. Marsh. 1996. Population estimates/population movements of Gila 

cypha, an endangered cyprinid fish in the Grand Canyon region of Arizona. Copeia 

1996:15–28. 

Gila cypha (the humpback chub) is a unique but endangered cyprinid fish endemic to the 

Colorado River system in western North America. Its distribution within the system is patchy; 

occurrence is restricted primarily to narrow, canyon-bound reaches of these rivers. Greatest 

abundance is achieved at the confluence of the Colorado and Little Colorado rivers in northern 

Grand Canyon (Coconino County, AZ). This study defines the nature and extent of G. cypha’s 

movements within the LCR, and tests the hypothesis that its duration of stay within that river is 

restricted to the reproductive period. 

 During 1991-1992, adult G. cypha were captured and tagged during 19 6-14 day 

sampling periods in three separate reaches of the LCR. From these data, population estimates 

were derived for each reach on a monthly basis, by month for the entire LCR, and over the entire 

study period. Results indicate an upriver migration by some individuals in early spring, followed 

by a slow, protracted post-reproductive movement downstream. Localized stasis by adults in the 

LCR, particularly summer through winter, is also strongly supported by the data. Movements by 

G. cypha in the LCR thus appears to be amalgam of two processes: upriver movement in spring 

coupled with localized movements by overwintering adults. The latter suggests a possible 

alteration in life-history strategy for the species and is discussed in the context of Glen Canyon 

Dam, built in 1963 to impound Lake Powell at the northern extent of Grand Canyon. 

Douglas, M.E. and P.C. Marsh. 1996. Survivability of an endangered species (Gila cypha) 

within the Grand Canyon region of Arizona. Section 4 in M.E. Douglas and P.C. Marsh, 

eds. Ecology and Conservation Biology of Humpback Chub (Gila cypha) in the Little 

Colorado River. Bureau of Reclamation, Salt Lake City, Utah. 

The primary focus of this paper is development of Cormack-Jolly-Seber (CJS) open 

population estimates for G. cypha during each of the 50 months, 16 seasons, and four years of 

this study. From these data, probabilities of yearly survival are then estimated for five different 

adult size-classes. The hypothesis under test is that overall survival rate is low for this species, 

particularly given massive anthropogenic modifications of the mainstem Colorado River. 
Humpback Chub Annotated Bibliography 33 September 2009

 

Fagan, W.F., C. Aumann, C.M. Kennedy and P.J. Unmack. 2005. Rarity, fragmentation, 

and the scale of dependence of extinction risk in desert fishes. Ecology 86(1):34–41. 

 Attributes of a species’ spatial distribution, such as the number of occurrences and the 

spatial distribution of those occurrences, can affect extinction risk. Extinction risk, however, is 

scale dependent, and it is unclear how scale dependency affects linkages between species’ 

distributions and extinction risk. Here, we evaluate the relationships between number of 

occurrences, distributional fragmentation, and extinction risk for a diverse assemblage of desert 

fishes across multiple spatial scales. We used the SONFISHES biodiversity database, which 

details occurrence patterns of 25 native fishes to contrast the species’ historical distributions with 

their much-reduced modern distributions. Defining occurrences (and losses to extinction) at each 

of five scales (5, 25, 100, 500, and 2500 km of stream reach), we found that range fragmentation 

was a stronger predictor of extinction risk than the number of occurrences for all scales of 

analysis. Furthermore, we detected scale dependence in the strength of the predictive relationship 

between fragmentation and extinction, with loss of occurrences at intermediate scales ( 100 km 

of stream reach) being most closely tied to range fragmentation. Importantly, our results proved 

insensitive to our definition of the historical and modern periods. These findings highlight the 

value of multi-scale analyses to investigations of extinction in species assemblages. 

Gorman, O.T., R.G. Bramblett, R.M. Hervin, D.R. Van Haverbeke and D.M. Stone. 2005. 

Distribution and abundance of native and non-native fishes of the Colorado River 

Ecosystem in Grand Canyon, Arizona. Page 78-94 in Proceedings of two symposia: 

restoring native fish to the lower Colorado River: interaction of native and non-native 

fishes. July 13-14, 1999. Las Vegas, Nevada. U.S. Fish and Wildlife Service, Southwest 

Region, Albuquerque, New Mexico. 

The Colorado River ecosystem in Grand Canyon is strongly impacted by operation of 

Glen Canyon Dam. Fluctuating releases of cold, hypolimnetic water from Lake Powell (~8oC) 

for peak hydroelectric power generation has had a profound impact on the formerly warm, silty 

Colorado River. Clear, cold stenothermal conditions preclude successful reproduction and 

recruitment of most native fishes in the mainstem and introduced trout have become dominant 

species in the fish community. To assess the effects of dam operations on the native fish 

assemblage, the distribution and abundance of native and non-native fishes of the Colorado River 

ecosystem in Grand Canyon were assessed in the first year of a two-year research and 

monitoring program funded by the Grand Canyon Monitoring and Research Center. Study sites 

were located along 159 miles of the Colorado River from the Paria River to below Havasu 

Creek. An intensive area of study was established from just above the confluence of the Little 

Colorado River (LCR) at RM 60 to Tanner Rapid at RM 68.6 (LCR inflow reach). Additional 

sampling was conducted in major tributaries (LCR, Bright Angel, Shinumo, Kanab, Havasu). 

Mini-hoopnets, minnow traps, electrofishing, trammel nets, and seines were used to sample fish 

during 120 days of fieldwork spread over four seasons between March 1998 and February 1999. 

Some 4,618 fish were captured in the Colorado River mainstem and tributaries. Non-native 

species dominated the catch in the mainstem Colorado River (1,515/2,565, 59%) and rainbow 

trout Oncorhynchus mykiss was the most common non-native species (N=955, 37%). Of 1,050 

native fish captured in the mainstem, speckled dace Rhinichthys osculus (N=463, 18%) and 

humpback chub Gila cypha (N=395, 15%) were the most abundant. The use of mini-hoopnets to 
Humpback Chub Annotated Bibliography 34 September 2009

 

sample fish in mainstem habitats revealed a relative abundance of humpback chub in the 

100-200 mm TL size class, a population feature not observed in previous studies. In the smaller 

tributaries (Bright Angel, Shinumo, Kanab, Havasu), native species dominated the catch 

(739/847, 87%). Speckled dace (n=370, 44%) and humpback chub (n=133, 16%) were the most 

abundant native fishes. The LCR assemblage was dominated by native species (963/1206, 80%) 

with humpback chub (N=515, 43%) and speckled dace (n=308, 19%) dominating. The pattern of 

appearance, distribution, and abundance of YOY humpback chub in the mainstem Colorado 

River observed in our study was consistent with a “source-sink” model of downstream dispersal 

from the LCR coupled with high mortality from predation in the mainstem Colorado River. The 

abundance of adult rainbow trout in the LCR inflow reach of the Colorado River coupled with 

their complementary distribution with juvenile humpback chub in January 1999 strongly 

suggests that predation by rainbow trout may have been responsible for the near disappearance of 

YOY humpback chub between late summer and early winter. Mortality rates for small fish are 

likely exacerbated by fluctuating flows, which disrupt habitat associations and increase the 

probability of downstream movement and dispersal. Fluctuating flows also reduce the suitability 

of river edge habitats and food resources needed for rearing small fish. The rarity of small 

humpback chub downstream of the LCR inflow coupled with high abundance of trout and cold 

fluctuating flows suggest that conditions for recruitment of YOY humpback chub in the 

Colorado River in Grand Canyon are extremely poor. In order to provide opportunities for 

increased survivorship of small humpback chub in Grand Canyon, resource managers should 

consider ways to stabilize flows and increase temperature in the mainstem Colorado River. 

Implementation of more natural flow and temperature conditions will increase the stability of 

shoreline habitat and cover, and likely result in increased food resources and growth rates in 

small fishes, and decrease mortality associated with piscivory. 

Hoffnagle, T.L., R.A. Valdez and D.W. Speas. 1999. Fish abundance, distribution, and 

habitat use. Pages 273-287 in R.H. Webb, J.C. Schmidt, G.R. Marzolf and R.A. Valdez, eds. 

The Controlled Flood in Grand Canyon. Geophysical Monograph 110, The American 

Geophysical Union, Washington, D.C. 

 The 1996 controlled flood in the Colorado River, Grand Canyon, was designed, in part, to 

improve conditions for juvenile native fishes by reshaping habitat and displacing non-native 

fishes. We examined changes in abundance and distributions of native and non-native fishes 

immediately before and after the controlled flood and recovery of affected species 2.5 and 6 

months after. CPUE of humpback chub and flannelmouth sucker did not differ in pre- versus 

post-flood periods. CPUE of plains killifish, bluehead sucker and fathead minnow decreased 

following the flood, and CPUE of speckled dace and rainbow trout increased. Juvenile 

humpback chub remained primarily along talus shorelines at all discharges, while at higher 

discharges, speckled dace shifted from mid-channel riffles to debris fans and talus and fathead 

minnows used primarily vegetated shorelines. There was evidence of some downstream 

displacement of plains killifish, fathead minnows and rainbow trout. Catch rates of all species 

showed seasonal variation following the flood, with summer recruitment of YOY, particularly 

fathead minnows and plains killifish. Although short-term reductions in catch rates of fathead 

minnows and plains killifish occurred, these populations returned to pre-flood densities by 6 

months after the flood. Catch rates of all species before and after the flood were similar to those 
Humpback Chub Annotated Bibliography 35 September 2009

 

recorded in previous years. We determined that the controlled flood did not significantly alter 

native fish distributions or abundances through Grand Canyon. 

Jackson, J.A. 2008. Population estimate for the humpback chub (Gila cypha) and 

roundtail chub (Gila robusta) in Western Canyon, Colorado River, Utah 2003-2005. Draft 

report Utah Division of Wildlife Resources, Moab, Utah. 

Humpback chub population estimates were determined for Desolation and Gray canyons 

(Deso/Gray), on the Green River, by conducting multiple pass capture-recapture sampling. 

Three sampling passes were conducted in 2001 and 2003, and two passes were conducted in 

2002 due to low water. In 2003, sampling was moved to the fall to avoid capturing Colorado 

pikeminnow that use Desolation Canyon for spawning. Twelve sites were sampled throughout 

the two canyons. Included within these sites, were four long-term sites sampled annually by 

Utah Division of Wildlife Resources, since 1989. Analysis of point estimates generated by 

capture-recapture data demonstrated that the adult humpback chub populations was composed of 

1,254 individuals in 2001, 2,612 individuals in 2002, and 937 individuals in 2003. Many factors 

were at play during the three-year period that may have contributed in the variation in point 

estimates among years. Non-biological factors complicating the validity of the estimates include 

moving sampling from summer to fall and low water conditions at the time of sampling. Factors 

that may have directly affected the humpback chub population biologically include: the Rattle 

Complex fire and subsequent fish kill in late summer 2002, and the apparent increase in 

smallmouth bass occupying Deso/Gray. The authenticity of the point estimates will be more 

clearly analyzed when population estimates are conducted consistently during the fall months of 

2006-2008. 

 Population estimates for the juvenile portion of the population could not be determined 

since very few individuals were collected each year. Numbers of humpback chub juveniles 

collected by all methods during the study period were: 5 in 2001, 24 in 2002, and 4 in 2003. To 

determine mean recruitment for juveniles into the adult population, we assumed that individuals 

from 200-220 mm would be first year adults. Point estimates for this size class were derived by 

taking the proportion of these fish relative to the total numbers used in the adult population 

estimates. Therefore, estimates of first year adults were 163 (95% CI=149-192) for 2001, 297 

(95% CI=275-343) for 2002, and 134 (95% CI=123-159) for 2003. In order to increase the catch 

of juvenile humpback chub we recommend the continuation of electrofishing to the extent 

possible, utilizations of hoop nets and minnow traps, and incorporation of smaller mesh trammel 

nets. 

 Catch rate data incorporated to analyze changes over time at four long-term sites 

illustrated that catch rates for humpback chub have not changed substantially since 1989. 

Furthermore, examination of pre-study and study period data suggest that catch rates can be 

extremely variable and possibly dependent on environmental factors during sampling. 

 This study represents the first sampling period since finalization of the amended recovery 

goals for humpback chub in 2002 and is valuable in the initial evaluation of population size of 

humpback chub in Deso/Gray. Furthermore, it serves to illuminate any necessary adjustments to 
Humpback Chub Annotated Bibliography 36 September 2009

 

the sampling design before population estimate sampling for humpback chub in Deso/Gray 

resumes in 2006. 

Olden, J.D., L. Poff and K.R. Bestgen. 2008. Trait synergisms and the rarity, extirpation, 

and extinction risk of desert fishes. Ecology 89(3):847–856. 

Understanding the causes and consequences of species extinctions is a central goal in 

ecology. Faced with the difficult task of identifying those species with the greatest need for 

conservation, ecologists have turned to using predictive suites of ecological and life-history traits 

to provide reasonable estimates of species extinction risk. Previous studies have linked 

individual traits to extinction risk, yet the non-additive contribution of multiple traits to the entire 

extinction process, from species rarity to local extirpation to global extinction, has not been 

examined. This study asks whether trait synergisms predispose native fishes of the Lower 

Colorado River Basin (USA) to risk of extinction through their effects on rarity and local 

extirpation and their vulnerability to different sources of threat. Fish species with ‘‘slow’’ life 

histories (e.g., large body size, long life, and delayed maturity), minimal parental care to 

offspring, and specialized feeding behaviors are associated with smaller geographic distribution, 

greater frequency of local extirpation, and higher perceived extinction risk than that expected by 

simple additive effects of traits in combination. This supports the notion that trait synergisms 

increase the susceptibility of native fishes to multiple stages of the extinction process, thus 

making them prone to the multiple jeopardies resulting from a combination of fewer individuals, 

narrow environmental tolerances, and long recovery times following environmental change. 

Given that particular traits, some acting in concert, may differentially predispose native fishes to 

rarity, extirpation, and extinction, we suggest that management efforts in the Lower Colorado 

River Basin should be congruent with the life-history requirements of multiple species over large 

spatial and temporal scales. 

Paukert, C.P., L.G. Coggins, Jr. and C.E. Flaccus. 2006. Distribution and movement of 

humpback chub in the Colorado River, Grand Canyon, based on recaptures. Transactions 

of the American Fisheries Society 135:539–544. 

Mark-recapture data from the federally endangered humpback chub Gila cypha in the 

Colorado River, Grand Canyon, were analyzed from 1989 to 2002 to determine large-scale 

movement patterns and distribution. A total of 14,674 recaptures from 7,127 unique fish were 

documented; 87% of the recaptures occurred in the same main-stem river reach or tributary as 

the original captures, suggesting restricted distribution of most fish. A total of 99% of all 

recaptures were from in and around the Little Colorado River (LCR), a tributary of the Colorado 

River and primary aggregation and spawning location of humpback chub in Grand Canyon. 

Time at liberty averaged 394 d, but some fish were recaptured near their main-stem capture 

location over 10 years later. Proportionally fewer large (>300 mm) humpback chub exhibited 

restricted distribution than small (<200 mm) fish. However, several fish did not move more than 

154 km throughout Grand Canyon between capture and recapture, suggesting that limited 

movement occurs throughout Grand Canyon. The majority of the recaptured fish remained in or 

returned to the LCR or the Colorado River near the LCR. Although many large-river fishes 

exhibit extensive migrations to fulfill their life history requirements, most of the humpback chub 

in Grand Canyon appear to remain in or come back to the LCR and LCR confluence across 
Humpback Chub Annotated Bibliography 37 September 2009

 

multiple sizes and time scales. Detecting trends in the overall abundance of this endangered fish 

in Grand Canyon can probably be accomplished by monitoring the area in and around the LCR. 

Program Director’s Office. 2006. Evaluation of population estimates for Colorado 

pikeminnow and humpback chub in the Upper Colorado River Basin. Upper Colorado 

River Endangered Fish Recovery Program, Lakewood, Colorado. 

 The Upper Colorado River Endangered Fish Recovery Program (UCRRP) coordinates 

population estimates for the endangered Colorado pikeminnow (Ptychocheilus lucius) and 

humpback chub (Gila cypha) in the Colorado River Basin. Reliable and precise estimates are 

needed by the U.S. Fish and Wildlife Service as part of recovery and demographic criteria 

provided in species recovery goals approved in August 2002. Population estimates are being 

conducted in eight regions of the Upper Colorado River Basin by state and federal agencies with 

assistance from universities and private individuals. Mark-recapture estimates are being obtained 

from field sampling of populations in each region for 3 consecutive years with 2 years off to 

minimize over-handling of fish. Estimates of Colorado pikeminnow began in 1992 in the Upper 

Colorado River Subbasin and in 2000 in the Green River Subbasin. Numbers of wild fish in the 

San Juan River Subbasin are currently too low for formal mark-recapture estimates, and hatchery 

augmentation is expected to increase population size for estimates by about 2006. 

 Estimates of humpback chub began in 1998 in Black Rocks and Westwater Canyon; 2000 

in Yampa Canyon; 2001 in Desolation/Gray Canyons; and 2003 in Cataract Canyon. Annual 

reports are submitted by respective researchers for each of the population estimates to the 

UCRRP and the San Juan River Basin Recovery Implementation Program, and findings are 

presented and discussed at the Annual Upper Basin Researchers Meeting. Two workshops of 

species experts and statisticians have been convened by the UCRRP to improve reliability and 

precision of population estimates, and an ad hoc committee of species experts and researchers 

has been established to ensure ongoing communication and evaluation of field sampling 

protocols and analytical methods. Precision criteria of capture probability (P-hat ≥0.10) and 

coefficient of variation (CV ≤0.15) are not being consistently met in all estimates. Researchers 

are refining field sampling protocols and analytical methods to improve precision but 

environmental variables, particularly flow, are uncontrolled and affect capture efficiency and 

hence, precision. Estimates will continue to be evaluated, but maximum achievable precision 

may be reflected in current estimates. 

Robinson, A.T. D.M. Kubly, R.W. Clarkson and E.D. Creef. 1996. Factors limiting the 

distributions of native fishes in the Little Colorado River, Grand Canyon, Arizona. 

Southwestern Naturalist 41(4):378–387. 

Native fishes are not distributed evenly in the terminal 21 km of the Little Colorado River 

(Blue Spring to the mouth); speckled dace (Rhinichthys osculus) are present throughout the 

21 km; humpback chub (Gila cypha), bluehead sucker (Pantosteus discobolus), and 

flannelmouth sucker (Catostomus latipinnis) are restricted to the 14.2 km below chute Falls. 

Water chemistry (primarily carbon dioxide concentration) and food resources have been 

hypothesized to limit fish distribution in the Little Colorado River. We sampled algae, 

invertebrates, and water chemistry in reaches above and below Chute Falls to determine if native 
Humpback Chub Annotated Bibliography 38 September 2009

 

fish distributions were limited by these parameters. Chlorophyll a content of algae samples 

collected from fine substrates was greatest above Chute Falls. Densities and biomasses of 

invertebrates known to be food items for native fishes were also greatest in that reach. 

Longitudinal water chemistry gradients were consistent across seasons; dissolved oxygen, pH, 

and conductivity generally decreased. To determine if native fishes other than speckled dace 

could survive in the waters above Chute Falls, we captured age-0 and age-1 humpback chub, and 

age-1 bluehead suckers near 10.5 km, relocated subsets to 12.5, 15, 17.5, and 20 km, and held 

them for three days. All age-1 humpback chub and bluehead suckers survived three days of 

relocation at all sites. Age-0 humpback chub and bluehead suckers survived three days of 

relocation at all sites. Age-0 humpback chub experienced significantly more mortality, and 

exhibited more stress behaviors at the 20 km relocation site than at any other site. Longitudinal 

food resource patterns and the results of the relocation experiment suggest that neither food 

resources nor water chemistry prohibit humpback chub and bluehead sucker from inhabiting the 

reach above Chute Falls. We believe that during base flow, Chute Falls is a physical barrier to 

upstream movement of fishes. If humpback chub and the two sucker species could transgress 

Chute Falls during high discharge, or if these species were artificially reintroduced above the 

falls, we believe that sufficient habitat and food resources are available to sustain populations. 

Robinson, A.T., R.W. Clarkson and R.E. Forrest. 1998. Dispersal of larval fishes in a 

regulated river tributary. Transactions of the American Fisheries Society 127:722–786. 

We investigated longitudinal distributions, near-shore movements, and drift of larval 

native fishes (humpback chub Gila cypha, speckled dace Rhinichthys osculus, bluehead sucker 

Catostomus discobolus, and flannelmouth sucker Catostomus latipinnis) in the Little Colorado 

River, a tributary to the regulated Colorado River in Grand Canyon, Arizona, to determine 

spawning sites, larval dispersal patterns, and amount of drift into the mainstem Colorado River. 

Larval distributions and drift indicated native fishes spawned throughout the terminal 14.2 km of 

the Little Colorado River. In addition, distribution, drift, and trap data suggest an active 

component to dispersal for all four native species. Drift of larval native fish was greater near 

shore than mid-channel, and except for speckled dace larvae, which were prone to drift at night, 

larval native fish did not exhibit diel periodicity in drift. During a 46-d period in 1993, we 

estimated that over 370,000 native fish larvae drifted out of the Little Colorado River into the 

Colorado River. Regulated discharge from Glen Canyon Dam has all but eliminated spring–

summer ponding of tributary mouths that occurred when ascending flows in the Colorado River 

coincided with descending and base flows in tributaries; thus, drifting larvae are allowed to pass 

directly into the Colorado River. Survival of larvae now transported into the Colorado River is 

probably poor because of perennially cold water temperatures and instability of near-shore 

habitats. 

U.S. Geological Survey. 2006. Grand Canyon humpback chub population stabilizing. U.S. 

Geological Survey Fact Sheet 2006–3109. Abstract was excerpted from report introduction 

and results. 

A number of factors have contributed to the decline of humpback chub and other native 

Colorado River fish. In 1967, the humpback chub was added to the federal list of endangered 

species and is today protected under the Endangered Species Act of 1973. Only six populations 
Humpback Chub Annotated Bibliography 39 September 2009

 

of humpback chub are currently known to exist, five in the Colorado River Basin above Lees 

Ferry, Arizona, and one in Grand Canyon, Arizona. Monitoring and research of the Grand 

Canyon population of humpback chub is overseen by the U.S. Geological Survey’s Grand 

Canyon Monitoring and Research Center (GCMRC) under the auspices of the Glen Canyon Dam 

Adaptive Management Program (GCDAMP). Recently collected data indicate that the number of 

adult (age-4+) humpback chub in the Grand Canyon stabilized between 2001 and 2005 after 

more than a decade of decline. 

 Since scientists began monitoring efforts in 1989, the population of adult humpback chub 

in the Grand Canyon has declined steadily until recently. The death of 15 to 20% of adult fish 

each year and a low rate of juvenile fish surviving into adulthood contributed to the decline. 

Adult mortality rates and the failure of juvenile fish to reach adulthood have been attributed to 

changes in Little Colorado River and Colorado River hydrology, the weakening of young fish by 

the nonnative Asian tapeworm (Bothriocephalus acheilognathi), and competition with and 

predation by nonnative fish species. 

Between 2001 and 2005, however, conditions appear to have improved, and the number 

of adult fish stabilized at an estimated 5,000 fish. Additionally, near the confluence of the 

Colorado and Little Colorado Rivers, catch-rate data from the monitoring program indicate an 

increased abundance of juvenile humpback chub between 2003 and 2005. Increases in juvenile 

fish during the same period were also apparent for other native species found near the 

confluence, including bluehead sucker (Catostomus discobolus), flannelmouth sucker 

(Catostomus latipinnis), and speckled dace (Rhinichthys osculus). 

Elsewhere in the Grand Canyon, catch rates for humpback chub produced in 2005 were 

higher than previous years in middle and lower Marble Canyon. Higher than average catch rates 

at these locations were unexpected because they are up to 25 river miles above the confluence of 

the Colorado and Little Colorado Rivers where spawning usually occurs. These findings suggest 

that more favorable conditions for spawning and incubation existed in the Colorado River main 

channel during 2005. 

U.S. Geological Survey. 2007. Grand Canyon humpback chub population improving. U.S. 

Geological Survey Fact Sheet 2007–3113. Abstract excerpted from report. 

The U.S. Geological Survey’s (USGS) Grand Canyon Monitoring and Research Center 

oversees monitoring and research activities for the Grand Canyon population under the auspices 

of the Glen Canyon Dam Adaptive Management Program (GCDAMP). Analysis of data 

collected through 2006 suggests that the number of adult (age 4+ years) humpback chub in 

Grand Canyon increased to approximately 6,000 fish in 2006, following an approximate 40–50% 

decline between 1989 and 2001 (Coggins 2007). Increasing numbers of adult fish appear to be 

the result of steadily increasing numbers of juvenile fish reaching adulthood beginning in the 

mid- to late-1990s and continuing through at least 2002. 

Humpback chub have been affected not only by changes in hydrology since the 

construction of the dam but also by competition with and predation by nonnative fishes. Fishes 

originating in many parts of the world are currently found in the Colorado River, including 
Humpback Chub Annotated Bibliography 40 September 2009

 

introduced species of trout, catfish, carp, and bass. Nonnative fish parasites, such as the Asian 

tapeworm (Bothriocephalus acheilognathi) and anchor worm (Lernaea cyprinacea), which infect 

some humpback chub, have also found their way into the Colorado River. 

Since 1989, when scientists began repeated monitoring efforts, the population of adult 

humpback chub in Grand Canyon has declined steadily until about 2001, when the population 

appeared to stabilize. More recently, the population appears to have increased, reaching an 

estimated 6,000 adult fish in 2006. Current estimates suggest that there has been an approximate 

increase of 20–25 percent in adult fish abundance since 2001. This increase in adult fish numbers 

since 2001 appears to be the result of increasing recruitment that began in the mid- to late-1990s 

and has continued through at least 2002. 

USGS scientists have been working to improve their ability to estimate the status and 

trends of the Grand Canyon population of humpback chub. They evaluated the age-structured 

mark-and-recapture models used to estimate adult humpback chub numbers and made 

refinements to ensure that current estimates are most consistent with the data. Model innovations 

included accounting for the impacts of seasonal and spatial variation in water temperature on fish 

growth. A new method was also developed for estimating the relation between fish age and 

length. Scientists also concluded that only large changes in recruitment caused by management 

actions can be readily detected, given the uncertainty in current assessment procedures. 

Valdez, R.A., W.J. Masslich and W. Leibfried. 1993. Present distribution of humpback 

chub Gila cypha in the mainstem Colorado River, Grand Canyon, Arizona. Proceedings of 

the Desert Fishes Council 24:66. 

 Ninety-five percent (1,324) of 1,392 humpback chub Gila cypha captured from the 

mainstem Colorado River in Grand Canyon, form October 1990 through June 1992, were found 

in a 13-km reach between RM 57 and 65, about equidistance upstream and downstream of the 

confluence with the Little Colorado River (LCR, RM 61.3). Bimonthly sampling conducted 

between RM 56 and 226 revealed that chubs were distributed between RM 57.0 and 221.8. 

Concentrations of chubs downstream of the LCR were encountered at Bright Angel Creek inflow 

(RM 87-88), Shinumo Creek inflow (RM 108-109), above Blacktail Canyon RM 119-120) 

Middle Granite Gorge (RM 126-127), Havasu Creek inflow (RM 155-157), and Pumpkin Spring 

(RM 213-214). Present distribution of humpback chub in the mainstem Colorado River is 

compared with historic distribution. 

Wasowicz, A. and R.A. Valdez. 1995. Historic and present distribution and abundance of 

humpback chub in Grand Canyon, Arizona. Proceedings of the Desert Fishes Council 

26:57. 

Archaeological and historic records indicate that the endangered humpback chub (Gila 

cypha) was once distributed throughout the Colorado River and its major tributaries in Grand 

Canyon. Following completion of Glen Canyon Dam in 1963 and until 1970, mainstem 

distribution of the species was reported as 412 km, from the tailwaters of the dam to Separation 

Canyon. Present distribution is 359 km, from RM 30 (South Canyon) to RM 253 (Maxson 

Canyon), with 88 percent of adults in an 11-km area, from RM 58.3 to RM 65.4. This population 
Humpback Chub Annotated Bibliography 41 September 2009

 

center for humpback chub in Grand Canyon is associated with the LCR, where the majority of 

mainstem adults and the LCR population component spawn. Limited mainstem spawning 

success is suspected, as indicated by ripe and gravid fish away from the LCR and few larval 

chubs. Distribution of humpback chub in the mainstem Colorado River in Grand Canyon is 

limited by cold, hypolimnetic releases from Glen Canyon Dam (8–10°C, which also limit 

reproduction), low food availability, large numbers of predators, and possibly habitat instability 

from dam operations. The species was reported in low numbers from lower areas of Bright Angel 

Creek, Shinumo Creek, Kanab Creek, Tapeats Creek, and Havasu Creek, where it is still found in 

very small numbers. The population component inhabiting the LCR, and spawners ascending 

from the mainstem, occur only in the lower 13 km of stream. Although the distribution of 

humpback chub in Grand Canyon has contracted since Glen Canyon Dam was built, changes in 

species abundance are difficult to assess. Historic records indicate higher abundances throughout 

the canyon, but it appears that densities may be higher within the LCR. 

3.3 HABITAT SELECTION 

Childs, M.R., R.W. Clarkson and A.T. Robinson. 1998. Resource use by larval and early 

juvenile native fishes in the Little Colorado River, Grand Canyon, Arizona. Transactions 

of the American Fisheries Society 127:620–629. 

We investigated resource use by early life stage (≤30 mm, total length) humpback chub 

Gila cypha, speckled dace Rhinichthys osculus, bluehead suckers Catostomus discobolus, and 

flannelmouth suckers C. latipinnis in the Little Colorado River, a tributary to the Colorado River 

in Grand Canyon, Arizona. Significant logistic regression models for habitat use were developed 

for all species pairwise combinations except flannelmouth sucker–humpback chub and 

flannelmouth sucker–speckled dace; correct classification probabilities ranged from 54% to 81%. 

Parameters used in discriminating among habitat use included depth, distance from shore, cover, 

and substrate. Logistic models were also developed to compare habitat use among larval stages 

within species, and most combinations produced significant models. Classification probabilities 

ranged from 60% to 95% in these models with the variables of depth, distance from shore, 

current velocity, cover, and substrate contributing to the various models. Behavioral observations 

revealed significant differences in vertical use of the water column and feeding locations among 

bluehead suckers and the two cyprinids. Diet analysis supported differences observed in feeding 

location and also identified some differences in diel feeding patterns. These differences in habitat 

use, behavioral time budgets, and diet indicate that some resource partitioning occurs among 

larval fishes in the Little Colorado River. Further laboratory study is needed to verify the 

mechanisms that sustain differential resource use in this system. 

Converse, Y.K., C.P. Hawkins and R.A. Valdez. 1998. Habitat relationships of subadult 

humpback chub in the Colorado River through Grand Canyon: spatial variability and 

implications of flow regulation. Regulated Rivers: Research and Management 14(3):267–

284. 

We examined subadult humpback chub densities along 24 km of the Colorado River in 

the Grand Canyon to: (1) identify geomorphic conditions in the study area; (2) determine 
Humpback Chub Annotated Bibliography 42 September 2009

 

associations between subadult humpback chub (<200 mm TL) habitat use and geomorphic 

differences; and (3) determine how discharge, during base flow conditions, was related to 

subadult humpback chub habitat conditions. 

 Habitat was categorized at two nested spatial scales: geomorphic reach and shoreline 

type. Within reaches, shoreline types were categorized according to geomorphology. We 

measured water depth, velocity and cover attributes along all shoreline types over a range of 

discharges to determine if habitat quality of reaches and shoreline types varied with discharge. 

Reaches 1 and 3 had narrow, deep corridors, whereas Reach 2 was a wide, shallow reach. 

Among shoreline types, depth, velocity and cover varied; however, differences were not 

consistent between reaches. Fish densities also varied among shoreline types and reaches. 

Vegetation, talus and debris fan shorelines had the highest densities of subadult humpback chub 

in a pattern similar to that of cover. In addition, subadult humpback chub presence was 

associated with a high frequency of cover regardless of shoreline designation. However, these 

relationships explained little of the overall variation in subadult densities. 

Lack of a strong association between fish density and geomorphology may be partially 

due to effects of discharge on habitat quality. The overall trend among shorelines (without regard 

to type) showed that cover decreased with increasing discharge, whereas depth and velocity 

increased. However, no consistent pattern between discharge and depth, velocity and cover 

among individual shoreline types was evident. 

Vegetated shorelines, consisting mainly of non-native tamarisk (Tamarix chinensis), had 

nearly twice the fish densities of talus and debris fan. Reasons are discussed as to why subadult 

humpback chub occupy naturalized habitat like vegetated shorelines in greater densities than 

natural habitats. The relationships observed in this study have important implications for 

humpback chub recovery and management of the Colorado River through Grand Canyon. 

Day, K. S., K. D. Christopherson and C. Crosby. 2000. Backwater use by young-of-year 

chub (Gila spp.) and Colorado pikeminnow (Ptychocheilus lucius) in Desolation and Gray 

Canyons of the Green River, Utah. Report B in Flaming Gorge studies: reproduction and 

recruitment of Gila spp. and Colorado pikeminnow (Ptychocheilus lucius) in the middle 

Green River. Final report of Utah Division of Wildlife Resources to Upper Colorado River 

Endangered Fish Recovery Program, Lakewood, Colorado. 

Backwater nursery habitat characteristics used by chubs (Gila spp.) and Colorado 

pikeminnow (Ptychocheilus lucius) were studied in Desolation and Gray canyons of the Green 

River, Utah, during 1994 and 1996. This study was conducted as part of the Recovery 

Implementation Program (RIP) for the Endangered Fish Species in the Upper Colorado River 

Basin, Scope-of-Work number FG-39. The Flaming Gorge Investigations are a five year program 

begun in 1992 to provide pertinent information on endangered fishes in the Green River and the 

effects of flow regulation by the dam. Results of the numerous studies conducted during this 

period will be used to develop a new Biological Opinion on the future operation of Flaming 

Gorge Dam. There were a total of ten project objectives, six dealt with biological component and 

four dealt with geomorphic component. Several of the objectives were handled by more than one 

research team and the results are reported in more than one final report. The specific tasks of this 
Humpback Chub Annotated Bibliography 43 September 2009

 

report were to: 1. determine reproductive success, growth rates, and backwater habitat use of 

early life stages of Gila spp. and Colorado pikeminnow; 2. continue PIT tagging all juvenile and 

adult Gila spp.; and 3. monitor apparent trends in the non-target fish community. A total 729 

backwater and low velocity flow habitats of Desolation and Gray canyons were sampled four 

times each year between 1994 through 1996 for the presence of endangered fish. Each backwater 

sampled was first categorized by physical type, and physical measurements were made after fish 

communities were sampled with a 3 mm mesh seine. Several statistical analyses were conducted 

to help interpret significant relationships. Linear regression was performed on four flow 

parameters peak flow, date of peak flow, flow and duration against backwater numbers, volume 

and area. Contingency table and X2 analysis were preformed to test preference for use of habitat 

classes. The Wilcoxon rank-sum tested the significant differences (P < 0.05) of habitat variables 

between occupied and unoccupied backwaters. Discriminant function analysis was also used to 

determine if Colorado pikeminnow use of nursery habitats could be predicted by a model of 

habitat characteristics. Models were developed for each season of each year, for each season for 

all years, for each year and for all seasons and years pooled. Numbers of backwaters sampled 

varied between years and seasons. The predominant backwater class was shoreline eddy. 

Correlations between backwater numbers and flow events could not be rigorously tested because 

this study represents only three years of flow data. Correlation analyses were run to determine if 

backwater types were influenced by flow events. Strong negative correlations were seen between 

the number of migrating sand wave backwaters sampled and annual peak flow and the duration 

of flow above 50% of the peak, when all sampling periods were included in the analysis. 

Secondary channel backwaters were negatively associated with duration of flows above 75% of 

the peak. Although shoreline eddy habitats were not significantly correlated with peak flow 

events, there was a negative correlation with flows during sampling periods. Chubs did not show 

a preference for backwater habitats based on method of formation. Backwaters containing chubs 

were significantly larger (length, area, depth, volume) and more turbid than unused backwaters, 

but preferences varied between months. Habitat selection by chubs showed considerable 

variability. Recent studies from the Grand Canyon indicate that chubs use in-channel shoreline 

habitats more than backwaters. Other studies show that chubs are often found in main channel 

habitats and are capable of movement into and through flow. Therefore, this study is likely 

insufficient for describing characteristics of chub recruitment and nursery habitat use in 

Desolation and Gray canyons. Colorado pikeminnow used scour-formed and migrating 

sandwave backwaters and avoided constricted reach eddies and shoreline eddies. Selection for 

scour backwaters matched patterns seen in floodplain reaches. Colorado pikeminnow chose 

larger (length, width, area, volume) backwaters with little cover. Habitat use criteria for this 

species appeared to be more consistent than for chubs. 

Discriminant function analyses could not separate backwaters inhabited by chubs and 

Colorado pikeminnow from those uninhabited. Discriminant models for Colorado pikeminnow 

were better than those for chubs, another indication of more definite selection patterns, but they 

were still not powerful enough for application. All sampled habitats were overwhelmingly 

dominated by nonnative species. Catch-per-unit effort for a few of these species was positively 

correlated with chubs and Colorado pikeminnow. 

Flow regulation alone may not be adequate for control of nonnative fish. It is 

recommended that additional studies be conducted on chub nursery habitat use. Additional 
Humpback Chub Annotated Bibliography 44 September 2009

 

studies should be conducted on effects of spring discharge, single year and multiple year 

interaction, on chubs and Colorado pikeminnow. Habitat associations and flow/recruitment 

relationships for non-listed native fishes should be analyzed. Nonnative fish recruitment and 

habitat use, as well as interactions with native fishes should be pursued. 

Gorman, O.T. 1995. Habitat use by the endangered humpback chub (Gila cypha) in the 

Little Colorado River, Grand Canyon. Bulletin of the Ecological Society of America 76 

(Suppl. 3):333. 

 The objective of USFWS research is to determine habitat use by the endangered 

humpback chub and other native fishes in the LCR and other tributaries of the Colorado River in 

the Grand Canyon, evaluate the potential for establishing a second spawning aggregation of 

humpback chub, and from the perspective of habitat requirements, evaluate the impact of Glen 

Canyon dam on native fishes. Research commenced in the LCR in July 1991 and in January 

1992 for other tributaries. Stream habitat in the lower 21 km of the LCR and lower 8 km of 

other tributaries has been mapped and sampled. Habitat use patterns were evaluated from 

seining, electrofishing, and hoopnetting. In the LCR, humpback chub were the predominant 

species and maintained a resident population. Preliminary analyses indicate that adult chubs are 

highly habitat specific and that juvenile chub show a very different pattern of habitat use. 

Gorman, O.T. D.M Stone, Z.M. Zdinak and V. Meretsky. 1995. Habitat use by the 

endangered humpback chub (Gila cypha) in the Little Colorado River, Arizona near Grand 

Canyon. Proceedings of the Desert Fishes Council 26:53. 

During the spring months (March, April, May) of 1993, 1994, and 1995, the Service 

conducted field studies to describe the habitat used by spawning humpback chub in the Little 

Colorado River. During the spring spawning season, ripe males congregated in shallow to 

moderately deep runs and eddies below travertine dam/reef complexes. These habitats had slow 

currents, complex structure and were associated with the presence of gravel substrates. Most ripe 

females appeared to be solitary and were captured in deeper downstream pool habitats. Capture 

of single ripe females in aggregations of ripe males indicated putative spawning sites. This 

pattern of spawning habitat use and behavior is concordant with published studies of minnow 

spawning ecology. The results of our work will serve as a model of habitat use by humpback 

chub and will be useful in efforts to establish additional spawning populations. 

Gorman, O.T., S.C. Leon and O.E. Maughan. 1993. Habitat use by humpback chub, Gila 

cypha, in the Little Colorado River and other tributaries of the Colorado 

River. Proceedings of the Desert Fishes Council 24:20-21. 

The objective of USFWS research is to determine habitat use by the endangered 

humpback chub and other native fishes in the LCR and other tributaries of the Colorado River in 

the Grand Canyon, evaluate the potential for establishing a second spawning aggregation of 

humpback chub, and from the perspective of habitat requirements, evaluate the impact of Glen 

Canyon dam on native fishes. Research commenced in the LCR in July 1991 and in January 

1992 for other tributaries. Stream habitat in the lower 21 km of the LCR and the lower 8 km of 

other tributaries has been mapped and sampled. Habitat use patterns were evaluated from 
Humpback Chub Annotated Bibliography 45 September 2009

 

seining, electrofishing, and hoopnetting. In the LCR, humpback chub were the predominant 

species and maintained a resident population. Preliminary analyses indicate that adult chubs are 

highly habitat specific and that juvenile chub show a very different pattern of habitat use. 

Hoffnagle, T.L., W.R. Persons and G. Doster. 1994. Use of backwater areas by juvenile 

native fishes in the Colorado River. Proceedings of the Desert Fishes Council 25:33-34. 

Use of backwater habitats in the Colorado River, Grand Canyon, by juvenile native fishes 

was studied over the past year. Comparisons of relative abundances within reaches revealed that 

speckled dace (Rhinichthys osculus) (48.5%) and flannelmouth sucker (Catostomus latipinnis) 

(32.5%) were the more common species in Reach 20 [Lee's Ferry (RM 0) to the LCR (RM 

61.5)]. Humpback chub (Gila cypha) (33.3%) was the most common species in Reach 30 [LCR 

to Bright Angel Creek (RM 87.6)]. In Reach 40 [Bright Angel Creek to National Canyon (RM 

166.4)], bluehead sucker (Catostomus discobolus) (35.7%) was most abundant. Speckled dace 

(33.8%) and bluehead sucker (24.6%) were the more common species in Reach 50 [National 

Canyon to Diamond Creek (RM 225.6)]. Comparisons among reaches showed that most 

bluehead suckers (66.5%), flannelmouth suckers (52.4%) and speckled dace (67.9%) were 

collected in Reach 50, whereas most humpback chubs (87.6%) were taken in Reach 30. 

Humpback chubs caught in backwaters at night were significantly larger than those taken during 

the day. No significant relationships were found for comparisons of catch rates with water 

temperature, substrate, depth, turbidity, or ambient light. Juvenile native fishes were more 

common in areas near known spawning areas for these species, and it appears that the measured 

environmental variables had little effect on their use of backwaters.

Orchard, K.L. and J.C. Schmidt. 2000. A geomorphic assessment of the availability of 

potential humpback chub habitat in the Green River in Desolation and Gray Canyons, 

Utah. Report A in Flaming Gorge studies: reproduction and recruitment of Gila spp. and 

Colorado pikeminnow (Ptychocheilus lucius) in the middle Green River. Final report of 

Utah Division of Wildlife Resources to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

The size and number of low-velocity eddies that may be preferred habitat for the 

endangered humpback chub (Gila cypha) in the Green River in Desolation and Gray Canyons 

changes with discharge and has changed since the early 1900’s. We determined the present 

extent and distribution of these habitats by mapping low-velocity eddies at a scale of 1:5000 at 5 

or 6 discharges between 2,100 and 27,000 cfs in four 8-km reaches that are regularly sampled by 

the Utah Division of Wildlife Resources. We also mapped the surficial geology of these study 

reaches and the distribution of bed substrate that are emergent at 2,000 cfs. We analyzed the 

distribution of these areas within a geographic information system. The availability of habitat 

prior to completion of Flaming Gorge Dam was estimated by matching old oblique photographs, 

analyzing old aerial photos, and recomputing habitat availability prior to channel change. The 

total area of low-velocity eddies, when summed for the 4 study reaches, does not change with 

discharge, but the relative distribution of these eddies among the 4 study reaches does change. 

Also, the type of eddies changes with discharge. At low discharge, the greatest proportion of the 

total area of low-velocity eddies occurs as small shoreline eddies, but the greatest proportion 

occurs in a few large eddies at higher discharges. At low discharge, the river bank is highly 
Humpback Chub Annotated Bibliography 46 September 2009

 

contorted and is dominantly bare sand and gravel. At high discharge, the river bank has a simpler 

shape, and much of the shoreline is inundated vegetation. 

The Green River channel is 19% narrower today than it was in the 1920’s, and riparian 

vegetation has established itself at low elevations and on formerly active mid-channel islands. 

We estimate that the substrate of most nearshore habitats was sand or gravel prior to channel 

narrowing. For purposes of developing flow recommendations, our results must be integrated 

with the results of ecological studies which identify the relative importance of the different 

habitats in the life history of the target species. 

Pimentel, R. and R.V. Bulkley. 1983. Concentrations of total dissolved solids preferred or 

avoided by endangered Colorado River fishes. Transactions of the American Fisheries 

Society 112(5):595–600. 

 Juveniles (age 0-1) of three endangered River Colorado fishes were subjected to a 

gradient of total dissolved solids (TDS) to determine the concentrations that they preferred or 

avoided. Preferred and avoided TDS concentrations, respectively, for juveniles of each species 

were: Colorado squawfish Ptychocheilus lucius, 560-1, 1,150 mg/liter and greater than 4,400 

mg/liter; humpback chub Gila cypha, 1,000-2,500 mg/liter and greater than 5,100 mg/liter; and 

bonytail Gila elegans, 4,100-4,700 mg/liter and less than 560 mg/liter or greater than 6,600 

mg/liter. Colorado squawfish and humpback clubs selected TDS concentrations that were similar 

to those in waters they now inhabit, but bonytail selected concentrations four times higher. 

Seals, J.M., O.T. Gorman and S.C. Leon. 1994. Stream fish habitat studies in the Little 

Colorado River: a microhabitat approach. Proceedings of the Desert Fishes Council 25:14-

15. 

The objective of USFWS research is to determine habitat use by the endangered 

humpback chub (Gila cypha) and other native fishes in the LCR. High conductivity, low 

visibility, extensive travertine structures, and prolonged periods of flooding prohibited 

conventional approaches to determining habitat use by fishes in the LCR. We developed an 

experimental passive sampling methodology that would allow us to determine microhabitat use 

by all adult and YOY fishes and to detect diurnal patterns of activity and habitat use. Our passive 

sampling was complemented with seining surveys, and when conditions permitted, observational 

surveys. Microhabitat use patterns determined from these other sampling methods corroborated 

the results of our passive sampling methodology. Our sampling methods have been used in 

studies of other tributaries in the Grand Canyon to evaluate their potential to support additional 

reproducing populations of humpback chub. 

Thieme, M.L., C.C. Mivor, M.J. Brouder and T.L. Hoffnagle. 2001. Effects of pool 

formation and flash flooding on relative abundance of young-of-year flannelmouth suckers 

in the Paria River, Arizona. 

Flannelmouth sucker, Catostomus latipinnis, a fish endemic to the Colorado River basin 

in the western United States, appears to experience poor recruitment to adult size in the Colorado 

River, downstream of Glen Canyon Dam. Lack or impermanence of rearing areas for YOY fish 
Humpback Chub Annotated Bibliography 47 September 2009

 

is hypothesized to be the problem. Knowing the importance of tributary mouths as rearing areas 

in other river systems, we studied use of the mouth of the Paria River, a tributary of the Colorado 

River, by YOY flannelmouth suckers, and the availability of rearing area in the mouth at 

different flow levels in the Colorado River in 1996 and 1997. We also examined the relationship 

between flash floods in the Paria River and catch-per-unit-effort (CPUE) of YOY in the Paria 

River between 1991 and 1996. 

Maximum mean daily discharge in the Paria River was inversely correlated with CPUE 

of YOY flannelmouth suckers (Spearman rho=-0.9856, p=0.0003) during their critical rearing 

period (15 March-30 June). Thus, it appears that YOY flannelmouth suckers rear longer in the 

Paria River in years when flash flooding is minimal. 

Recruitment of YOY flannelmouth suckers at the Paria River may also be improved by 

enhancing pool formation during spring and summer rearing seasons. YOY flannelmouth sucker 

was captured in a pool created by high Colorado River flows (336 m3/s) that inundated the mouth 

of the Paria River during spring and summer, 1996. In 1997, high flows (about 550-750 m3

/s) in 

the Colorado River during winter and spring initially inundated the Paria River and formed a 

pool in the mouth. However, these high flows eventually caused 0.5-1.0 m of suspended 

sediment from the incoming Paria River to deposit in the mouth. Thus, despite higher flows than 

1996, the slackwater area formed only occasionally in 1997. Differences in pool formation 

between 1996 and 1997 demonstrate that pool formation cannot be inferred solely from Colorado 

River flows. 

Tyus, H.M. and C.A. Karp. 1989. Habitat use and streamflow needs of rare and 

endangered fishes, Yampa River, Colorado and Utah. U.S. Fish and Wildlife Service 

Biological Report 89:1–27. 

In the Yampa River, stream habitat needs and life history requirements of Colorado 

squawfish (Ptychocheilus lucius), humpback chub (Gila cypha), razorback sucker (Xyrauchen 

texanus), and other native Colorado River fishes are presently maintained by flow regimens 

approximating natural conditions. Yampa River flows are also important in reducing adverse 

water management practices in the downstream Green River. Management for recovery of 

endangered fishes in the Yampa River will require specific flows to provide seasonal 

requirements at different locations: high spring flows associated with the initiation of Colorado 

squawfish spawning migrations, humpback chub and razorback sucker spawning, and 

maintenance of spawning bars and eddy habitats; descending summer flows associated with 

Colorado squawfish spawning, downstream transport of larvae, and creation of nursery habitat; 

stable winter flows to remove the threat of ice damage to shoreline areas used by many species. 

Acquisition of Yampa River water rights may be the decisive factor in conservation of 

endangered fish species in the Green River basin. 

Valdez, R.A., P.B. Holden and T.B. Hardy. 1990. Habitat suitability index curves for 

humpback chub of the Upper Colorado River Basin. Rivers 1:31–42. 

Habitat suitability index (SI) curves were developed for the endangered humpback chub 

(Gila cypha) using previously-collected microhabitat data from the Upper Colorado River Basin. 
Humpback Chub Annotated Bibliography 48 September 2009

 

Data selection, partitioning and pooling, as well as curve development were decided by 

consensus by a panel of species experts during two week-long workshops. The result was a total 

of 14 riverine SI curves associating four life stages (larvae, YOY, juvenile, and adult) with three 

microhabitat parameters (water depth, velocity, and substrate). The SI curves were developed to 

best fit actual field data, and modified by the experts according to biological judgment. The 

species experts classified these as "interim SI curves" and recommended application of only the 

adult curve set, recognizing that much information still needs to be gathered on the rare fishes of 

the upper basin. The process by which these SI curves were developed is recommended in 

dealing with large volumes of pre-existing microhabitat information scattered through many 

literature sources and reports. The concept of assimilating the data for evaluation by a panel of 

species experts was sound in that it allowed for a joint review by the experts without each 

investing large amounts of time to independently research the data. The idea of open workshops, 

in which experts and participants were given equal opportunity to express opinions, also worked 

well, although a third workshop was recommended to allow the experts to participate in 

generation of weighted usable area and evaluation of the streamflow to habitat relationships.

Wick, E.J., J.A. Hawkins and T.P. Nesler. 1991. Occurrence of two endangered fishes in 

the Little Snake River, Colorado. Southwestern Naturalist 36:251–254. 

The Little Snake River (Colorado) delivers significant amounts of water and sediments to 

the Yampa River yet generally has been disregarded as a potential habitat for endangered fishes. 

Collection of humpback-like chubs of the Gila complex led to funding of studies to determine 

the extent of use of the lower Little Snake River by endangered and other native fishes. Two 

radiotagged Colorado squawfish were contacted by radiotelemetry in the Little Snake River. 

Sampling for adult fishes in the Little Snake River was initiated during spring runoff and 

continued into baseflow periods in July and October. Among the 308 adult and large juvenile 

fish collected were seven suspected humpback chub, two suspected hybrids of humpback chub x 

Colorado roundtail chub, and one Colorado squawfish. Numerically dominant species collected 

were Colorado roundtail chub (53%), flannel-mouth sucker (20%), common carp (11%), and 

channel catfish (9%). Species collected in small numbers (< 3%) included bluehead sucker, black 

bullhead, and white sucker. Collections with fine-mesh seine and dipnet yielded 1,260 young 

fish, of which 82% were flannel-mouth sucker and 17% were bluehead sucker. Other species 

collected in small numbers included sand shiner, speckled dace, and Colorado roundtail chub. 

The Little Snake River provided habitat for Colorado squawfish and humpback chub during the 

spring, when high discharge provided suitable habitat. It appeared that Colorado squawfish left 

the Little Snake River prior to spawning. Occurrence of suspected humpback chub in the canyon 

section of the Little Snake River also appears to be restricted to the spring runoff period.
Humpback Chub Annotated Bibliography 49 September 2009

 

3.4 STREAM FLOW

Muth, R.T., L.W. Crist, K.E. LaGory, J.W. Hayse, K.R. Bestgen, T.P. Ryan, J.K. Lyons 

and R.A. Valdez. 2000. Flow and temperature recommendations for endangered fishes in 

the Green River downstream of Flaming Gorge Dam. Final report to Upper Colorado 

River Endangered Fish Recovery Program, Lakewood, Colorado. 

The Green River system of the upper Colorado River basin in Utah and Colorado 

supports populations of three endangered fishes — humpback chub Gila cypha, Colorado 

pikeminnow Ptychocheilus lucius, and razorback sucker Xyrauchen texanus—and it historically 

supported the endangered bonytail Gila elegans. Bonytails are almost unknown in recent 

collections. Humpback chubs still reproduce and recruit in the Green River system, but their 

long-term viability in the system is uncertain. System-wide reductions in spatial and temporal 

components of habitat complexity, attributed to past and ongoing alterations in river flow and 

temperature, have been implicated as major factors contributing to the decline of all the 

endangered fishes. 

Operation of Flaming Gorge Dam, which is located on the upper main-stem Green River, 

strongly influences downstream flow and temperature regimes and the ecology of riverine biota, 

including native fishes. The USFWS, in its 1992 Biological Opinion on Operation of Flaming 

Gorge Dam (Biological Opinion), concluded that continuation of historic operations at Flaming 

Gorge Dam was likely to further reduce the distribution and abundance of these federally 

protected species and thus jeopardize their continued existence. The Biological Opinion 

identified a reasonable and prudent alternative containing several related elements. These 

elements included (1) refine the operation of Flaming Gorge Dam so that flow and temperature 

regimes more closely approximate historic conditions; (2) conduct a 5-year research program 

(“Flaming Gorge Flow Recommendations Investigation”) to include implementation of winter 

and spring “research flows” beginning in 1992, to allow for potential refinement of flows for 

those seasons; (3) determine the feasibility and effects of releasing warmer water during the late 

spring through summer period and investigate the feasibility of retrofitting river bypass tubes to 

include power generation capability, thereby facilitating higher spring releases; (4) legally 

protect Green River flows from Flaming Gorge Dam to Lake Powell; and (5) initiate discussions 

with the USFWS after conclusion of the Flaming Gorge Flow Recommendations Investigation to 

examine further refinement of flows and temperatures for the endangered fishes. 

The Flaming Gorge Flow Recommendations Investigation, which began in 1992 but also 

included research conducted in 1990 and 1991 (while the Biological Opinion was being 

prepared), was conducted under the auspices of the Upper Colorado River Endangered Fish 

Recovery Program. The purpose of the investigation was to evaluate and refine the original flow 

and temperature recommendations given in the Biological Opinion as part of the reasonable and 

prudent alternative. Specifically, the Flaming Gorge Flow Recommendations Investigation was 

intended to determine the biological and physical responses of the Green River system to 

seasonal flow modifications, develop data for refinement of flow recommendations, and 

investigate the potential effects of increasing the temperature of water released from Flaming 

Gorge Dam. Specific objectives of the investigation were to (1) track reproduction of the 

endangered fishes and determine relationships among seasonal flows, water temperatures, and 
Humpback Chub Annotated Bibliography 50 September 2009

 

reproductive success; (2) evaluate recruitment of the endangered fishes from age-0 to subsequent 

life-history stages and determine relationships among seasonal flows, water temperatures, and 

survival of young fish; (3) monitor the relative abundance and population structure of the 

endangered fishes in order to acquire information on interactions among fish species and how 

flows may differentially affect populations; and (4) determine how releases from Flaming Gorge 

Dam and flows from tributaries affect the formation and maintenance of important habitats for 

the endangered fishes throughout the Green River. To accomplish these objectives, a series of 

long-term studies was conducted to track changes in populations, reproductive success, and 

habitats. In addition, shorter-duration studies were conducted to examine specific hypotheses and 

flow relationships. This report summarizes and synthesizes the results of the Flaming Gorge 

Flow Recommendations Investigation as well as other relevant information to provide 

recommended flow and temperature regimes that would benefit the endangered fishes in the 

Green River. 

Data gathered during the Flaming Gorge Flow Recommendations Investigation and other 

studies were used to develop descriptions of the basic life history, habitat use, and population 

status of the Colorado pikeminnow, razorback sucker, and humpback chub in the Green River 

system downstream of Flaming Gorge Dam. Reproduction and recruitment of humpback chubs 

occur in Desolation and Gray Canyons in Reach 3. A few humpback chubs occur in Whirlpool 

and Split Mountain Canyons of upper Reach 2, but the current abundance and life history of 

chubs in those areas are unknown. High spring flows prepare spawning habitats and provide the 

fish with cues for spawning, which occurs as runoff declines in late spring. Young fish inhabit 

low-velocity shorelines and backwater habitats as flow decreases during summer. Older juveniles 

inhabit deeper offshore eddies, often in association with boulders or other cover. Large eddies 

form at high flow and provide habitat in which humpback chubs spawn and feed on entrained 

allochthonous materials. Complex shoreline habitats used by larvae and juveniles are available at 

relatively low base flows during summer and autumn. 

Information on each endangered fish species was used to develop integrated flow and 

temperature recommendations for the Green River downstream of Flaming Gorge Dam. The goal 

of the recommendations is to provide the annual and seasonal flow and temperature patterns in 

the Green River that would enhance populations of the endangered fishes. Six objectives were 

developed to achieve this goal: (1) provide appropriate conditions that allow gonadal maturation 

and environmental cues for spawning movements and reproduction; (2) form low-velocity 

habitats for pre-spawning staging and post-spawning feeding and resting areas; (3) inundate 

floodplains and other off-channel habitats at the appropriate time and for an adequate duration to 

provide warm, food-rich environments for fish growth and conditioning and to provide river 

floodplain connections for the restoration of natural ecosystem processes; (4) restore and 

maintain the channel complexity and dynamics needed for the formation and maintenance of 

high-quality spawning, nursery, and adult habitats; (5) provide base flows that promote favorable 

conditions in low-velocity habitats during summer, autumn, and winter; and (6) minimize 

differences in water temperature between the Green River and Yampa River in Echo Park to 

prevent temperature shock and possible mortality to larval Colorado pikeminnow transported 

from the Yampa River and into the Green River during summer. 
Humpback Chub Annotated Bibliography 51 September 2009

 

To achieve these objectives, Flaming Gorge Dam releases should provide a wide range of 

peak and base flows, and daily fluctuations in downstream reaches due to hydropower generation 

should be moderated. Providing greater inter-annual flow variability would maintain and restore 

important geomorphic and biological processes and improve the spatial and temporal habitat 

complexity in the system, which is required by the endangered fishes. Such inter-annual 

variability should be achieved by providing flows consistent with hydrologic conditions in the 

upper Green River basin in a given year. Flow recommendations were based on the following 

information or assumptions: (1) populations of the endangered fishes and habitats required by all 

life stages are concentrated in Reaches 2 and 3 of the Green River; (2) habitat for endangered 

fishes in Reach 1 is limited to Lodore Canyon because the summer water temperatures upstream 

are too cold; (3) providing suitable habitat conditions through flow and temperature management 

at Flaming Gorge Dam will enhance endangered fish populations in the Green River; (4) current 

hydrology of the upper Green River basin, including inflows to Flaming Gorge Reservoir and 

available release volumes from Flaming Gorge Dam, will remain largely unaltered; and 

(5) changes in flow, temperature, and sediment regimes in Green River tributaries (particularly 

the Yampa and White Rivers) will be consistent with known or pending biological opinions. 

Stanford, J.A. 1994. Instream flows to assist the recovery of endangered fishes of the 

Upper Colorado River basin: review and synthesis of ecological information, issues, 

methods and rationale. U.S. Fish and Wildlife Service, Denver, Colorado. FLBS Open File 

Report 130-93. Abstract excerpted from results and conclusions. 

The purpose of this study was to review the science pertaining to the issue of flow 

provision, to identify critical uncertainties and to provide recommendations for determining the 

instream flow needs of the endangered fishes. Studies to date strongly indicate that truncation of 

peak flows and higher fluctuating base flows (loss of seasonality) resulting from river regulation 

have altered complex biophysical processes (detailed herein) that form and maintain low velocity 

habitats required for survival of the various life history stages of the fishes. An ecological 

tradeoff apparently exists: very high flows are needed occasionally to produce habitats that the 

fish need to survive, but at the expense of reproductive success. Based on review of the 

ecological information and recognizing the problems in the methodological approaches that were 

used to derive flow recommendations, several key uncertainties appear to be critical to the goal 

of establishing flow regimes that will ultimately recover the endangered fishes: 

 Flow seasonality and its correlates (e.g., temperature and physical habitat) may not be the 

factor(s) limiting recovery of the native fishes. 

 Given the high societal value placed on tailwater trout fisheries, and the high priority 

placed on meeting entitlements under the Colorado compact and current water law 

(i.e., the “law of the river”), water volume in the Colorado and Green Rivers may be 

insufficient to produce flows required to recover the fishes. 

 Channel and floodplain morphology in time and space is not a simple flow-area 

relationship, and complex interactions not yet fully understood may emerge that will 

compromise recovery of the fish. 
Humpback Chub Annotated Bibliography 52 September 2009

 

 What is the tradeoff between the propensity of endangered fish larvae to drift 

downstream and the need for high flows to maintain connectivity between the channel 

and backwaters and wetlands? 

 Can food webs reestablish in key low velocity habitats (backwaters) to the extent needed 

to recover the fishes, given the windows permitted or needed for hydropower operations? 

 Can the endangered fishes expand their range and productivity, given the downstream 

extension of cold water environments caused by regulation, and is the locality of the 

transition zone between cold and warm reaches likely to stay constant as deregulated 

flow regimes are implemented? 

 Interactions with nonnative fishes may limit recovery of endangered fishes regardless of 

flow provisions. 

 The report concludes with recommendations that couple management action 

(implementation of interim flow regimes) with additional study to resolve the 

uncertainties presented above. The suite of recommendations constitute an ecosystem 

approach to resolution of flows needed to protect and enhance the endangered fishes of 

the upper Colorado River basin. In essence, these recommendations constitute a new, 

holistic instream flow methodology. 

 Implement interim flows that reestablish seasonality with spring peaks that approach the 

amplitude and frequency of preregulation events and summer and winter base flows with 

daily changes (not daily volume) limited to near preregulation conditions (likely no more 

than about 5% per day). 

 Provide common understanding of water availability so that interim flows can be 

provided in relation to precipitation and legal flow abstraction in each sub-basin 

 

 Improve the standardized monitoring program as a mechanism to evaluate the 

effectiveness of interim flows by adding a community ecology perspective. 

 Diversify the research program to resolve critical uncertainties associated with interim 

flows. 

 Implement a peer review process to insure that research and monitoring objectives are 

based on solid science and are responsive to the need to resolve uncertainties associated 

with the interim flows. 

 Implement a management plan that can adaptively change the interim flows as new 

implications from monitoring and research are forthcoming. 

The recommended methodology needs unambiguous endorsement to be successful. Success or 

failure will be judged by long-term trends in the populations of the endangered fishes. 
Humpback Chub Annotated Bibliography 53 September 2009

 

Tyus, H.M. and C.A. Karp. 1991. Habitat use and streamflow needs of rare and 

endangered fishes, Green River, Utah. U.S. Fish and Wildlife Service, Vernal, Utah. 

In the Yampa River, stream habitat needs and life history requirements of Colorado 

squawfish (Ptychocheilus lucius), humpback chub (Gila cypha), razorback sucker (Xyrauchen 

texanus), and other native Colorado River fishes are presently maintained by flow regimens 

approximating natural conditions. Yampa River flows are also important in reducing adverse 

water management practices in the downstream Green River. Management for recovery of 

endangered fishes in the Yampa River will require specific flows to provide seasonal 

requirements at different locations: high spring flows associated with the initiation of Colorado 

squawfish spawning migrations, humpback chub and razorback sucker spawning, and 

maintenance of spawning bars and eddy habitats; descending summer flows associated with 

Colorado squawfish spawning, downstream transport of larvae, and creation of nursery habitat; 

stable winter flows to remove the threat of ice damage to shoreline areas used by many species. 

Acquisition of Yampa River water rights may be the decisive factor in conservation of 

endangered fish species in the Green River basin. 

Valdez, R.A., T.L. Hoffnagle, C.D. McIvor, T. McKinney and W.C. Leibfried. 2001. 

Effects of a test flood on fishes of the Colorado River in Grand Canyon, Arizona. 

Ecological Applications 11:686–700. 

A beach/habitat-building flow (i.e., test flood) of 1,274 m3

/s, released from Glen Canyon 

Dam down the Colorado River through Grand Canyon, had little effect on distribution, 

abundance, or movement of native fishes, and only short-term effects on densities of some 

nonnative species. Shoreline and backwater catch rates of native fishes, including juvenile 

humpback chub (Gila cypha), flannelmouth suckers (Catostomus latipinnis), and bluehead 

suckers (C. discobolus), and all ages of speckled dace (Rhinichthys osculus), were not 

significantly different before and after the flood. Annual spring spawning migrations of 

flannelmouth suckers into the Paria River and endangered humpback chub into the LCR took 

place during and after the flood, indicating no impediment to fish migrations. Pre-spawning 

adults staged in large slack water pools formed at the mouths of these tributaries during the 

flood. Net movement and habitat used by nine radio-tagged adult humpback chub during the 

flood were not significantly different from prior observations. Diet composition of adult 

humpback chub varied, but total biomass did not differ significantly before, during, and after the 

flood, indicating opportunistic feeding for a larger array of available food items displaced by the 

flood. Numbers of nonnative rainbow trout (Oncorhynchus mykiss) <152 mm total length 

decreased by -8% in electrofishing samples from the dam tailwaters (0-25 km downstream of the 

dam) during the flood. Increased catch rates in the vicinity of the LCR (125 km downstream of 

the dam) and Hell’s Hollow (314 km downstream of the dam) suggest that these young trout 

were displaced downstream by the flood, although displacement distance was unknown since 

some fish could have originated from local populations associated with intervening tributaries. 

Abundance, catch rate, body condition, and diet of adult rainbow trout in the dam tailwaters were 

not significantly affected by the flood, and the flood did not detrimentally affect spawning 

success; catch of YOY increased by 20% in summer following the flood. Post-flood catch rates 

of nonnative fathead minnows (Pimephales promelas) in shorelines and backwaters, and plains 

killifish (Fundulus zebrinus) in backwaters decreased in the vicinity of the LCR, and fathead 
Humpback Chub Annotated Bibliography 54 September 2009

 

minnows increased near Hell’s Hollow, suggesting that the flood displaced this nonnative 

species. Densities of rainbow trout and fathead minnows recovered to pre-flood levels eight 

months after the flood by reinvasion from tributaries and reproduction in backwaters. We 

concluded that the flood was of insufficient magnitude to substantially reduce populations of 

nonnative fishes, but that similar managed floods can disadvantage alien predators and 

competitors and enhance survival of native fishes. 

Van Steeter, M.M. and J. Pitlick. 1998. Geomorphology and endangered fish habitats of 

the upper Colorado River, 1. Historic changes in streamflow, sediment load and channel 

morphology. Water Resources Research 34:287–302. 

The hydrologic, geomorphic, and ecologic effects of reservoir operations are thought to 

be key factors in the decline of native fishes in the upper Colorado River basin. The present 

paper examines the extent to which changes in streamflow and sediment loads have affected 

alluvial reaches of the Colorado River near Grand Junction, Colorado. The analysis shows that 

since 1950, annual peak discharges of the Colorado River and its major tributary, the Gunnison 

River, have decreased by 29–38%. The total volume of runoff delivered to the study area has not 

changed significantly over the period of record, but the annual hydrograph has been modified 

greatly by reductions in peak flows and augmentation of base flows. Annual suspended sediment 

loads of the Colorado River and Gunnison River have likewise decreased. This was particularly 

apparent during the period from 1964 to 1978, when annual sediment loads were 40–65% less 

than the long-term average. Analysis of aerial photographs indicates that between 1937 and 1993 

the main channel of the Colorado River has narrowed by an average of 20 m and about 1/4 of the 

area formed by side channels and backwaters has been lost. 

3.5 TEMPERATURE 

Gloss, S.P. and L.G. Coggins. 2005. Fishes of Grand Canyon. Pages 33-49 in Gloss, S.P., 

J.E. Lovich and T.S. Melis, eds., The state of the Colorado River ecosystem in Grand 

Canyon. A report of the Grand Canyon Monitoring and Research Center 1991-2004. USGS 

Circular 1282. U.S. Geological Survey, Flagstaff, Arizona. 

 Fishes of the Colorado River vary from coldwater trout species found in the river’s 

mountainous headwaters to uniquely adapted desert river species found at lower elevations. 

Within the study area, the Colorado River corridor between Glen Canyon Dam and the western 

boundary of Grand Canyon National Park (hereafter Grand Canyon), the Colorado River was a 

seasonally warm and turbid river characterized by large seasonal variations in flow before it was 

altered by the closure of Glen Canyon Dam in 1963. Although water temperatures fluctuated 

between 32°F (0°C) during winter to a high approaching 86°F (30°C) during late summer, 

several warmwater native fish species successfully inhabited this stretch of the river. Because of 

the harsh environment created by dramatic seasonal fluctuations in the river’s pre-dam flow and 

temperature, only 8 of the 32 species of native fish historically found in the Colorado River were 

common in the Grand Canyon reach of the river. Other native fishes within the study area were 

restricted to small tributary streams or occurred only in transient or seasonal numbers. Of the 
Humpback Chub Annotated Bibliography 55 September 2009

 

eight fish species that were originally common to the study area, only four species are known to 

persist today. 

Korman, J., M. Kaplinski and J. Buszowski. 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 to U.S. Geological Survey, Grand Canyon Monitoring and Research Center, 

Flagstaff, Arizona. 

Backwater and other shoreline environments are preferentially used by native juvenile 

fish for rearing. The objective of this study was to better determine the extent to which daily 

variation in flow from Glen Canyon Dam effects water temperature regimes in shoreline 

environments. Continuously recording temperature loggers were deployed at –3.5 mile (Glen 

Canyon), 44.6 mile (Eminence), and 64.5 mile (Salt Mines). Loggers were deployed along chains 

extending from the shoreline towards the thalweg, allowing us to record the gradient in 

temperatures between backwaters and the mainstem, and in mainstem shoreline environments. 

Temperature loggers were deployed in 3 habitat types: backwaters; low angle mainstem 

shorelines; and talus mainstem shoreline. Loggers were deployed in mid-August and retrieved in 

early-November, 2004. 

Maximum warming in low angle shorelines was observed in August in Glen Canyon 

when the difference between mainstem water temperatures and air temperatures was greatest. 

Across the three habitat types, the extent of warming depended on the extent of isolation from 

the mainstem, with backwaters showing the greatest warming, low angle shorelines showing 

moderate warming, and virtually no warming seen in well mixed steep talus environments. 

Greater fluctuations in flow reduced the extent of warming in backwaters due to increased 

exchange with mainstem water. The extent of this effect was variable and depended on the 

timing of daily maximum and minimum flows and the topography of the backwater. With the 

exception of backwater temperatures at Eminence in September, shoreline temperatures were a 

maximum of 2-3°C (Celsius) warmer than the mainstem and typically these larger differences 

only occurred in the fluctuating zone. Vertical stratification in water temperature was observed in 

all backwaters. Stratification patterns were dynamic and varied over a 24 hr. period with changes 

in flow and air temperature. Surface waters in backwater and talus environments were a 

maximum of 3-7°C and 1°C warmer than bottom water, respectively. 

Marsh, P.C. 1985. Effect of incubation temperature on survival of embryos of native 

Colorado River fishes. Southwestern Naturalist 30:129–140. 

Razorback sucker (Xyrauchen texanus), bonytail (Gila elegans) and humpback (G. 

cypha) chubs, and Colorado squawfish (Ptychocheilus lucius) comprise the endemic “big river” 

fish fauna of the Colorado River, western North America. All are near extirpated in the wild. 

Effects of incubation temperature upon embryo hatch success were experimentally examined to 

evaluate potential impacts of cold hypolimnetic reservoir releases upon species reproductive 

success. Eggs were spawned and fertilized at 18°C, and embryos incubated at 5, 10, 15, 20, 25, 

and 30°C. Total mortality of embryos of all species occurred in 12 - 96 hours at 5, 10, and 30°C; 

and in 48–60 hours at 15°C for P. luscious only. Survival and percentage hatch were highest at 
Humpback Chub Annotated Bibliography 56 September 2009

 

15 and 20°C (G. elegans) or 20°C (all others). Hatched prolarvae were 0.2–1.3 mm TL longer at 

20° C than at 15 or 25 C. Spinal or other anomalies were more frequent at 15 and 25°C than at 

20°C. Development rates (V) were similar for all species, 4.4–6.1 (15°C), 8.4–9.9 (20°C), and 

12.4–18.8 (25°C). Because of lower survival and higher incidence of anomalies at 15 and 25°C, 

optimal temperatures for development and hatching are probably neat 20°C. Reproduction may 

thus be limited in the wild by low water temperatures, although successful hatching is certainly 

not precluded. Other hypotheses to explain the demise of these fishes in thermally suitable 

portions of the Colorado River, such as predation among young, should be examined. 

3.6 FORAGING AND DIET 

Clarkson, R.W. 1993. Foods of young-of-year native fishes in the Little Colorado River, 

Arizona, and infestation patterns by Asian fish tapeworm Bothriocephalus 

acheilognathi. Proceedings of the Desert Fishes Council 24:27. 

Foods and tapeworm infestation rates were examined from stomachs of larvae, early 

post-larvae, and juvenile speckled dace (Rhinichthys osculus), bluehead sucker (Pantosteus 

discobolus), and humpback chub (Gila cypha) from the LCR in 1990-1991. Chironomidae was 

an important food item for all three species, with the two cyprinids reducing their utilization of 

this component with age, and bluehead sucker increasing its use with age. Ostracods were used 

most often by larval and early-larval dace, and by juvenile chub. Vascular plant material was 

noteworthy in stomachs of younger dace and chub, while bluehead sucker frequently contained 

inorganic materials. Asian fish tapeworm suddenly appeared in chub stomachs in 1990. Three 

larvae, 11 early post-larvae, and 47 adult and sub-adult chub examined from 1989 did not 

contain tapeworms, while chub larvae collected from May-June 1990 (N=24) exhibited a 91.7% 

infestation rate, older 1990 YOY specimens (N=15) exhibited a 100% infestation rate, and 44% 

of 18 adults examined from 1990 were infested. In contrast, tapeworms did not appear in 1991 

YOY chub stomachs until they exceeded 50 mm in length beginning in September. A low 

incidence in speckled dace was noted in 1991. Effects of the tapeworm on its hosts are well 

studied, but may include reduced growth, depressed swimming ability via elevated muscle 

fatigue, other debilitating effects, and elevated mortality. 

Leibfried, W.C. and R.A. Valdez. 1995. Food habits and electivity indices of the 

endangered humpback chub, Gila cypha form the Colorado River in Grand Canyon 

National Park. Proceedings of the Desert Fishes Council, Flagstaff, Arizona. 

 The diets of humpback chub from the Colorado River in Grand Canyon National Park 

were analyzed from three locations along the river during 1991, 1992, and 1993. A total of 168 

chub were pumped and variation between season and location determined for stomach contents 

both by volume and abundance. The amphipod, Gammarus lacustris, chironomids, simuliids, 

terrestrial invertebrates, and the green alga, Cladophora glomerata dominated stomach contents. 

Significant variation in invertebrate numbers and volume of gut contents occurred between 

locations sampled. Significant seasonal variation within locations was also determined for some 

food items. Chub stomachs sampled from locations away from the Little Colorado River (LCR) 

had significantly greater numbers and volumes of terrestrial and other forms of aquatic 
Humpback Chub Annotated Bibliography 57 September 2009

 

invertebrates. Electivity indices (Ivlev 1961) were calculated to compare food habits of 

humpback chub to food availability from instream drift. Chub above the LCR showed a more 

generalized feeding strategy than below the LCR which selected for Gammarus. Chub from the 

Middle Granite Gorge tended to select terrestrial and other aquatic invertebrates. 

Robinson, A.T. 1993. Feeding behavior and ecology of young-of-the-year native fish in the 

Little Colorado River of the Grand Canyon. Proceedings of the Desert Fishes Council 

24:39. 

The feeding behavior and ecology of three YOY native fish species (Gila cypha, 

Rhinichthys osculus, Catostomus discobolus) was studied in the Little Colorado River of the 

Grand Canyon. Feeding behavior was recorded within four general habitat localities: bottom, 

plants, water column, and surface. A habitat variable, vertical positioning in the water column, 

was noted as individuals began new behaviors. Specimens of each species were collected and 

preserved, and their stomach contents were analyzed in the laboratory. Drift samples were 

collected and analyzed for invertebrate composition. 

Foraging humpback chubs partitioned their habitat by feeding extensively off of the 

vegetation. Bluehead suckers on the other hand feed primarily on the bottom, and to a lesser 

extent on algae and aquatic macrophytes. Humpback chub and speckled dace YOY utilize the 

upper pelagic and surface zones preferentially to other vertical zones. Humpback chubs and 

speckled dace had diets that did not differ significantly from each other, however, both species 

differed from bluehead suckers. Humpback chubs had diets that were most similar in 

invertebrate composition to what occurred in the drift samples. The behavioral, spatial use, and 

diet differences may help to reduce any possible competition between species. 

Shannon, J.P., D.W. Blinn, G.A. Haden, E.P. Benenati and K.P. Wilson. 2001. Food web 

implications of σ13 C and σ15 N variability over 370 km of the regulated Colorado River 

USA. Isotopes in Environmental and Health Studies 37(3):179-191. 

Dual stable isotope analysis in the regulated Colorado River through Grand Canyon 

National Park, USA, revealed a food web that varied spatially through this arid biome. Downriver enrichment of δ13C data was detected across three trophic levels resulting in shifted food 

webs. Humpback chub δ13C and δ15N values from muscle plugs and fin clips did not differ 

significantly. Humpback chub and rainbow trout trophic position is positively correlated with 

standard length indicating an increase in piscivory by larger fishes. Recovery of the aquatic 

community from impoundment by Glen Canyon Dam and collecting refinements for stable 

isotope analysis within large rivers are discussed. 

Stone, D.M. 2004. Differential detection of ingested items evacuated from genus Gila 

cyprinids by two nonlethal alimentary tract lavage techniques. Journal of Freshwater 

Ecology 19:559–565. 

Two nonlethal alimentary tract lavage techniques were conducted on ten bonytail chub 

(Gila elegans, 211-241 mm TL) that had previously ingested 2-4 rainbow trout (Oncorhynchus 

mykiss, apprx40 mm TL) to evaluate their capabilities of detecting piscivory in the field. 

Each fish was initially lavaged with water down its buccal cavity and out its anal vent using the 
Humpback Chub Annotated Bibliography 58 September 2009

 

Wasowicz and Valdez (W-V) technique and then immediately flushed in the opposite direction 

with the Baker and Fraser (B-F) method. Microscopic examination of evacuated 

material revealed only three identifiable rainbow trout scales and other assorted clumps of 

presumably well-digested body material. Overall, 30% of bonytail chub expelled rainbow trout 

scales and/or other body material during the initial W-V lavage, and 60% expelled 

material during the B-F flush. Dissections of four bonytail, seven humpback (G. cypha), and four 

roundtail chubs (G. robusta) revealed that their intestines were similarly curved and tapered to 

ltoreq50% of the anterior widths. Whereas the B-F method pushes ingested items backwards 

through the increasingly larger intestinal circumferences in these Gila fishes, it is more apt to 

retrieve greater quantities of food items. Food preference studies based on findings from a 

highly size-selective lavage technique will likely be biased in favor of smaller, less-digestible 

prey items, such as invertebrates with chitinous exoskeletons. Use of the B-F rather than W-V 

technique should lessen this bias. 

Tyus, H.M. and W.L. Minckley. 1988. Migrating Mormon crickets, Anabrus simplex 

(Orthoptera: Tettigoniidae), as food for stream fishes. Great Basin Naturalist 48:25–30. 

Migrating bands of Mormon crickets (Anabrus simplex ) were observed crossing the 

Green and Yampa rivers in Dinosaur National Monument, Colorado and Utah, in 1986 and 1987. 

Swimming cricket were swept downstream and eaten by four endemic and seven introduced fish 

species. Included were two endangered fishes, Colorado squawfish (Ptychocheilus lucius) and 

humpback chub (Gila cypha). Direct and indirect effects to aquatic food webs associated with 

application of pesticides for Mormon cricket control may pose a threat to these fishes and to 

man.

3.7 SUPPORTING ARTICLES 

Bartley, D., M. Bagley, G. Gall and B. Bentley. 1992. Use of linkage disequilibrium data to 

estimate effective size of hatchery and natural fish populations. Conservation Biology 

6:365–375. 

 A primary parameter in the assessment of the viability of a population is its effective 

population size (Ne). Allozyme analysis of four groups of fishes provided data on linkage 

disequilibrium, which were then used to estimate Ne. The groups included hatchery samples of 

juvenile rainbow trout, Oncorhynchus mykiss, from Shasta hatchery, and juvenile Chinook 

salmon, O. tshawytscha, from Coleman National Fish hatchery. The fourth sample consisted of 

juvenile Chinook salmon from the threatened winter run in the upper Sacramento River. The 

groups of fish were chosen to represent different applications of the methodology to conservation 

of fishes. For a variety of reasons, Ne may considerably lower than census counts of fish present 

in the parental populations. The Ne of the hatchery broodstock that produced the sample of 

juvenile white seabass was estimated to be approximately 10, although 25 adult white seabass 

were present in a mass spawning tank. Ne estimates for the Shasta and Coleman Hatchery 

samples were 35.8 and 132.5, respectively. The actual number of fish spawned at the Shasta 

hatchery was approximately 40, where nearly 10,000 salmon spawned at the Coleman Hatchery. 

The threatened winter run of Chinook salmon had estimated Ne of 85.5 and approximate run size 
Humpback Chub Annotated Bibliography 59 September 2009

 

of 2000 salmon. The method estimating effective population size from linkage disequilibrium 

data appears to result in realistic estimates of effective population size when adequate sample 

size and sufficient number of polymorphic loci are available. 

Bestgen, K.R. 1996. Growth, survival and starvation resistance of Colorado squawfish 

larvae. Environmental Biology of Fishes 46:197–209. 

Growth and survival of Colorado squawfish, Ptychocheilus lucius, larvae under 

fluctuating 18, 22, and 26°C (5°C diel fluctuations) and constant 18, 22, 26°C, and 30°C 

temperature conditions and ration size corresponding to 12.5, 28, 64, 142, 320 brine shrimp 

nauplii/fish/day was determined from laboratory experiments. Growth was optimal at 31°C and 

high at temperatures of 26°C to 30°C, at the highest food abundance. Lowest growth was under 

lowest food rations and highest temperatures. Growth of Colorado squawfish larvae declined 

substantially at temperatures < 22°C. Neither growth nor survival was significantly different 

between fluctuating or constant regimes. Survival of Colorado squawfish larvae was highest 

(95%) at 26.2°C and 235 nauplii/fish/day and high at temperatures of 20 to 30°C with food 

abundance > 180 nauplii/fish/day. Survival was lowest when food abundance was low and 

temperature was high. Highest mortality occurred more than 20 days after experiments began 

and mortalities occurred sooner in higher than lower temperatures. Colorado squawfish larvae 

denied food for 5, 10, or 15 d after first feeding could have begun (6 d), had survival greater than 

87% which was equivalent to continuously fed controls. Survival of fish denied food for 17.5 d 

after feeding could have begun declined from 84% before feeding to 57% after feeding. Point of 

no return was estimated between 17.5 and 20 d. Colorado squawfish have relatively high 

starvation resistance. Low, stable flows that simulate natural hydrographs may enhance growth, 

survival, and recruitment of early life stages of Colorado squawfish by increasing water 

temperature and food abundance in regulated rivers of the Colorado River basin. 

Bestgen, K.R. 1997. Interacting effects of physical and biological processes on recruitment 

of Colorado squawfish. Doctoral Dissertation, Chapter 4. Colorado State University, Fort 

Collins. 

Recruitment is central to population ecology because the abundance of young individuals 

often drives dynamics of subsequent life stages. Recruitment variation of age-0 Colorado 

squawfish Ptychocheilus lucius in the Green River, Colorado River basin, was related to physical 

and biological factors that were important at both intra-annual and annual time scales. 

Distributions of squawfish hatching dates derived from otolith increment analyses in 1991 and 

1992 indicated that larvae in cohorts that hatched early survived poorly to fall. Growth rate 

comparisons suggested that the few early-hatched fish that survived were a fast-growing subset 

of the fish present in the same cohort in summer. I attributed this to a biological factor, sizeselective predation mortality by nonnative fishes. In contrast, larvae that hatched late grew 

relatively slowly but survived at higher rates due to environmental factors and to declines in 

abundance of predaceous red shiners Cyprinella lutrensis by mid-summer. An independent 

individual-based computer simulation model which had gape-limited red shiners as predators and 

Colorado squawfish larvae as prey produced similar size-selective survival patterns. Model 

simulations also showed that fish with moderate growth rates survive at twice the rate of fish 

with low-growth rates. Growth reductions caused by competition with non-native fishes or 
Humpback Chub Annotated Bibliography 60 September 2009

 

starvation would extend the time that Colorado squawfish were susceptible to predation but by 

themselves would not explain the size-selective patterns observed. Reduced growth rates of 

Colorado squawfish, which were temporally correlated with a stochastic physical factor, flooding 

from summer thunderstorms, may have combined with size-selective predation to cause very low 

recruitment in the lower Green River in 1992. Otherwise, recruitment was not correlated with 

discharge and temperature regimes in the summers of 1991 and 1992. Over a 17-year record, 

mean July-August discharge had no effect on annual abundance of Colorado squawfish juveniles 

in backwaters in the fall except at relatively high discharge. Low abundance of juvenile Colorado 

squawfish in 1991 and 1992 when size-selective patterns were evident suggested that predation 

may regulate recruitment in most years. Therefore, discharge management that emphasizes 

habitat enhancement should be supplemented with strategies to reduce effects of nonnative 

fishes. 

Bestgen, K.R., D.W. Beyers, J.A. Rice and G.B. Haines. 2006. Factors affecting 

recruitment of young Colorado pikeminnow: Synthesis of predation experiments, field 

studies and individual-based modeling. Transactions of the American Fisheries Society 

135:1722–1742. 

Predation experiments, field studies, and individual-based models (IBM) simulations 

revealed that factors that affected the survival of early life stages of endangered Colorado 

pikeminnow Ptychocheilus lucius in the Green River basin, Utah and Colorado. Small-bodied, 

non-native red shiners Cyprinella lutrensis attacked Colorado pikeminnow larvae an average of 

once per minute, and predation success approached 30% in laboratory aquaria. Attack rate was 

also high in mesocosm experiments; turbidity and alternative prey reduced predation success. 

Distributions of hatching dates derived from otolith daily increment analysis showed that large 

cohorts of Colorado pikeminnow larvae that hatched in the Green River in early summer had low 

survival to autumn and that the few survivors were fast growing. Larvae hatched in midsummer 

or later had higher survival. Autumn juveniles grew 12-73 and faster than summer juveniles, 

which suggested differential mortality of slow-growing fish. The IBM simulations integrated 

size-dependent pikeminnow growth, Green River predator size-structure dynamics, seasonally 

variable Green River water temperatures, and turbidity and alternative prey availability effects; 

the simulations showed that red shiner predation interacting with environmental variables may 

significantly reduce age-0 pikeminnow recruitment in autumn. Recruitment and growth patterns 

from simulations and field observations were consistent and suggested that the IBM is useful in 

evaluating management scenarios. Experiments, field studies, and predictive modeling provided 

consistent evidence that interacting effects of predation and environmental variables, including 

flow fluctuations, may structure intra-annual growth and recruitment patterns of age-0 Colorado 

pikeminnow. Flow management to benefit growth and survival of young pikeminnow, 

particularly early hatching ones, and reduced nonnative predator abundance in Green River 

backwaters may enhance the Colorado pikeminnow populations. 
Humpback Chub Annotated Bibliography 61 September 2009

 

Bestgen, K.R. and J.M. Bundy. 1998. Environmental factors affect daily increment 

deposition and otolith growth in young Colorado squawfish. Transactions of the American 

Fisheries Society 127:105–117. 

Otolith microstructure of endangered Colorado squawfish Ptychocheilus lucius was 

investigated to determine patterns of otolith growth and to validate daily deposition of 

increments. Sagittae and lapilli formed prior to hatching. After fish hatched, otolith increments 

were deposited daily whether larvae were reared at a constant 22°C temperature or subjected to 

fluctuating temperatures (± 2.5°C d) centered at 18, 22, or 26°C. Otolith increments were clearer 

and counts of increments were more accurate for fish reared at fluctuating than at constant 

temperatures. Otolith growth was lower at 18°C than at 22 or 26°C, but evidence of a direct 

effect of temperature on otolith growth was inconclusive. Lapillus diameters of slow-growing 

Colorado squawfish were larger than those of similar-sized but fast-growing fish, indicating that 

fish and otolith growth rates were not proportional. When larvae were starved, growth in body 

length generally ceased immediately but otolith growth continued for up to 15 d. Otolith growth 

was reduced for up to 5 d after starved fish began to feed. Timing of starvation and reduced 

growth may not be accurately recorded by reduced otolith increment spacing. Low-contrast 

otolith increments in wild fish may indicate periods of low food abundance and starvation. 

Increased otolith growth early in life could reflect the start of exogenous feeding by Colorado 

squawfish larvae, a habitat shift to warmer water, or both. Otolith analysis will be useful for 

elucidating age, growth, and recruitment patterns of young Colorado squawfish. 

Bestgen, K.R., R.T. Muth and M.A. Trammell. 1998. Downstream transport of Colorado 

squawfish larvae in the Green River drainage: temporal and spatial variation in 

abundance and relationships with juvenile recruitment. Final report of Colorado State 

University Larval Fish Laboratory to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

This study was initiated in 1990 and was part of the Five-Year Flaming Gorge Flow 

Recommendations Investigations, 1992-1996. It was designed to assess aspects of reproduction, 

recruitment, and status of Colorado squawfish in the Green and Yampa Rivers. Colorado 

squawfish reproduced in early to mid-summer in the Green River basin. Initiation of 

reproduction by Colorado squawfish each year was generally associated with increasing water 

temperature and diminishing spring runoff. Earlier spawning was associated with earlier 

occurrence of peak runoff and warmer water temperatures. 

No single variable accurately predicted when Colorado squawfish first reproduce among 

sites or years. Water temperature at initiation of reproduction ranged from 16.0 to 22.3°C in the 

lower Yampa River and was 19.8 to 23.0°C in the lower Green River. In the lower Yampa River, 

Colorado squawfish generally initiated reproduction a few days prior to or within a few days 

after mean daily water temperature exceeded 18°C. In contrast, Colorado squawfish in the lower 

Green River initiated reproduction after mean daily temperature exceeded 18°C for 13 to 39 

days. Time of year and accumulated degree days were also reasonable predictors of initiation of 

reproduction by Colorado squawfish. Initiation of reproduction was not closely associated with 

days post-peak discharge. 
Humpback Chub Annotated Bibliography 62 September 2009

 

 Abundance of larvae was generally higher in the Yampa River than in the lower Green 

River, and varied widely on diel, spatial, intra-annual and inter-annual scales. High transport 

abundance of larvae associated with increased turbidity, discharge, and darkness may be due to 

several factors including loss of orientation. High transport abundance under those conditions 

may also be a behavioral response to avoid sight-feeding predators. Increased transport 

abundance during turbidity events may have been caused by increased sediment deposition in 

interstitial spaces in the substrate, a stress which may have motivated larvae to emerge and drift. 

Differences in transport abundance of larvae across years and the patterns of abundance within a 

year may be due to several factors including timing of arrival, condition, and number of 

reproducing adults at the spawning areas. 

 Transport abundance appeared to be associated with discharge only during extreme years. 

High discharge was negatively associated with transport abundance in both the lower Yampa 

River and the lower Green River while low discharge was negatively associated with transport 

abundance only at the Yampa River station. Low abundance during either low or high discharge 

years could be a consequence of low abundance of adults and low production of larvae at 

spawning areas, high mortality of eggs or larvae at spawning areas or during downstream 

transport, sampling error, or other factors. 

 High intra-annual recruitment variation of juvenile Colorado squawfish in both the lower 

and middle Green River, 1990–1996 was not usually the result of inadequate numbers of larvae 

produced from spawning areas. Instead, high annual recruitment variation may be a consequence 

of factors that differentially affect growth and survival of early life stages. Colorado squawfish 

seem well-adapted to the fluctuating environmental conditions with which they have evolved. 

Thus, physical factors may regulate recruitment of age-0 Colorado squawfish only in relatively 

rare instances. Understanding the relative importance of mechanisms regulating recruitment of 

Colorado squawfish, including effects of discharge, habitat availability, and non-native fish 

predators, is critical to management and recovery of this species. 

Bestgen, K.R. and M.A. Williams. 1994. Effects of fluctuating and constant temperatures 

on early development and survival of Colorado squawfish. Transactions of the American 

Fisheries Society 123:574–579. 

A laboratory study was conducted to determine the effects of four constant temperatures 

(18, 22, 26, and 30°C) and three fluctuating temperatures (diel fluctuations of ± 2.5°C around 18, 

22, and 26°C) on early development and survival of Colorado squawfish Ptychocheilus lucius, 

which is listed as an endangered species by the U.S. Department of the Interior. Average hatch in 

constant and fluctuating temperatures was 72% at 18°C, 67% at 22°C, 62% at 26°C, and 38% 

(constant temperature only) at 30°C. There was no significant difference in hatch between 

constant and fluctuating temperatures. Average survival of larvae to 7 d post-hatch in constant 

and fluctuating temperatures was 68% at 18°C, 64% at 22°C, 83% at 26°C, and 13% (constant 

temperature only) at 30oC. Survival of larvae at 30°C may have been confounded by a relatively 

low hatch of embryos and poor condition of larvae. Survival of larvae was 10–31% higher in 

fluctuating than in constant temperatures. Incidence of abnormalities was 2–22% at 18–26°C and 

100% at 30°C. Differences in abnormality rates were not detectable between constant and 

fluctuating temperatures. Times to start of hatch, swim bladder inflation, and exogenous feeding 
Humpback Chub Annotated Bibliography 63 September 2009

 

were shorter at higher temperatures. First feeding occurred about 31 h earlier in fluctuating 

temperatures than in constant temperatures. Differences in lengths of larvae at hatching and on 

day 7 post-hatch at the venous test temperatures were small and not considered ecologically 

significant. Tolerance of a relatively wide range of high-water temperatures by Colorado 

squawfish embryos and larvae may reflect the historically variable Colorado River environments 

in which the species evolved. Low summer water temperatures caused by mainstream dams have 

eliminated Colorado squawfish from portions of its historic range in the Colorado River basin. 

Water temperatures that more closely reflect historic regimes are necessary to restore selfsustaining populations of Colorado squawfish in those areas. 

Beyers, D.W., R.T. Muth and M.S. Farmer. 1994. Experimental evidence of competition 

between larvae of Colorado squawfish and fathead minnow. Final report of Colorado State 

University Larval Fish Laboratory to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

Quantitative study of resource competition has been frustrated by an inability to separate 

effects of intraspecific and interspecific competition. Two types of experimental design are 

commonly used to study competition in two- species assemblages (1) replacement designs, and 

(2) additive designs. We used an experimental design and analysis that incorporated the positive 

attributes of replacement and additive designs to study resource competition between larvae of 

federally endangered Colorado squawfish, Ptychocheilus lucius, and a widely distributed 

nonnative species, the fathead minnow, Pimephales promelas. Effects of competition were 

inferred by feeding fish known quantities of zooplankton and comparing relative growth in 

single- and mixed-species assemblages. Effects of intraspecific exploitative competition were 

accounted for by using regression to describe the density-dependent relation between relative 

growth and feeding regime in single-species assemblages, and then subtracting these effects from 

the response of relative growth in mixed-species assemblages. Relative growth of Colorado 

squawfish and fathead minnow in single- and mixed-species assemblages was compared using a 

one-sample t-statistic, regression analysis, and an index of competitive ability. Conclusions of 

statistical analyses were confirmed by study of diet overlap. 

 The response of each species to competition was consistent with that predicted by 

ecological theory: relative growth of both fishes was reduced by competition (i.e., -/-). Negative 

competitive effects were asymmetrical, and quantitatively greater and more frequent for 

Colorado squawfish than for fathead minnow. Study of diet overlap confirmed conclusions of 

relative growth analysis. Diet overlap was reduced in the lowest feeding regime where resource 

competition was intense. Paradoxically, at higher feeding regimes diet overlap increased 

although analysis of relative growth suggested competition occurred at those feeding regimes as 

well. The insensitivity of diet overlap at higher feeding regimes may have been due to a lack of 

alternative prey, or may suggest that the response variable, relative growth, integrated effects of 

two qualitatively different competitive mechanisms without reflecting a change because intensity 

of competition remained relatively constant. These results emphasize the need for more detailed 

ecological investigations of interactions between early life stages of Colorado squawfish and 

potential non-native competitors. In addition, this study demonstrated that under experimental 

conditions, effects of intra- and interspecific competition can be separated and the outcome of 

exploitative resource competition can be determined. 
Humpback Chub Annotated Bibliography 64 September 2009

 

Bulkley, R.V. and R. Pimental. 1983. Temperature preference and avoidance by adult 

razorback suckers. Transactions of the American Fisheries Society 112:601–607. 

 Final thermal preferendum for the razorback sucker Xyrauchen texanus, a rare endemic 

species of the Colorado River basin, was estimated to lie between 22.9 and 24.8°C based on 

electronic-shuttlebox studies. Estimates of upper and lower avoidance temperature ranged from 

27.4 to 31.6°C and from 8.0 to 14.7°C, respectively. Lower, but not upper, avoidance 

temperature was positively correlated with acclimation temperature. Results indicated that new 

water-control structures on the upper Colorado River drainage should be designed to provide 

summer water temperatures between 22 and 25°C if preservation of habitat for this species is a 

consideration. 

Chao, A. 1989. Estimating population size for sparse data in capture-recapture 

experiments. Biometrics 45:427–438. 

Estimators of population size under two commonly used models (the time-variation 

model and the heterogeneity model) for sparse capture-recapture data are proposed. A real data 

set of Illinois mud turtle (Kinosternon flavescens spooneri) is used to illustrate the methods and 

to compare them with other estimators. A simulation study was carried out to show the 

performance and robustness of the proposed estimators. 

Collins, K.P. and D.K. Shiozawa. 1996. The effects of fish predation on backwater 

invertebrate communities of the Green River, Utah (Ouray National Wildlife Refuge 

reach). Final report of Brigham Young University Department of Zoology to Upper 

Colorado River Endangered Fish Recovery Program, Lakewood, Colorado. 

The potential role of fish predation on the structure of invertebrate communities in 

backwater habitats of the Green River, a large river in eastern Utah, was examined by placing a 

series of complete, partial, and no fish exclosures in backwater habitats and sampling benthic and 

planktonic communities periodically through the summer. The taxa showing the greatest direct 

treatment effects were the chironomid genus Tanypus, the Corixidae, and the planktonic adult 

copepod. The benthic densities of the naupliar and copepodite stages of copepods showed a 

negative response to fish exclusion, probably the result of increased levels of Corixidae and 

Tanypus, which are known to prey on benthic organisms. This study indicates that backwater 

fishes may impact food resources, although invertebrate predation may act in a compensatory 

manner on certain invertebrate species. This suggests that Colorado squawfish Ptychocheilus 

lucius may undergo resource competition during their post-larval stage. More research is 

necessary to determine if this is the case. 
Humpback Chub Annotated Bibliography 65 September 2009

 

Day, K.S., K.D. Christopherson and C. Crosby. 1999. An assessment of young-of-year 

Colorado pikeminnow Ptychocheilus lucius use of backwater habitats in the Green River, 

Utah. Report B in Flaming Gorge Studies: Assessment of Colorado pikeminnow nursery 

habitat in the Green River. Final report to Upper Colorado River Endangered Fish 

Recovery Program. Utah Division of Wildlife Resources, Salt Lake City, Utah. 

Colorado pikeminnow nursery habitat characteristics and selection focusing fall sampling 

for YOY recruitment in backwater habitats were studied in a 16.1 km study reach at Ouray 

National Wildlife Refuge, Utah, from 1990 to 1996 using Interagency Standardized Monitoring 

Program (ISMP). The information generated by this study was used for development of a model 

to predict Colorado pikeminnow use of backwaters based on physical parameters, relationships 

between spring flows, and nursery habitat formation. This report was generated from the 

Recovery Implementation Program Scope-of-Work number FG-33. The specific task of this 

project was to study the Green River within the boundaries of Ouray National Wildlife Refuge 

to: 1) determine the relationship between quantity of nursery habitats available in the summer 

period to the number of YOY Colorado pikeminnow present in nursery habitats during the 

autumn period; 2) describe the relationship between nursery habitat availability and fish habitat 

selection; and 3) compare intensive sampling and standardized monitoring to assess ways of 

refining standardized monitoring and ways to make greater use of available data. 

 A total of 1,043 backwaters and low velocity habitats were sampled three times each year 

from August 1990 through September 1996 for the presence of endangered fishes. Each 

backwater sampled was first categorized by physical type; which was determined by its method 

of formation or current condition. To avoid disturbing the fish, all physical measurements were 

made after fish communities were sampled with a 3 mm mesh seine. Several statistical analyses 

were conducted to help interpret significant relationships. Linear regression was performed on 

four flow parameters peak flow, date of peak flow, flow and duration against backwater 

numbers, volume and area. Contingency table and X2

 analysis were preformed to test preference 

for use of habitat classes. The Wilcoxon rank-sum tested the significant differences (p < 0.05) of 

habitat variables between occupied and unoccupied backwaters. Discriminant function analysis 

was also used to determine if Colorado pikeminnow use of nursery habitats could be predicted 

by a model of habitat characteristics. Models were developed for each season of each year, for 

each season for all years, for each year and for all seasons and years pooled. Correlation analysis 

on catch-per-unit-effort (CPUE) data for all species to show correlation between species CPUE. 

No consistent trend was found between native and non-native species. 

 Findings of this study show that Colorado pikeminnow use large, deep backwaters with 

high turbidity, and backwaters used by Colorado pikeminnow in the spring were larger and 

deeper than those used in the summer and fall. Water temperature did not have as much 

influence on Colorado pikeminnow use of backwaters as expected. Temperature differentials 

between backwaters and main channel were significant only in the spring. Backwater area and 

volume available at Ouray NWR was negatively related to peak flows in the preceding spring for 

all seasons, and no relationship existed between numbers of backwaters available and spring 

flows. The catch-per-unit-effort of Colorado pikeminnow was positively correlated with 

bluehead sucker catch, and was not related to spring flows. This was true for most other species 

captured. 
Humpback Chub Annotated Bibliography 66 September 2009

 

 We recommend that periodic high spring flows are needed to rebuild the river channel 

and re-establish secondary channel backwaters used by Colorado pikeminnow. This rebuilding 

event should be followed with several years of variable flow aimed at maintaining channel 

diversity and secondary channel backwaters. Determination of flow events and timing should be 

based on geologic and hydrologic studies, concurrently being completed. There are two possible 

modification that should be considered for ISMP YOY sampling. These include a measure of 

turbidity and dropping the minimum depth restriction to 0.20–0.25 m. Although not fully 

addressed here, it is recommended that the final Green River flow regime take into account other 

species of native fish that show different responses to spring flows and habitats. Variability of 

the Green River flow regime is likely the best scenario for adequate management of the entire 

system. Considerable information concerning backwater use by the remaining Green River fish 

community is still available in this data set, and personnel, time and funding should be dedicated 

to continue analyses. 

Filbert, R.B. and C.P. Hawkins. 1995. Variation in condition of rainbow trout in relation 

to food, temperature and individual length in the Green River, Utah. Transactions of the 

American Fisheries Society 124:824–835. 

 We examined how condition (weight at length) of rainbow trout Oncorhynchus mykiss

varied in relation to availability of drifting invertebrates and temperature at two locations over 

four seasons in the Green River, Utah. Food availability (daytime drift density) varied more than 

17-fold across sites and seasons, and rainbow trout experienced an 11°C range in mean monthly 

temperature. Both rainbow trout gut fullness and condition increased as joint, nonlinear functions 

of increasing food availability and increasing temperature. Variation in condition decreased with 

fish size, although condition of intermediate sized fish was most strongly related to variation in 

food and temperature. Observed relationships between rainbow trout condition, drift abundance, 

and temperature were qualitatively consistent with bioenergetic models that predict fish growth 

should vary as a joint function of food and temperature. However, the inferred temperature 

optima for rainbow trout seemed to be significantly higher than predicted. Our results support a 

growing body of evidence that stream trout may be frequently food-limited in nature. 

Freeman, M.C., Z.H. Bowen, K.D. Bove and E.R. Irwin. 2001. Flow and habitat effects on 

juvenile fish abundance in natural and altered flow regimes. Ecological Applications 

11(1):179-190. 

Conserving biological resources native to large river systems increasingly depends on 

how flow-regulated segments of these rivers are managed. Improving management will require a 

better understanding of linkages between river biota and temporal variability of flow and 

instream habitat. However, few studies have quantified responses of native fish populations to 

multiyear (>2 yr) patterns of hydrologic or habitat variability in flow-regulated systems. To 

provide these data, we quantified YOY fish abundance during four years in relation to 

hydrologic and habitat variability in two segments of the Tallapoosa River in the southeastern 

United States. One segment had an unregulated flow regime, whereas the other was flowregulated by a peak-load generating hydropower dam. We sampled fishes annually and explored 

how continuously recorded flow data and physical habitat simulation models (PHABSIM) for 
Humpback Chub Annotated Bibliography 67 September 2009

 

spring (April-June) and summer (July- August) preceding each sample explained fish 

abundances. Patterns of YOY abundance in relation to habitat availability (median area) and 

habitat persistence (longest period with habitat area continuously above the long-term median 

area) differed between unregulated and flow-regulated sites. At the unregulated site, YOY 

abundances were most frequently correlated with availability of shallow-slow habitat in summer 

(10 species) and persistence of shallow-slow and shallow-fast habitat in spring (nine species). 

Additionally, abundances were negatively correlated with 1-h maximum flow in summer (five 

species). At the flow-regulated site, YOY abundances were more frequently correlated with 

persistence of shallow-water habitats (four species in spring; six species in summer) than with 

habitat availability or magnitude of flow extremes. The associations of YOY with habitat 

persistence at the flow-regulated site corresponded to the effects of flow regulation on habitat 

patterns. Flow regulation reduced median flows during spring and summer, which resulted in 

median availability of shallow-water habitats comparable to the unregulated site. However, 

habitat persistence was severely reduced by flow fluctuations resulting from pulsed water 

releases for peak-load power generation. Habitat persistence, comparable to levels in the 

unregulated site, only occurred during summer when low rainfall or other factors occasionally 

curtailed power generation. As a consequence, summer-spawning species numerically dominated 

the fish assemblage at the flow-regulated site; five of six spring-spawning species occurring at 

both study sites were significantly less abundant at the flow-regulated site. Persistence of native 

fishes in flow-regulated systems depends, in part, on the seasonal occurrence of stable habitat 

conditions that facilitate reproduction and YOY survival. 

Gido, K.B., D.L. Propst and M.C. Molles. 1997. Spatial and temporal variation of fish 

communities in secondary channels of the San Juan River, New Mexico and Utah. 

Environmental Biology of Fishes 49:417–434. 

Spatial and temporal variation of fish communities in four secondary channels of the San 

Juan River between Shiprock, NM and Bluff, UT were investigated from July 1993 through 

November 1994. Fish abundance and habitat availability data were collected to determine if 

physical attributes of sites influenced spatial and temporal variation in their fish communities. 

Stability of habitat was shown to positively influence the stability of the fish community. 

Analysis of variance revealed greater spatial than temporal variation in the abundance of red 

shiner, Cyprinella lutrensis, fathead minnow, Pimephales promelas, and flannelmouth sucker 

Catostomus latipinnis, while speckled dace, Rhinichthys osculus showed greater temporal 

variation. Ordination, using detrended correspondence analysis, revealed variation in fish 

communities by site, date, and sample year. Spatial variation was greatest during low-flow 

periods when the greatest differences in habitat among the four sites occurred. Spring runoff had 

the greatest temporal effect on the fish communities in secondary channels and appeared to 

reset the communities by displacing those species that were less resistant to increased current 

velocities. This annual event may help maintain native fish species adapted to these conditions in 

the San Juan River while moderating the abundance of nonnative fish species.
Humpback Chub Annotated Bibliography 68 September 2009

 

Haines, G.B., D.W. Beyers and T. Modde. 1998. Estimation of winter survival, movement 

and dispersal of young Colorado squawfish in the Green River, Utah. Final report of U.S. 

Fish and Wildlife Service, Vernal, Utah, to Upper Colorado River Endangered Fish 

Recovery Program, Lakewood, Colorado. 

Population estimates for age-0 and age-1 Colorado squawfish in two 32-km reaches of 

the Green River were made using capture-recapture procedures. Comparisons of autumn and 

spring population estimates were used to assess overwinter survival and evaluate factors that 

affect it. Previous research using traditional methodology has demonstrated that estimates 

obtained using catch per unit effort (CPUE) are unreliable for assessing overwinter survival. 

Capture-recapture provides a more rigorous basis for estimating abundance of young Colorado 

squawfish because it can account for variable capture probabilities. 

Objectives of this study were to employ capture-recapture methods to (1) compare 

estimates of abundance from capture-recapture and CPUE methods; (2) estimate overwinter 

survival of age-0 Colorado squawfish; (3) estimate seining catchability coefficients for autumn 

and spring sampling; (4) determine extent of downstream movement of marked Colorado 

squawfish between 1 November and 1 April; and (5) determine the effect of timing and 

magnitude of spring flows on dispersal of age-1 Colorado squawfish. 

We found little evidence that abundance estimates from CPUE accurately reflect the 

number of young Colorado squawfish in study reaches in the Green River. There was only a 

weak correlation (R=0.30, P=0.47) between estimates of abundance from CPUE and capturerecapture. On several occasions, CPUE estimates had precision that was comparable to that 

achieved with capture-recapture, but the estimates differed by as much as 217%. Inaccuracy and 

greater variability of CPUE was attributed to effects of water temperature on capture probability. 

Evidence suggests that young Colorado squawfish are less likely to be caught when water 

temperatures are cool, regardless of their abundance. 

Overwinter survival probabilities of age-0 fish ranged from 0.06 to 0.62. Three of four 

estimates were similar and ranged from 0.56 to 0.62. Low overwinter survival (0.06) during 

1995-1996 may have been due to small size of age-0 fish in autumn or relatively high winter 

discharge. 

Recaptures of marked age-0 and age-l Colorado squawfish showed that they moved less 

than 16 km downstream during sampling periods that ranged from 2 to 21 days Similarly, age-0 

fish that were marked in autumn and recaptured the following spring moved less than 16 km 

downstream after being at large for 170 to 200 d. The role of spring flooding in redistribution of 

age-1 Colorado squawfish remains unclear because few fish were captured during post-runoff 

surveys conducted in July and August. 
Humpback Chub Annotated Bibliography 69 September 2009

 

Haines, G.B. and H.M. Tyus. 1990. Fish associations and environmental variables in age–0 

Colorado squawfish habitats, Green River, Utah. Journal of Freshwater Ecology 5:427–

436. 

Colorado squawfish (Ptychocheilus lucius), the largest North American minnow, was 

once abundant and widely distributed. It now exists in less than about 20% of its historic range, 

and is classified as an endangered species. The species associations of age-0 Colorado squawfish 

were evaluated in the Green River, Utah , from their hatching through the first growing season, 

and the influence of several variables (i.e. backwater area, depth, and temperature; peak spring 

and summer discharge) on the relative abundance and distribution of the more common fishes 

was determined. Drifting larval fish (<30 mm total length (TL) were sampled in the Yampa 

River and Green River on dates corresponding to larval emergence and downstream drift of 

Colorado squawfish. The age-0 squawfish were sympatric with seven native and fifteen 

introduced fishes in the Green River. Larval squawfish was the most abundant fish captured in 

summer drift (38%) which included suckers, Catostomus spp. (33%), speckled dace, Rhinichthys 

osculus (14%), and channel catfish, Ictalurus punctatus (3%). However, ephemeral shoreline 

embayments used by Colorado squawfish as nursery habitats were dominated by introduced 

fishes, including red shiner, Notropis lutrensis (87%) in summer, and red shiner (65%) and 

fathead minnow, Pimephales promelas (16%) in autumn. Abundance of most fishes was highest 

in years of lower, more historic summer flow. Most fishes in backwaters inhabited a wide range 

of environmental conditions, but were most abundant in habitats deeper than 15 cm. No 

segregation in habitat use was detected between young Colorado squawfish and non-native 

fishes. Hydrologic conditions in the regulated Green River presumably favor the establishment 

and proliferation of fish invaders from more mesic environments. 

Hedrick, P.W., D. Hedgecock and S. Hamelberg. 1995. Effective population size in winterrun chinook salmon. Conservation Biology 9:615–624. 

Winter-run chinook salmon from the Sacramento River, California is federally listed as 

endangered. Since 1989 there has been a program to augment the natural population by capturing 

adults, artificially spawning them, raising the young, and releasing the smolt. Here we estimate 

the effective population size of these captive-raised fish, the natural run, and the combination of 

both groups over the three-year period from 1991 to 1993. We find that the most appropriate 

estimate of the effective population size of the captive-raised progeny is a variance estimate of 

effective population size standardized so that the number of released smolts returning to spawn 

was the same as the number of spawners used to produce the smolts originally. We have 

generated 10,000 random samples to simulate returns from these released progeny. The estimates 

of the effective population sizes in 1991, 1992, and 1993 were only 7.02, 19.07, and 7.74, 

respectively. We then determined limits on the effective population size of the natural run based 

on 0.1 and 0.333 of the run-size estimates. Using estimates of the captive proportion of the run, 

the minimum estimates of the effective population size of the overall run for the three years were 

21.9, 127.3, and 39.0, and the maximum estimates were 61.6, 401.0, and 108.7. It does not 

appear that the hatchery program has reduced the overall effective population size. The run sizes 

in each year are extremely low, however, and it is possible that fish will be lost from this run in 

one of the years in the immediate future, making reestablishment of a healthy run even more 

difficult. 
Humpback Chub Annotated Bibliography 70 September 2009

 

Houde, E.D. 1987. Fish early life dynamics and recruitment variability. American 

Fisheries Society Symposium 2:17–29. 

Tenfold or greater fluctuations in fish recruitment can be precipitated by relatively small 

variation in mortality rates, growth rates, or stage durations in the early life of fishes. An analysis 

of dynamics for 5 species in the egg, yolk-sac larva, larva, and juvenile stages, based on field, 

laboratory, and enclosure data from the literature, demonstrated that growth rate variability and 

its effect on stage durations can be a major factor affecting recruitment level. Recruitments of 

anchovy-like species, with high larval growth and mortality rates, and relatively large size at 

metamorphosis, are probably regulated in the larval stage. Cod-like or herring-like species with 

slow larval growth, low larval mortality, and relatively small size at metamorphosis could be 

regulated during the juvenile stage, although control in the larval stage seems more likely. A 

stage-specific analysis of growth rate variability in early life, which may be more reliable than 

survey estimation of mortality rates, can provide important insight into fluctuating recruitment 

levels. 

Irving, D. and T. Modde. 2000. Home-range fidelity and use of historical habitat by adult 

Colorado squawfish (Ptychocheilus lucius) in the White River, Colorado and Utah. Western 

North American Naturalist 60:16–25. 

Twelve wild adult Colorado pikeminnow (Ptychocheilus lucius), captured in the 

tailwaters of Taylor Draw Dam on the White River, Colorado, were implanted with radio 

transmitters and their movement patterns monitored from 1992 to 1994. The spawning migration 

of these fish was extensive. In 1993, the only full year of the study, the fish migrated an average 

of 658 km from the White River to spawning sites in the Yampa or Green rivers and back to the 

White River. Eight of these fish were translocated in the river upstream of the dam in April 1993. 

These fish and the 4 others below the dam remained in the river until May 1993. All 12 had 

migrated down the White River to spawning sites in the Green and Yampa rivers by July 1993. 

The fish that were located above the dam successfully passed over the dam during their 

downstream migration. Seven fish migrated upstream toward the Yampa River Canyon spawning 

site and 5 migrated downstream toward the Green River Desolation/Gray Canyon spawning site. 

Five of 7 Yampa River fish were found at the spawning site. The other 2 were found 5–8 km 

downstream of the site. One of 5 Green River fish was found at the spawning site, the other 4 

between 16 and 62 km upstream of the site. All fish migrated back to the White River by August 

1993 and were found near the dam by October 1993. Two fish were recaptured and translocated 

above the dam in September 1993. Five fish were located below the dam and 2 above the dam in 

April 1994. By July 1994 seven of the same fish that had migrated toward the Yampa River in 

1993 were found at the Yampa Canyon spawning site. At the same time, 3 of 5 fish that migrated 

toward the Green River in 1993 were found at the Desolation/Gray Canyon spawning site. This 

included 2 fish that had been found upstream of the site in 1993. 

The 12 fish traveled an average of 6 km/d (range: 4–10 km/d) during the migration period 

from May through October 1993. Generally, fish moved faster to the spawning site than back 

from the site to the White River. 
Humpback Chub Annotated Bibliography 71 September 2009

 

These fish moved very little within their home ranges in the White River. Six fish tagged 

in 1992 moved only 0.1–2.3 km in the tailwater reach below Taylor Draw Dam from September 

1992 through April 1993. All fish, after their spawning runs, had moved up to or near the dam by 

October 1993. These fish were not tracked again until April 1994. Their movement patterns in 

April 1994 were similar to those observed in April 1993. The greatest amount of fish movement 

in the White River was displayed by the 8 fish placed above Taylor Draw Dam in April 1993 and 

the 2 placed in Kenney Reservoir in September 1993. They moved 1.1–40.6 km in the river 

before and after their spawning migration in spring and autumn 1993. 

These spawning migrations suggest that adult Colorado pikeminnow in the White River 

were recruited from both Green and Yampa river spawning populations and were presumably 

imprinted to these respective spawning sites. Those fish placed above Taylor Draw Dam 

established home ranges in habitats previously occupied by Colorado pikeminnow before the 

dam was completed. They remained there until they migrated downstream during the spawning 

period. Although we did not study fish passage, our study demonstrates that adult Colorado 

pikeminnow will use habitat if access is provided. Translocation of wild adult fish into historic 

but unoccupied habitats may be a valuable recovery option. 

Mabey, L.W. and D.K. Shiozawa. 1993. Planktonic and benthic microcrustaceans from 

floodplain and river habitats of the Ouray Refuge on the Green River, Utah. Department of 

Zoology, Brigham Young University, Provo, Utah. 

This study compares microcrustacean densities and species occurrence of benthic and 

planktonic copepods and cladocerans in backwater, river channel, and floodplain habitats of the 

Green River, Utah. Samples were taken during the summer of 1991. Samples were taken using a 

1.27-cm diameter benthic core sampler and vertical plankton tows with a 63-micron plankton 

net. In all, 28 species were collected. The copepods are represented by six species of cyclopoids, 

six species of calanoids, and two species of harpacticoids. Fourteen species of cladocerans were 

collected. The highest densities were found in the floodplain. Benthic densities ranged from 

4,896–23,059/m2

 in backwater habitats, 948–6,138/m2 in river habitats, and 85,812–262,808/m2

in floodplain habitats. Plankton densities ranged from 1,450–63,353/m3

 in backwaters, 317–

1,312/m3 in the river, and 205,923–690,187/m3 in the floodplain. A comparison of the first 

sample periods for the floodplain (June), the Ouray backwater (July), and river sites (July) 

indicate that the density of the benthos was 41 times greater in the floodplain than in the other 

habitats, and the plankton density in the floodplain was 29 times greater than the backwater and 

157 times greater than the river. 

McKinney, T. and D.W. Speas. 2001. Observations of size-related asymmetries in diet and 

energy intake of rainbow trout in a regulated river. Environmental Biology of Fishes 

61(4):435–444. 

We examined diet and diel energy intake of rainbow trout, Oncorhynchus mykiss, of 

different lengths captured by electrofishing between 1991 and 1997 in the Lee’s Ferry tailwater, 

Colorado River, below Glen Canyon Dam, Arizona. Trout diets reflected a depauperate food 

base and indicated limited potential of different fish size-groups to partition food resources. As 

evidenced by relative stomach volumes of ingested matter, mid-sized and large trout tended to 
Humpback Chub Annotated Bibliography 72 September 2009

 

consume more algae than did small fish, suggesting that they consumed diets of lower nutritional 

quality. An energy intake model indicated that median consumers among mid-sized and large 

fish generally failed annually to surpass estimated maintenance energy requirements and that 

median consumers among mid-sized trout failed to meet or exceed maintenance requirements 

during all seasons. In contrast, median consumers among small trout met or surpassed 

maintenance energy requirements during most years and in summer. Results support a 

hypothesis that larger rainbow trout in lotic systems are food-limited more often than smaller 

fish. 

Meffe, G.K. and W.L. Minckley. 1987. Persistence and stability of fish and invertebrate 

assemblages in a repeatedly disturbed Sonoran Desert stream. American Midland 

Naturalist. 117:177–191. 

Persistence, a measure of presence or absence of species, and stability, an estimate of 

assemblage equilibrium measured as constancy in species ranks or densities, should both be 

considered when assessing temporal change in natural assemblages. We measured persistence 

and stability in two distinct animal assemblages frequently disturbed by natural and severe 

flooding events, the fishes and benthic invertebrates in a Sonoran Desert stream. A persistence 

index (derived from colonization/extinction analyses) indicates high persistence of fishes for 

several decades, while benthic invertebrates were persistent except in periods of severe flooding. 

Stability of taxon rankings (measured by Kendall’s W) was high for both assemblages, even 

though absolute population sizes fluctuated. Fish populations resisted even the most severe flood 

disturbances, whereas benthic invertebrates were decimated by particular frequent and intensive 

flooding. The latter were resilient, however, and quickly recovered due to life history characters 

favoring rapid post-flood recolonization. Although absolute numbers of organisms varied 

through orders of magnitude, more general aspects of assemblage structure (species’ presence or 

absence, and relative rankings) remained relatively constant despite repeated and potentially 

devastating natural perturbations.

Mills, L.S. and F.W. Allendorf. 1996. The one-migrant-per-generation rule in 

conservation and management. Conservation Biology 10:1509–1518. 

 In the face of continuing habitat fragmentation and isolation, the optimal level of 

connectivity between populations has become a central issue in conservation biology. A 

common rule of thumb holds that one migrant per generation into a subpopulation is sufficient to 

minimize the loss of polymorphism and heterozygosity within subpopulations while allowing for 

divergence in allele frequencies among subpopulations. The one-migrant-per-generation rule is 

based on numerous simplifying assumptions that may not hold in natural populations. We 

examine the conceptual and theoretical basis of the rule and consider both genetic and 

nongenetic factors that influence the desired level of connectivity among subpopulations. We 

conclude that one migrant per generation is a desirable minimum, but it may inadequate for 

many natural populations. We suggest that a minimum of 1 and a maximum of 10 migrants per 

generation would be an appropriate general rule for genetic purposes, bearing in mind that 

factors other than genetics may further influence the ideal level of connectivity. 
Humpback Chub Annotated Bibliography 73 September 2009

 

Muth, R.T. and D. E. Snyder. 1995. Diets of young Colorado squawfish and other small 

fish in backwaters of the Green River, Colorado and Utah. Great Basin Naturalist 55:95–

104. 

We compared diet of YOY Colorado squawfish (Ptychocheilus lucius), an endangered 

cyprinid, with diets of other fish < 75 mm total length (TL) collected from backwaters of the 

Green River between river kilometers 555 and 35 during summer and autumn 1987. Species 

included native Rhinichthys osculus, Catostomus discobolus, and C. latipinnis, and nonnative 

Cyprinella lutrensis, Notropis stramineus, Pimephales promelas, Ictalurus punctatus, and 

Lepomis cyanellus. For each species, diet varied with size and between upper and lower river 

reaches but not between seasons for fish of similar size. Larval chironomids and ceratopogonids 

were principal foods of most fishes. Copepods and cladocerans were important in diets of P. 

lucius < 21 mm TL and L. cyanellus < 31 mm TL. Catostomus discobolus was the only species 

that ate moderate amounts of algae. Fish (all larvae) were in digestive tracts of only 10 P. lucius 

(21–73 mm TL), about 1% of P. lucius analyzed. High diet overlap occurred between some sizereach groups of P. lucius and C. lutrensis, R. osculus, C. latipinnis, L. punctatus, and L. 

cyanellus. Potential for food competition between YOY P. lucius and other fishes in backwaters 

appeared greatest with the very abundant C. lutrensis. 

Muth, R.T. and E.J. Wick. 1997. Field studies on larval razorback suckers in 

Canyonlands National Park and Glen Canyon National Recreation Area, 1993–1995. Final 

report of Colorado State University Larval Fish Laboratory to U.S. National Park Service, 

Rocky Mountain Region, Denver, Colorado. 

Field studies on larval razorback suckers (Xyrauchen texanus) were conducted during 

spring–summer 1993–1995 in reaches of the lower Green River (from Millard Canyon, RK 53.9, 

downstream to Holeman Canyon, RK 45.1) or middle Colorado River (from the Gooseneck area, 

RK 58.4, downstream to Lathrop Canyon, RK 37.6) within or bordering Canyonlands National 

Park and in the lower 47 km of the Colorado River inflow to Lake Powell within Glen Canyon 

National Recreation Area. Studies and key findings included: 

1. Fish collections using floating quatrefoil light traps and seines in quiet-water flooded or 

backwater habitats (1993–1995). 

 Nonnative minnows (e.g., red shiner Cyprinella lutrensis, sand shiner Notropis 

stramineus, and fathead minnow Pimephales promelas) dominated all fish collections 

(76–99% of total catch from each sampling area over all sampling periods). Native fishes 

collected included larval razorback suckers (185 total – 122, 47, and 1 from the lower 

Green River in 1993, 1994, and 1995, respectively; 15 from the Colorado River inflow to 

Lake Powell in 1993), and larval or early juvenile Colorado squawfish Ptychocheilus 

lucius (12 larvae and 133 juveniles total – 12 larvae and 6 juveniles in 1993 and 5 

juveniles in 1994 from the Colorado River inflow to Lake Powell in 1993; 1, 36, and 82 

juveniles from the lower Green River in 1993, 1994, and 1995, respectively; 3 juveniles 

from the middle Colorado River in 1994). Of all razorback suckers collected, 168 were 

captured by light traps and 17 (from the lower Green River) by seines. Colorado 

squawfish larvae were caught in light traps and juveniles were caught in seines. 
Humpback Chub Annotated Bibliography 74 September 2009

 

 The collection of razorback sucker larvae from the lower Green River suggests localized 

spawning. 

 Collections of razorback sucker and Colorado squawfish larvae from the Colorado River 

inflow to Lake Powell in 1993 suggest that flowing, lotic conditions throughout the 

inflow are necessary to transport larvae produced in upstream river reaches into inflow 

nursery habitats. Larval suckers were efficiently and accurately identified alive in the 

field, but procedures for successfully transporting wild razorback sucker larvae caught in 

remote areas (e.g., lower Green River) to rearing facilities require further development. 

2. Description of the diet of adult nonnative red shiners captured from the lower Green and 

middle Colorado rivers (1994). 

 Digestive tracts of 22 adult red shiners (5% of those examined) contained cypriniform 

fish larvae, most were catostomids. Insects, including parts, chironomid larvae, simuliid 

pupae, and corixids, were the principal identifiable food items. Adult red shiners may be 

an important predator on native fishes in the Colorado River basin, especially in habitats 

with low invertebrate forage during spring and early summer. 

3. Initial evaluation of a method to partially block access of adult red shiners into portions of 

important nursery habitats for larval razorback suckers in the lower Green River using net 

exclosures (1995). 

 Netting effectively blocked access of adult red shiners into exclosed portions of nursery 

habitats while allowing passage of sucker larvae; results suggest that this method of 

nonnative fish control could be adapted for broader-scale use. 

4. Field marking of sucker larvae using techniques developed in the laboratory for 

incorporating fluorescent chemicals into otoliths (1995). 

 Laboratory techniques for marking otoliths in larval razorback suckers were successfully 

applied to sucker larvae in the field. Otolith aging of wild-caught razorback sucker larvae 

can be used to determine growth rates and exact time of spawning, data which can then 

be used to document environmental parameters associated with spawning and nursery 

habitats and evaluate factors influencing growth and survival of larvae. 

Papoulias, D. and W.L. Minckley. 1992. Effects of food availability on survival and 

growth of larval razorback suckers in ponds. Transactions of the American Fisheries 

Society 121:340–355. 

 The reasons for consistent failure of razorback sucker Xyrauchen texanus year-classes in 

Lake Mohave, Arizona–Nevada, are not entirely understood. To date, egg and larval predation 

by nonnative fishes is considered the most likely explanation, but food limitation may influence 

larval mortality. Our experiments in rearing razorback sucker larvae in ponds fertilized at three 

levels ("high," "medium," and "low") with mean invertebrate densities of 43.3, 23.7, and 12.5 
Humpback Chub Annotated Bibliography 75 September 2009

 

organisms/L, respectively, did not result in significant differences in larval survival (77.0, 89.8, 

and 67.4%, respectively). However, total larval growth was greater at the two higher invertebrate 

densities. Biovolume of food but not numbers of food organisms in guts increased linearly with 

growth of larvae. Numbers and biovolumes of food items did not differ relative to fertilization 

treatment. First foods of larval razorback suckers were diatoms, detritus, and algae, Soon 

thereafter, small rotifers and chironomids were taken, and larger organisms, primarily 

cladocerans, were selected by larger larvae. Year-class failure of razorback sucker in Lake 

Mohave may be attributable to nutritional deficiency at the lowest recorded densities of reservoir 

zooplankton. However, starvation or food-related problems do not seem likely at the higher Lake 

Mohave zooplankton densities, which are at least as great as the invertebrate densities in our 

low-fertilization treatment ponds. 

Rakowski, C.L. and J.C. Schmidt. 1999. The geomorphic basis of Colorado pikeminnow 

nursery habitat in the Green River near Ouray, Utah. Report A in Flaming Gorge Studies: 

Assessment of Colorado pikeminnow nursery habitat in the Green River. Final report to 

Upper Colorado River Endangered Fish Recovery Program. Utah Division of Wildlife 

Resources, Salt Lake City, Utah. 

Nursery habitat availability is considered a bottleneck to successful recruitment of 

Colorado pikeminnow (Ptychocheilus lucius). Detailed geomorphic studies were conducted in a 

1.5-km reach to examine channel response to flows and the geomorphic setting of nursery 

habitats during a 2-year period. Videography was used to extend relationships in the 1.5-km 

reach to a longer 10-km reach. 

Nursery habitat availability varied yearly with little persistence in location or geomorphic 

setting of individual habitats for the 2 years of this study. A small number of habitats provided 

most of the area of high-quality (i.e., deep) habitat, and most of the total area of habitat was 

formed by three geomorphic classes. Although the 1993 flood reduced the area of available 

habitat, area of deep habitat increased. The 1994 low-peak flood increased the area of habitat, but 

most habitats were shallow. 

The 1993 and 1994 multi-peaked habitat availability curves for the 1.5-km-reach bankattached bar were the result of the superposition of curves from habitats in each geomorphic 

classification, and showed that the discharge that maximized habitat availability changed yearly. 

A complexity index was evaluated for the 10-km reach as a surrogate for habitat availability. 

Total base-flow habitat availability was significantly correlated to the complexity index, but deep 

habitat availability was not. 

Measured channel topography was used as input to a flow and sediment transport model. 

Simulated hydrograph runs produced greater bank-attached bar aggradation and thalweg scour 

than steady flows, although some unrealistic patterns of scour occurred. 

New flow recommendations must include occasional high flows sufficient to rebuild 

channel topography. Flaming Gorge Dam releases should be used to augment the Yampa River 

flood peak, but not increase low flood-peak duration. The conceptual model for habitat 

availability developed here may be used to target the formation and availability of habitats. Base 
Humpback Chub Annotated Bibliography 76 September 2009

 

flow recommendations designed to maximize habitat availability should be evaluated annually. 

Winter flows should be reevaluated for their negative effects on habitat. 

Schmidt, J.C. and J. Brim Box. 2004. Application of a dynamic model to assess controls on 

age-0 Colorado pikeminnow distribution in the middle Green River, Colorado and Utah. 

Annals of the Association of American Geographers, Vol. 94 (3):458–476. 

Analysis of field data and development and application of a dynamic model indicate that 

the processes that control the number and distribution of age-0 Colorado pikeminnow in the 

middle Green River are poorly understood. Colorado pikeminnow are a federally endangered 

species endemic to the Colorado River basin that utilize backwaters during their larval stage. The 

present agency-mandated field sampling program for backwater habitats may be inadequate 

because it takes place at a time when the model predicts that most larval fish have drifted beyond 

the study area. The model predicts that water releases from Flaming Gorge Dam have a large 

potential effect on larval drift, because high releases at the time of drift greatly increase the 

proportion of the population transported beyond the study area to unfavorable river 

environments. Development of the model shows that the role of the geomorphic and hydraulic 

attributes that control larval drift and transport into backwaters, and that were parameterized in 

the model, are not well known. Resolution of these uncertainties by field study and 

experimentation would lead to refining this river management tool. 

Schmidt, J.C., K.L. Orchard and S.P. Holman. 1996. Spatial and temporal patterns of 

habitat availability in Desolation and Gray Canyons. 1995 Annual report and 1996 field 

progress report, Department of Geography and Earth Resources, Utah State University. 

Logan. 

Available shoreline habitat along the Green River in Desolation and Gray Canyons is 

strongly influenced by geology and discharge although the relationship between the three has not 

been readily apparent. To better associate the two, we established four geomorphic study reaches 

within the canyons. Within each reach, a series of cross sections was measured at different 

discharges. Surficial geology of the river corridor was mapped, and historic oblique photos were 

matched to establish the geomorphic organization of the canyon and assess changes that have 

occurred over the past century. Maps were also made of the distribution of eddies, low-velocity 

zones, and the distribution of shoreline habitat. These maps were repeated at several discharges 

including base flow and bank full discharge. 

Preliminary results show that low-velocity zones occur predominantly in the lee of 

obstructions caused by debris fans. Debris fans in Desolation Canyon are predominantly 

expansive and of low gradient. Only the small portion of the fan that is active delivers sediment 

that restricts flow and causes rapids and eddies, while the main fan is so large that it acts more as 

a meander bend as the river flows around the fan. As discharge increases the total area of eddies 

increases, however, at bankfull discharge many of the relatively small active portions of the fans 

are overtopped, and eddy frequency decreases. Although very large debris fans dominate the 

river corridor, fine-grained alluvium is the most abundant bank material at low discharge, and 

vegetated fine-grained alluvium dominates at higher flows. 
Humpback Chub Annotated Bibliography 77 September 2009

 

Schultz. A.A., O.E. Maughan, S.A. Bonar and W.J. Matter. 2003. Effects of flooding on 

abundance of native and nonnative fishes downstream from a small impoundment. North 

American Journal of Fisheries Management 23:503–511. 

Flooding can benefit native fishes in southwestern streams by disproportionately 

displacing nonnative fishes. We examined how the presence of an upstream impoundment 

affected this relationship in lower Sonoita Creek, Arizona. Nonnative species not found in the 

reservoir decreased in abundance in lower Sonoita Creek after flooding. The catch and relative 

abundance of some nonnative species found in both the reservoir and the creek increased in 

lower Sonoita Creek after flooding. Movement of nonnative fishes out of the reservoir via the 

spillway during periods of high water probably contributes to the persistence and abundance of 

these species downstream. Both preventing nonnative fishes from escaping reservoirs and the 

release of flushing flows would aid conservation of native southwestern fishes downstream. 

Shaffer, M.L. 1981. Minimum population sizes for species conservation. Bioscience 

31:131–134. 

In this paper, the author proposes tentative criteria for successful preservation at the 

population level, discusses the various methods available for determining the population sizes 

and their area requirements to meet these criteria, and relates both to overall conservation 

strategy. 

Trammell, M. A. and T. E. Chart. 1999. Colorado pikeminnow young-of-year habitat use, 

Green River, Utah, 1992-1996. Report C in Flaming Gorge Studies: Assessment of 

Colorado pikeminnow nursery habitat in the Green River. Utah Division of Wildlife 

Resources, Final report to Upper Colorado River Endangered Fish Recovery Program, 

Lakewood, Colorado. 

This nursery habitat study was conducted from 1992 to 1996 under the auspices of the 

Recovery Implementation Program, to further define Colorado pikeminnow use of habitat. The 

relationships between peak and sampling flows, habitat availability, temperature, Colorado 

pikeminnow catch and growth rates, and density of sympatric non-native cyprinids were 

examined. The objectives of this study included: 1) determine the relationship between 

availability, formation, and maintenance of Colorado pikeminnow nursery habitat and test 

release flows from Flaming Gorge Dam; 2) describe the relationship between nursery habitat 

types available to and selected by Colorado pikeminnow; 3) describe the relationship between 

degree-day accumulation in main channel and nursery habitat areas, 4) determine the relationship 

between degree-day accumulation in all potential nursery habitat areas and those utilized by 

young Colorado pikeminnow; 5) determine the relationship between the quantity of nursery 

habitats available in the summer period to the number of young Colorado pikeminnow present in 

nursery habitats during the autumn period; 6) determine the usefulness of video imagery as a 

predictor of year class strength of Colorado pikeminnow; 7) refine the interpretation of video so 

that “quality” nursery habitats can be distinguished; and 8) compare intensive sampling data and 

the concept of habitat utilization to standardized monitoring data to assess a) ways of refining 

standardized monitoring procedures and b) ways of making greater use of the data currently 

being collected. 
Humpback Chub Annotated Bibliography 78 September 2009

 

Colorado pikeminnow prefer backwater habitats that are formed behind large sandbars 

from scour channels, and are larger, deeper and more persistent than other habitats. Non-native 

cyprinids also preferred this habitat. All types of habitat including quality habitat increased in 

quantity during low water years, and decreased in high water years. There were slight decreases 

associated with higher sampling flows. Non-native cyprinids were positively associated with 

increased habitat availability, while Colorado pikeminnow were negatively associated. Total 

degree day accumulation was higher in low water years, which in turn was positively correlated 

with high growth rates for pikeminnow, and with high overwinter survival rates. The density of 

non-native cyprinids was negatively correlated with Colorado pikeminnow catch rates. Colorado 

pikeminnow are limited more by the presence of non-native cyprinids than by habitat availability 

in the lower Green River. We recommend managing the river system for a variety of flow 

scenarios to emulate the natural hydrograph. The standardized monitoring program sampling 

protocol is sufficiently representative of Colorado pikeminnow annual trends. We recommend no 

changes. 

Tyus, H.M. 1991. Movements and habitat use of young Colorado squawfish in the Green 

River, Utah. Journal of Freshwater Ecology 6:43–51. 

Habitat use and movements of young Colorado squawfish Ptychocheilus lucius were 

determined by seining 1,194 of the fish in shoreline areas. A total of 922 of these was fin-clipped 

in selected habitats and 230 (25%) were subsequently recaptured. Most young Colorado 

squawfish were captured in shallow shoreline embayments (backwaters; 85% of captures), where 

they were most abundant in spring (April; 68%). Some individuals used more than one habitat 

and moved between backwaters, shoreline eddies, and main-channel runs. A diel pattern of 

backwater use was associated with warmer water temperatures, especially in spring (April) when 

backwater temperature exceeded river temperatures. 

Tyus, H.M. and G.B. Haines. 1991. Distribution, habitat use and growth of age–0 

Colorado squawfish in the Green River basin, Colorado and Utah. Transactions of the 

American Fisheries Society 120:79–89. 

 Age-0 Colorado squawfish Ptychocheilus lucius (N=11,379) were captured as larvae and 

post-larvae in drift nets and seines in the Green and Yampa rivers from 1979 to 1988. Larvae 

were captured in drift nets (N=601) for 2–6 weeks in June and July. Small post-larvae (N=3,079) 

were captured by seining shoreline habitats in July and August. In September and October, postlarvae were most abundant (N=6,459) in low-gradient reaches of the Green River. Catch data 

indicated that the post-larvae moved from the Yampa and Green river spawning areas and were 

concentrated about 150 km downstream by autumn of each year. Spring sampling indicated that 

young fish (N=1,240) overwintered in areas occupied the previous autumn. Post-larvae captured 

in the Green River (N=5,043) most frequently occupied shoreline embayments (backwaters) that 

were relatively warm (mean, 17.0°C), deep (mean, 38 cm), large (mean, 826 m2

), and turbid. 

Abundance and size of young Colorado squawfish in the Green River were inversely correlated 

with high summer and autumn flows, which inundated nursery habitats. Seine catches of young 

squawfish in 4 years of sampling the upper and lower Green River in autumn and the following 

spring were not reliable in assessing overwintering mortality of age-0 Colorado squawfish, 
Humpback Chub Annotated Bibliography 79 September 2009

 

presumably due to differences in capture vulnerability between seasons. Survival of small fish in 

spring indicated their tolerance of prevailing winter conditions. 

Tyus, H.M. and C.W. McAda. 1984. Migration, movements and habitat preferences of 

Colorado squawfish, Ptychocheilus lucius, in the Green, White and Yampa Rivers, 

Colorado and Utah. Southwestern Naturalist 29:289–299. 

 A total of 31 Colorado squawfish, Ptychocheilus lucius, endemic were collected from the 

Green River in 1980 and the Green, White, and Yampa rivers in 1981. the fish were surgically 

implanted with radiotransmitter modules and their movement monitored for up to five months 

each year. Two movement patterns were linked to fish maturity: mature fish were highly mobile; 

immature fish were sedentary. A spawning migration of up to 205 km one-way was documented 

in 1981. Fish migrated upstream and downstream to reach a common spawning ground in the 

lower Yampa River canyon. Diel studies indicated no diel rhythm in movement existed until 

after spawning, when the fish were more active from 0800-1200 h. Colorado squawfish were 

monitored primarily in shoreline habitat over sand substrates. There were significant differences 

recorded for water depths and velocities selected by Colorado squawfish between Green, White, 

and Yampa rivers, but no difference occurred between 1980 and 1981 values in the Green River. 

Walters, C. and J. Korman. 1999. Linking recruitment to trophic factors: revisiting the 

Beverton-Holt recruitment model from a life history and multispecies perspective. Reviews 

in Fish Biology and Fisheries 9(2):187-202. 

The Beverton–Holt recruitment model can be derived from arguments about evolution of 

life history traits related to foraging and predation risk, along with spatially localized and 

temporarily competitive relationships in the habitats where juvenile fish forage and face 

predation risk while foraging. This derivation explicitly represents two key biotic factors, food 

supply (I) and predator abundance (R), which appear as a risk ratio (R/I) that facilitates modeling 

of changes in trophic circumstances and analysis of historical data. The same general recruitment 

relationship is expected whether the juvenile life history is simple or involves a complex 

sequence of stanzas; in the complex case, the Beverton–Holt parameters represent weighted 

averages or integrals of risk ratios over the stanzas. The relationship should also apply in settings 

where there is complex, mesoscale variation in habitat and predation risk, provided that animals 

sense this variation and move about so as to achieve similar survival at all mesoscale rearing 

sites. The model predicts that changes in food and predation risk can be amplified violently in 

settings where juvenile survival rate is low, producing large changes in recruitment rates over 

time. 

Ward, D.L. and S.A. Bonar. 2003. Effects of cold water on susceptibility of age-0 

flannelmouth sucker predation by rainbow trout. Southwestern Naturalist 48:43–46. 

We conducted laboratory tests to evaluate the effects of an abrupt 10°C decrease in water 

temperature on ability of age-0 flannelmouth suckers (Catostomus latipinnis) to escape predation 

by rainbow trout (Oncorhynchus mykiss). Juvenile flannelmouth suckers (58 mm mean total 

length) were maintained at 20°C and introduced individually, without acclimation, into tanks 

containing a single adult rainbow trout (246 mm mean total length) at 10 or 20°C. Rainbow trout 
Humpback Chub Annotated Bibliography 80 September 2009

 

attacked suckers more often at 20°C, but were more likely to capture them at 10°C. Age-0 

flannelmouth suckers experience an abrupt temperature decrease when they exit warm tributaries 

and enter cold hypolimnetic water released from Glen Canyon Dam on the Colorado River. This 

temperature change might increase susceptibility of young flannelmouth suckers to predation by 

rainbow trout, which are abundant in the Colorado River in Glen, Marble, and Grand canyons. 

Williams, J.E., D.B. Bowman, J.E. Brooks, A.A. Echelle, R.J. Edwards, D.A. Hendrickson 

and J.J. Landye. 1985. Endangered aquatic ecosystems in North American deserts, with a 

list of vanishing fishes of the region. Journal of the Arizona–Nevada Academy of Sciences. 

Habitat degradation and the introduction of exotic species are endangering an increasing 

number of fishes and other aquatic organisms in the desert areas of North America. We identify 

164 fishes from North American deserts as endangered, vulnerable, rare, or of intermediate 

status. Forty-six of these are herein considered endangered. Additionally, 18 recently extinct 

fishes are recorded from the region. Fifteen ecosystems are identified as providing habitat for 83 

of these vanishing fishes. These highly significant aquatic ecosystems, with locations given 

parenthetically, are: Cuatro Cienegas (Coahuila), Gila River (New Mexico, Arizona, and 

Sonora), Rio Grande (New Mexico, Texas, Chihuahua, Coahuila, Nuevo Leon, and Tamaulipas), 

Pecos River (New Mexico and Texas), Railroad Valley (Nevada), Colorado River (Colorado, 

Utah, New Mexico, Arizona, Nevada, California, Baja California del Norte, and Sonora) Green 

River (Wyoming, Colorado, and Utah), Paharanagat Valley (Nevada), Parras Valley (Coahuila) 

La Media Luna (San Luis Potosi), Ash Meadows (Nevada), Upper White River (Nevada), Moapa 

River (Nevada), Rio Yaqui (Arizona, Chihuahua, and Sonora), and Upper Klamath Basin 

(Oregon and California). A discussion of these ecosystems and their vanishing fishes, 

amphibians, reptiles, and invertebrates are provided. Protection of remaining natural habitats 

and communities within these areas provide the best opportunity for long-term survival of the 

constituent rare organism. 

Wolz, E.R. and D.K. Shiozawa. 1995. Soft sediment benthic macroinvertebrate 

communities of the Green River at the Ouray National Wildlife Refuge, Uintah County, 

Utah. Great Basin Naturalist 55:213–224. 

Benthic macroinvertebrates from four habitat types (river channel, ephemeral side 

channel, river backwater, and seasonally inundated wetland) were examined from the Green 

River at the Ouray National Wildlife Refuge, Uintah County, UT, June–August 1991. Four 

major taxa (Nematoda, Oligochaeta, Diptera, Ceratopogonidae, and Chironomidae) were 

quantified. Cluster analysis of densities showed that habitat types with comparable flow 

conditions were the most similar. Highest to lowest overall benthic invertebrate densities of the 

four habitats were as follows: ephemeral side channel, river backwater, seasonally inundated 

wetland, and river channel. Nematodes were the most abundant taxon in all habitat types and 

sample dates except the August sample of the river channel and river backwater and the July 

sample of the seasonally inundated wetland. 
Humpback Chub Annotated Bibliography 81 September 2009

 

4 IMPACTS OF DAM OPERATIONS 

4.1 EFFECTS ON FLOW 

Chart, T.E. and L.D. Lentsch. 1999. Flow effects on humpback chub (Gila cypha) in 

Westwater Canyon. Final report of Utah Division of Wildlife Resources to Upper Colorado 

River Endangered Fish Recovery Program, Lakewood, Colorado. 

This five-year study to determine the effect of Colorado River flows on humpback chub 

(Gila cypha) reproduction and recruitment is a component of the Recovery Implementation 

Program (RIP) Aspinall Studies. The goal of this project was to develop relationships between 

observed flows and humpback chub life history responses, concentrating on the earlier life 

stages. To meet this goal, the following study objectives were identified: determine spawning 

and nursery requirements, describe the relationship between geomorphic processes of sediment 

transport and nursery habitat formation, identify and describe reproductive isolating mechanisms, 

and assess recruitment. Similar research is being conducted on the Green River in Desolation 

Canyon as part of the Flaming Gorge Studies. Three components of the Westwater Canyon fish 

community were studied: the YOY, juveniles (AGE1+ and 2+) and late juvenile/adults. Both 

humpback chub (Gila cypha) and roundtail chub (G. robusta) are common in Westwater 

Canyon. Unlike some Upper Basin chub populations, the adults of these two Gila spp. are 

morphologically distinct in Westwater Canyon. However, young chubs are difficult to identify 

to species wherever more than one of these species is found. YOY sampling was therefore 

broken into sub-reaches: above Westwater Canyon (where only roundtail chubs are common), 

within Westwater Canyon (roundtail and humpback are equally represented in the adult fish 

community) and below the canyon (where roundtail chubs are present in low numbers and 

humpback chub are absent). YOY were sampled with seines. Juvenile chubs were monitored 

with shoreline electrofishing in the canyon, and late juvenile and adults were sampled with hoop 

and trammel nets as well as with electrofishing. The design of the study focused on YOY 

densities (fish/m2 of seined habitat) and habitat use to establish relationships with observed 

flows. Juvenile chubs (still not readily identified to species) were monitored in the canyon to take 

the flow/reproduction relationship to the next step. Only three of the five cohorts produced 

during this study (1992, 1993, and 1994) could be tracked past their first summer (age 0); the 

1995 cohort was virtually non-existent and further monitoring of the 1996 cohort was beyond the 

scope of this study. Late juvenile and adult chubs were monitored to determine population trend 

and stability in light of the recent recruitment. Pre-project data were incorporated into these 

analyses. Hatching time and growth of young Gila spp. were correlated with flow parameters 

(peak flow at State Line gage and pre-peak flow in excess of 6000 cfs (a cumulative flow metric 

similar to degree days)) and water temperature (degree days > 10°C prior to June 15). In general, 

YOY chubs hatched earlier above the canyon indicating roundtails likely spawned earlier than 

humpbacks. Catch rates of YOY Gila spp. were greatest in the above-canyon sub-reach with a 

project high density, 0.679, recorded there during July and August of 1993. The greatest density 

of YOY chubs within Westwater Canyon was nearly as high, 0.673, recorded during the summer 

of 1996. The catch rates of chubs were significantly higher in the above-canyon and canyon subreaches than in the sub-reach below the canyon. Reproductive success as measured by densities 

of YOY chubs was positively correlated with the previous year’s peak flow, and negatively 
Humpback Chub Annotated Bibliography 82 September 2009

 

correlated with the amount the June monthly mean flow deviated from the historic monthly 

mean. The greatest canyon catch rates occurred when the river peaked near 30,000 cfs. A 

multinomial analysis indicated YOY chubs used backwater habitats as they were available, but 

did not select for them. Similar use was recorded in embayments and shoreline habitats within 

Westwater Canyon. Habitat availability within Westwater Canyon was not dependent on the 

spring peak as much as instantaneous flow. Nursery habitats were basically any low velocity 

area, whether that be a typical secondary channel backwater or merely a sculpted area in the 

shoreline bedrock (referred to as embayments). A chi-square analysis of presence/absence YOY 

chub in Westwater Canyon by habitat depth indicated no selection, supporting the finding of 

opportunistic habitat use. Habitat depth was positively correlated with peak flows and more 

strongly correlated with flows at the time of sampling. Shallow habitats were defined as those 

having a maximum depth < 0.7 m. Much of the available habitat within Westwater Canyon was 

not formed by sediment deposition as the classic Colorado pikeminnow nursery areas are. Nonnative species were found in lower densities in Westwater Canyon than above or below the 

canyon, again a function of canyon habitat availability. Non-native densities were negatively 

correlated with the peak flow at the State Line gage. The analysis of chub recruitment was based 

on a comparison of cohort (as determined by length frequency analysis) densities (electrofishing 

CPE) relative from year to year. From this analysis, it appeared the 1994 cohort recruited the 

best; the 1993 cohort the worst. YOY produced in 1994, although not particularly abundant, had 

grown larger (45 mm TL by mid-August) than either the 1992 or 1993 cohorts. In addition, 

overwinter flows for the 1994 YOY cohort were lower and more stable than experienced by the 

other two cohorts. Survival of all juvenile chubs (> 100 mm TL) appeared to be high, although 

not quantified. The humpback chub population in Westwater Canyon was monitored at three 

sites established for the Interagency Standardized Monitoring Program (ISMP): Miner’s Cabin 

(RK 199.9–198.6), Cougar Bar (RK 194.4–193.6), and Hades bar (RK 192.2–191.8). Densities 

of adult humpback chub, as referenced by trammel net CPE (fish/23 m net hour), fluctuated 

greatly from trip to trip but overall remained fairly stable, with the trend in CPE slightly up at 

Miner’s Cabin and slightly down at the other two. The same data for roundtail chub indicated a 

relatively strong downward trend at all sites. Lincoln-Peterson population estimates, although 

compromised by large 95% confidence intervals, showed a similar trend in population size for 

the two species. 

Goeking, S.A., J.C. Schmidt and M.K. Webb. 2003. Spatial and temporal trends in the 

size and number of backwaters between 1935 and 2000, Marble and Grand Canyons, 

Arizona. Department of Aquatic, Watershed and Earth Resources. Utah State University. 

report prepared for U.S. Geological Survey, Grand Canyon Monitoring and Research 

Center, Flagstaff, Arizona. 

The decline in native fish populations in the Colorado River in Marble and Grand 

Canyons over the past few decades has led biologists and river managers to investigate possible 

causes of that decline. One potential cause is declining habitat availability, including changes in 

the conditions of the backwater habitats used by nursery fish. Backwaters of the post-dam 

Colorado River in Grand Canyon occur in inundated return current channels in the lee of eddy 

bars. We evaluated spatial and temporal trends in backwater size and number based on: 

1) analyses of detailed ground survey data from five eddy bars, and 2) interpretation of historical 

aerial photographs of five reaches totaling 21 km. From the survey data, we developed 
Humpback Chub Annotated Bibliography 83 September 2009

 

topographic maps of each eddy bar and evaluated the potential backwater area and volume at 

each survey site as a function of discharge. The results of this analysis indicated that the 

relationship between discharge and backwater condition changes from year to year at each site, 

and it also varies among sites in a given year. Variations in backwater volume were larger than 

variations in backwater area, demonstrating that volume is the more sensitive indicator of 

backwater condition because it accounts for differences in size between deep backwaters and 

shallow ones. Analyses of aerial photographs involved delineation of all backwaters in five study 

reaches between 1984 and 2000, and we delineated all backwaters between 1935 and 2000 

within two study reaches. In all reaches, backwater size was greater in October 1984 than at any 

other time during the period of record; the number of backwaters was largest in 1984 and 1990. 

Time series of backwater conditions within each reach showed qualitatively that floods tended to 

increase backwater area and the absence of floods tends to decrease backwater area, while there 

was no apparent relationship between floods and backwater numbers. Although the area and 

number of backwaters in each reach showed large temporal variation, this variation appeared to 

be within the range of variability observed during the period of record. We found no evidence for 

a progressive increase or decrease in the availability of backwater habitats. 

Harpman, D.A. and A.J. Douglas. 2005. Status and trends of hydropower at Glen Canyon 

Dam. Pages 165-176 in Gloss, S.P., J.E. Lovich and T.S. Melis, eds., The state of the 

Colorado River ecosystem in Grand Canyon. A report of the Grand Canyon Monitoring 

and Research Center 1991-2004. USGS Circular 1282. U.S. Geological Survey, Flagstaff, 

Arizona. 

 Approximately 7% of the electricity in the United States is generated by hydroelectric 

powerplants. These plants are an invaluable component of the Nation’s interconnected electric 

power system in which generation resources consist of thermal, nuclear, solar, wind, and other 

sources. Hydroelectric powerplants are characterized by exceptionally low costs of operation, are 

highly reliable, and produce electricity without burning fossil fuels and producing air pollution. 

In addition, they provide voltage control, system regulation, and other ancillary services which 

help ensure the reliability and electrical integrity of the system. Although they play an important 

role in the electric power system, hydroelectric powerplants, such as the one at Glen Canyon 

Dam, have some widely recognized environmental effects. Large hydro facilities have blocked 

the spawning of anadromous and migratory aquatic species, eliminated the downstream transport 

of sediment, fundamentally altered the seasonal hydrograph, affected water chemistry, and 

changed the downstream temperature regime. Furthermore, the operation of these plants, 

particularly those used to produce peaking, or variable, power, causes hourly variations in stream 

flow and elevation, thereby adversely affecting downstream aquatic and riparian communities 

and recreation. The unveiling of plans to construct Glen Canyon Dam spurred a nationwide 

protest. Construction of the dam started a public environmental discourse which continues to this 

day. 
Humpback Chub Annotated Bibliography 84 September 2009

 

Hickman, T.J. 1983. Effect of habitat alterations by energy resource developments in the 

Upper Colorado River basin on endangered fishes. Aquatic Resources Management of the 

Colorado River Ecosystem: Proceedings of the 1981 Symposium on the Aquatic Resources 

Management of the Colorado River Ecosystem November 16-18, 1981, Las Vegas, NV. Ann 

Arbor Science, Ann Arbor, MI. pp 1537–550. 

 The upper Colorado River system is the habitat of several endangered fish: Kendall 

Warm Springs dace, Colorado squawfish, humpback chub, and bonytail chub. The single most 

important factor contributing to the decline of these species has been the construction and 

operation of dams and reservoirs, which have effected flow, temperature, chemistry, biota, and 

migration routes. Water depletion amounting to about 25% of the total has also had similar 

effects, particularly by eliminating the backwater nursery areas. A predicted decrease in 

agricultural use and increase in energy development use would decrease the amount of used 

irrigation water percolating back into the groundwater and streams. In addition, water allocated 

for irrigation is not always used, whereas energy use would be more uniform. In order to 

preserve the endangered fish, cooperation between diverse groups is needed. This may require 

that some dam projects may be abandoned and that others may be changed or delayed. Reducing 

demands on the river’s water supply can also aid in protecting the fish. This could take the form 

of energy alternatives (solar), water conservation, technological improvements, use of 

groundwater where feasible, and weather modification. Other habitat preservation activities are 

purchase of water rights, habitat manipulation and construction, fish passageways, and artificial 

propagation. 

Hoffnagle, T.L. 1996. Changes in water quality parameters and fish usage of backwaters 

during fluctuating vs. short-term steady flows in the Colorado River, Grand Canyon. 

Arizona Game and Fish Dept. Prepared for Glen Canyon Environmental Studies, U.S. 

Bureau of Reclamation. 

The changes in water quality of backwaters and their use by fishes during fluctuating vs. 

short-term steady flows were examined in the Colorado River, Grand Canyon, 25-31 May 1994. 

Temperature gauges were deployed in four backwaters in the vicinity of the confluence of the 

Colorado and Little Colorado Rivers. Thirteen backwaters were sampled for fish use. 

Temperature, dissolved oxygen, and pH fluctuated daily under both fluctuating and steady flow 

regimes. Mean mainchannel temperatures was warmer under steady flows. Mean, minimum, 

maximum, and diel range of backwater temperatures were higher under steady flows. Mean and 

minimum dissolved oxygen were lower under steady flows. Specific conductance and pH did 

not vary between flow regimes. Catch-per-unit effort in backwaters did not differ under either 

flow regime. These results indicated that steady flows will cause warming of the mainchannel 

Colorado River and its backwaters and changes in other water quality parameters. These 

changes may both positively and negatively affect fish populations directly and indirectly 

through their influence on primary and secondary productivity and the potential for an increase 

in parasite and disease prevalence. These factors should be more closely examined before 

implementation of a steady flow regime or other changes that might increase water temperatures 

in the river. 
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Johnson, R.R. and S.W. Carothers. 2005. External threats: the dilemma of resource 

management on the Colorado River in Grand Canyon National park, USA. Environmental 

Management 11(1):99–107. 

The United States Congress established Grand Canyon National Park in 1919 to preserve 

for posterity the outstanding natural attributes of the canyon cut by the Colorado River. In some 

cases National Park Service attempts to maintain Grand Canyon’s natural environment have been 

thwarted by activities outside the park. One of the most obvious external threats is Glen Canyon 

Dam, only 26 km upstream from the park boundary. Constructed in 1963, this gigantic dam has 

greatly altered the physicochemical and biological characteristics of 446 km of the Colorado 

River in Grand Canyon National Park. The river’s aquatic ecosystem has been greatly modified 

through the loss of indigenous species and the addition of numerous exotics. We consider this an 

exotic ecosystem. The riparian ecosystem has been less modified, with addition of a few exotics 

and no loss of natives—this we consider a naturalized ecosystem. 

The great dilemma now faced by park managers is that, after 20 years of managing 

resources along a river controlled by Glen Canyon Dam, the Bureau of Reclamation has 

proposed major changes in operational procedures for the dam. Scientists and managers from the 

National Park Service, Bureau of Reclamation, and cooperating federal and state resource 

management agencies are using a systems analysis approach to examine the impacts of various 

Colorado River flow regimes on aquatic, riparian, and recreational parameters in the park. This 

approach will help in the development of management alternatives designed to permit the most 

efficient use of that river’s natural resources without their destruction. 

Korman, J. and S.E. Campana. 2009. Effects of hydropeaking on nearshore habitat use 

and growth of age-0 rainbow trout in a large regulated river. Transactions of the 

American Fisheries Society 138(1):76–87. 

We evaluated the effects of hourly variation in flow caused by power load following at 

Glen Canyon Dam (“hydropeaking”) on the nearshore habitat use and growth of age-0 rainbow 

trout Oncorhynchus mykiss downstream from the dam in the Colorado River, Arizona. Reduction 

in the extent of hydropeaking is a common element of restoration efforts in regulated rivers, but 

empirical support for such a practice is limited. Our assessment was based on a comparison of 

abundance in shoreline areas determined by electrofishing at different flows as well as analysis 

of otolith microstructure. The catch rates of age-0 rainbow trout in nearshore areas were at least 

two- to fourfold higher at the daily minimum flow than at the daily maximum, indicating that 

most age-0 rainbow trout do not maintain their position within immediate shoreline areas when 

flows are high. A striping pattern, identified by the presence of atypical daily increments formed 

every 7 d, was evident in over 50% of the 259 otoliths examined in 2003 but in only 6% of the 

334 examined in 2004. The weekly pattern corresponded to a reduction in the extent of hourly 

flow fluctuations on Sundays during the growing season, which occurred in 2003 but not in 

2004. The atypical increments were 25% wider than the adjacent increments and were indicative 

of significant (F sub(15, 235) = 19.2, P < 0.0001) short-term increases in otolith growth. The 

somatic growth rate among fish with otoliths where striping was present (11.2 mm/month) was 

slightly greater than that among fish with otoliths without striping (10.8 mm/month), but the 

difference was not significant. We provide evidence suggesting that otolith growth improved on 
Humpback Chub Annotated Bibliography 86 September 2009

 

Sundays in 2003 because it was the only day of the week when most age-0 fish were found in 

immediate shoreline areas, where higher water temperatures and lower velocities provided better 

growing conditions. 

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

fluctuating flows from Glen Canyon Dam in 2003 and 2004 on the early life history stages 

of rainbow trout in the Colorado River. Final report to Grand Canyon Monitoring and 

Research Center, Flagstaff, Arizona. 

An experimental alteration of the hydrograph from Glen Canyon Dam (GCD), targeted at 

reducing the survival rate of young rainbow trout through increased daily fluctuations in flow, 

was implemented from January through March in 2003 and 2004. This report describes the 

impact of the experimental flow regime on the early life stages of rainbow trout below Glen 

Canyon Dam. The study consisted of five components. We measured the timing of redd 

excavation and the distribution of redds across elevations (i.e., redd hypsometry) in Glen Canyon 

to estimate the potential egg and alevin mortality caused by the experimental flow regime. We 

quantified the relationships between spawning habitat preference and depth, velocity, and 

substrate in Glen Canyon to evaluate the feasibility of controlling spawning elevations through 

changes in discharge. We obtained monthly samples of YOY from Glen Canyon to compare 

length-frequencies over time and among habitat types to make qualitative inferences regarding 

the seasonal timing of hatch, and YOY survival, growth, and movement among habitat types. We 

analyzed the microstructure of otoliths from a subsample of fish to establish length-age 

relationships and evaluate the effects of dam operations on YOY growth. These data were used 

in a stock synthesis model to estimate seasonal trends in the number of rainbow trout emerging 

from the gravel, and their subsequent survival rates and movement among habitat types. Finally, 

we conducted rainbow trout spawning habitat, redd, and fry surveys from Lees Ferry to the 

confluence of the Little Colorado River (LCR) to evaluate the extent of natural reproduction in 

this reach. 

There was minimal spawning prior to mid-January in both 2003 and 2004 and peak 

counts of approximately 1,000 redds were obtained by late-March/early-April. We estimated that 

4,000 and 2,100 redds were excavated in 2003 and 2004, respectively. The average percentage of 

redds above 12, 8, and 5 kcfs at high elevation spawning sites was 27%, 54%, and 82%, 

respectively. The system-wide redd survey documented a total of 27 spawning locations in the 

Glen Canyon with the majority of redds located at elevations below 8 kcfs. Intergravel water 

temperatures at Four Mile and Powerline Bars increased with elevation and exceeded the lethal 

egg incubation limit of 16°C by mid-March at higher elevations. Estimates of the percentage of 

redds that did not produce viable young for Glen Canyon were 23% and 33% in 2003 and 2004, 

respectively. Mortality in 2004 was higher because of the implementation of a daytime Sunday 

steady flow of 8 kcfs between January and March. Under normal Record of Decision (ROD) 

operations from January to March with a similar total volume released from Glen Canyon Dam 

(GCD) to the volumes in 2003 and 2004, the model predicted a redd loss of 19% in January and 

33% from February to March when the majority of spawning occurs. Thus, there was likely very 

little additional incubation mortality associated with the higher experimental fluctuations in 

January to March of 2003 and 2004. We estimated that between 1988 and 1991, when daytime 

low flows during the spawning and incubation period averaged 1-3 kcfs, total redd loss likely 
Humpback Chub Annotated Bibliography 87 September 2009

 

exceeded 75%. We predicted that redd loss rates could be increased to over 50% if a daytime 

Sunday steady flow of 5 kcfs was implemented. 

The spawning habitat preference models we developed for rainbow trout in Glen Canyon 

were useful for evaluating the extent to which increased discharge during the January to March 

experimental flow period altered the elevations where spawning occurred. Depths of 0.5 – 1.5 m, 

velocities of 0.3 – 1 m/sec, and D85 values of 15-45 mm were preferred. Weighted useable area 

computations showed that higher discharges increased total spawning habitat availability at sites 

that had spawning habitat located at higher stages such as Four Mile and Powerline Bars, and 

reduced spawning habitat availability at deep-water redd sites such as Ferry Swale. The model 

also showed that the stages of preferred suitable spawning habitat at Four Mile and Powerline 

Bars were increased under higher discharges. Such changes in spawning habitat availability 

would increase the proportion of redds that would be desiccated and increase the duration of 

exposure. The redd hypsometry study showed that there was a significant proportion of redds 

excavated in deep-water that would not be dewatered at flows as low as 5 kcfs. The large decline 

in spawning habitat availability at Ferry Swale under high discharge suggests that spawning at 

deep-water sites could be suppressed through maintenance of high flows through the entire 

spawning period; however this conclusion needs to be validated by direct field observations. This 

uncertainty is important as 40-50% of the redds in Glen Canyon were located below 5 kcfs. 

Seasonal changes in length frequencies of YOY in Glen Canyon showed effects of hatch 

timing, growth, survival variation, and movement from low to steep angle shorelines. Substantial 

decreases in density following the early-September reduction in the minimum daily flow from 

10 to 5 kcfs were observed in both 2003 and 2004, and a very big drop in density in steep angle 

habitats following the November 2004 42.5 kcfs beach habitat building flow was also seen. 

Catch rates obtained at the minimum daily flow were 3- to 5-fold higher compared to those 

during the daily maximum and these differences were statistically significant. A weekly striping 

pattern was evident in at least 51% of the 255 otoliths examined in 2003 but in only 5% of the 

334 otoliths in 2004. The atypical weekly increment was 25% wider compared to the other 

increments and indicated enhanced growth during Sunday steady flow periods. There was little 

weekly striping in 2004 because daytime flows were not steady on Sundays during the summer 

of 2004. Age determinations based on analysis of otolith microstructure were made from 237 and 

318 fish in 2003 and 2004, respectively. Variation in length-at-age was very low with logistic 

growth models predicting 86-87% of the variation in forklength as a function of the number of 

days from hatch. YOY in steeper habitats were significantly larger at age than those in low angle 

habitats for fish that were at least 3 months old. Hatch date distributions for the total YOY catch 

in 2003 (N=966) and 2004 (N=4,647) were computed by length back-calculation. The 

correspondence between the back-calculated hatch date distributions and those inferred from 

redd counts was very strong, indicating that there was limited variation in mortality rates over the 

incubation period. The observation that YOY generally remain at the daily minimum flow 

elevation, and the post-September density reductions documented in Glen Canyon, coupled with 

the substantial literature on stranding impacts, support the need to evaluate a ‘stranding’ flow 

operation from GCD targeted at reducing YOY recruitment. 

Estimates of YOY weekly survival rate from the stock synthesis model in both low and 

steep angle habitats were approximately 0.85 and were not dependent on the form of the hatch 
Humpback Chub Annotated Bibliography 88 September 2009

 

timing distribution. The constant and variable survival rate models provided good fits to the 

length frequency data and the improved fit of the latter models was useful in untangling were 

significantly lower than in the previous (0.91 and 0.95) and following intervals (0.87 and 0.90). 

This change may have been caused by the reduction in the daily minimum flow from 10 to 5 kcfs 

in early-September. However, it is also possible that the decrease in survival we estimated was a 

natural occurrence, possibly driven by a normal ontogenetic habitat shift and/or densitydependent mortality. In steep habitats, weekly survival rates dropped from 0.90 for the period 

spanning early-September to early-November, to 0.59 for the period between November and 

December. This change was likely related to the 42.5 kcfs Beach Habitat-Building Flow 

(BHBF), although it could also have been caused by a natural or flow-induced habitat shift 

rather. Uncertainty in survival rate estimates was generally larger in low angle habitats because 

of lower sample size. Hatch timing-patterns estimated from the model were highly uncertain 

when survival rates were allowed to vary among sample periods. The juvenile stock synthesis 

modeling approach we have developed represents a potential advance in monitoring the response 

of salmonid populations to habitat alterations. However, we caution that it does not replace the 

need to track trends in the adult population. Without this supporting data, it will be uncertain 

whether a measured change in the mortality at an early juvenile stage will be compensated by a 

subsequent change in density-dependent mortality. 

Exposed gravels and cobbles above 8 kcfs were generally much too coarse and poorly 

sorted to support spawning between Lees Ferry and the confluence with the Little Colorado 

River. We observed a handful of very small areas (10-400 m2

) that contained appropriate grain 

sizes for spawning, however no redds were observed at any of these locations. Due to high 

turbidity we were unable to survey for spawning habitat or redds in Marble Canyon below the 

daily minimum flow elevation of 8 kcfs on the April 2004 trip. In June 2004 water clarity was 

adequate and suitable spawning substrate below 8 kcfs was found at a number of locations in 

Marble Canyon, with the majority of larger sites located between the confluence of Nankoweap 

Creek and Kwagunt rapid (river miles 52 and 56, respectively). The vast majority of these sites 

were located at the downstream end of riffles or small rapids at depths of 3-10 m at a discharge 

of ca. 9 kcfs. Nankoweap Creek was accessible to fish in the Mainstem Colorado River in 2004 

and could support at least a few thousand spawners between January and early-February when 

water temperatures are suitable. We did not catch recruitment and survival effects in the length 

frequency data. Survival rates for the period between the August and September samples for low 

and steep angle habitats of 0.84-0.85 any YOY rainbow trout in Nankoweap Creek during the 

April 2004 survey and saw only limited spawning activity. 

Relative to Glen Canyon, we found very few YOY rainbow trout between Lees Ferry and 

the LCR confluence during the June and August 2004 surveys. Across gear types, densities of 

YoY rainbow trout in Glen Canyon were 12-fold higher than in Marble Canyon in June and 15-

fold higher in August. Densities of YoY in Marble Canyon were highest in the 15-mile reach 

immediately below Lees Ferry and increased between June and August in the first 30 miles 

downstream of Lees Ferry. Length-at-age and hatch date distributions for YOY trout caught in 

Glen and Marble Canyons were very similar. These data suggest that the limited number of YOY 

caught in Marble Canyon in 2004 likely originated from Glen Canyon. The reach between river 

mile 45 and 60 had the lowest densities of YoY fish of all the reaches in Marble Canyon with 

only 14 and 4 YOY caught in June and August, respectively. Although this reach had the greatest 
Humpback Chub Annotated Bibliography 89 September 2009

 

amount of spawning habitat in the mainstem and a tributary that could support a substantial 

amount of spawning (Nankoweap Creek), these habitats clearly did not produce a significant 

number of viable young in 2004. 

If our surveys in Marble Canyon are representative of reproductive conditions for 

rainbow trout in future years, it is unlikely that flows from GCD can be used to reduce the 

survival rate of young trout in this reach. There was virtually no spawning habitat above 8 kcfs 

that could potentially be dewatered. The limited area of spawning habitat that was observed was 

well below 5 kcfs. The very low densities of YOY observed in 2004 indicate that recruitment to 

the Marble Canyon population is already quite low, thus the incremental effect of destabilizing 

shoreline habitats would be very small. Our results cannot be used to definitively determine the 

origin of the current population of rainbow trout in Marble Canyon. It is possible that these fish 

originated in Marble Canyon and that the limited reproduction we observed in 2004 was a unique 

occurrence. Continued documentation of YOY absence in Marble Canyon over the next few 

years, combined with observations of a constant or increasing adult population above the 

mechanical removal reach, would provide strong evidence that this population is supported by 

downstream dispersal from Glen Canyon. Alternatively, if downstream dispersal is not a 

significant process, and if the lack of local reproduction in Marble Canyon continues, the 

rainbow trout population in this reach should decline substantially over the next few years. 

Korman, J., S.M. Wiele and M. Torizzo. 2004. Modelling effects of discharge on habitat 

quality and dispersal of juvenile humpback chub (Gila cypha) in the Colorado River, 

Grand Canyon. Regulated Rivers 20:379-400. 

 A two-dimensional hydrodynamic model was applied to seven study reaches in the 

Colorado River within Grand Canyon to examine how operation of Glen Canyon Dam has 

affected availability of suitable shoreline habitat and dispersal of juvenile humpback chub (Gila 

cypha). Suitable shoreline habitat typically declined with increasing discharges above 226–

425m3

/s, although the response varied among modeled reaches and was strongly dependent on 

local morphology. The area of suitable shoreline habitat over cover types that are preferred by 

juvenile humpback chub, however, stayed constant, and in some reaches, actually increased with 

discharge. In general, changes in discharge caused by impoundment tended to decrease 

availability of suitable shoreline habitat from September to February, but increased habitat 

availability in spring (May–June). Hourly variation in discharge from Glen Canyon Dam 

substantially reduced the amount of persistent shoreline habitat at all reaches. Changes in 

suitable shoreline habitat with discharge were shown to potentially bias historical catch per unit 

effort indices of native fish abundance up to fourfold. Physical retention of randomly placed 

particles simulating the movement of juvenile humpback chub in the study reaches tended to 

decline with increasing discharge, but the pattern varied considerably due to differences in the 

local morphology among reaches and the type of swimming behavior modeled. Implications of 

these results to current hypotheses about the effects of Glen Canyon Dam on juvenile humpback 

chub survival in the mainstem Colorado River are discussed. 
Humpback Chub Annotated Bibliography 90 September 2009

 

McGuinn-Robbins, D.K. 1995. Comparisons in the number and area of backwaters 

associated with the Colorado River in Glen, Marble and Grand Canyons, Arizona. Draft 

report to Glen Canyon Environmental Studies, U.S. Bureau of Reclamation. Arizona Game 

and Fish Department, Phoenix, Arizona. 

Backwaters provide important rearing habitat for larval and juvenile native fishes in 

Marble and Grand Canyons. Geomorphology, sediment supply, and antecedent flow conditions 

dictate backwater location, number, and size. Size and number of backwaters have important 

implications for native fish populations. 

 This study compared the number and size of backwaters greater than 100 m2

 recorded by 

aerial videography in Glen, Marble, and Grand Canyons of the Colorado River at 227 m3

/s 

constant flows of 1990, 1992, 1993, and 1994. Number of backwaters among years was 

significantly different (G-test, P<0.025). Number of backwaters decreased from 146 in 1990 to 

70 in 1992. Following winter flooding of the Little Colorado River in January and February 

1993, and a concurrent input of sediment, number of backwaters increased to 113 in 1993. 

Number of backwaters decreased to 89 in 1994. More backwaters occurred in wide reaches than 

in narrow reaches (G-test, P<0.025). Crucial reaches for native fishes are found above and 

below the Little Colorado River confluence and below the Havasu Creek confluence Mean area 

of backwaters during constant 227 m3

/s flows in 1990 (733 m2), 1992 (450 m2), 1993 (649 m2) 

and 1994 (798 m2

) was not significantly different (Kruskal-Wallis test, P=0.099, N=55 for each 

year). 

 Number of backwaters at 142 and 227 m3/s flows during 1990 for river kilometers 89.3 to 

122.3 were also compared. Significantly more backwaters appeared at the 142 m3/s discharge 

level (42) than at the 227 m3/s level (21) (G-test, P<0.05). Mean backwaters in 1990 at 227 m3/s 

(741 m2

) was greater than those at 142 (493 m2), but was not significantly different (MannWhitney test, P=0.307). 

McKinney, T. and W.R. Persons. 1999. Rainbow trout and lower trophic levels in the Lee’s 

Ferry tailwater below Glen Canyon Dam, Arizona: a review. Arizona Game and Fish 

Department report to U.S. Geological Survey, Grand Canyon Monitoring and Research 

Center, Flagstaff, Arizona. Abstract excerpted from study conclusions.

Alterations in flow regimes in regulated rivers profoundly influence fish populations. 

Our review similarly indicates that operations of Glen Canyon Dam influence Lee Ferry’s 

rainbow trout population. Widely fluctuating discharges and particularly extended periods of 

flow reductions to between 28 m3/s and 142 m3/s are detrimental to trout health, condition, 

growth, reproduction, recruitment, and population size and structure. Negative impacts of dam 

operations result from the following influences: 

(1) Disrupted or seasonally restricted spawning; 

(2) Desiccation of redds; 

(3) Stranding mortality of larvae, fry, and older fish; 
Humpback Chub Annotated Bibliography 91 September 2009

 

(4) Reduced suitable habitat, influencing survival of fry, environmental stress, and lowered 

health and condition of fish; 

(5) Reduced available food base due to losses and slow recolonization of periphyton, 

submerged macrophytes, and benthic macroinvertebrates in the varial zone; 

(6) Increased metabolic demands associated with local displacements and greater densityrelated stress (competition for food and space); and 

(7) Reduced recruitment to sexual maturity associated with lower growth rates. 

 Conversely, more stable daily and seasonal flow regimes such as provided by interim 

flow (IF) and modified low fluctuating flows (MLFFs) operating alternatives for Glen Canyon 

Dam (GCD) benefit the rainbow trout fishery through the following influences: 

(1) Increased suitable habitat for fry and older fish; 

(2) Extended spawning; 

(3) Reduced desiccation of redds; 

(4) Prevention of stranding mortality due to restricted ramping rates and the magnitude of 

daily flow fluctuations; 

(5) Improved health and condition; 

(6) Increased aquatic food base due to the greater permanently wetter perimeter of the river 

channel; 

(7) Reduced local displacement, density-related stress, and metabolic demands; and 

(8) Greater recruitment due to increased growth rates. 

In summary, the IF and MLFF operating alternatives benefited the Lee’s Ferry 

recreational fishery by development of a self-sustaining rainbow trout population and increased 

fish densities and recreational use by anglers. Present resource quality likely will be sustained 

within the foreseeable future under current policies of dam operations (MLFF) and fisheries 

management. However, importance of density- and food-related factors and changing nutrient 

concentrations since 1993-1994 in affecting the fishery remain to be evaluated. Continued 

monitoring, research, and management efforts are essential to increase the knowledge base from 

which to manage the fishery in relation to operations of GCD. Greater consideration of habitat 

suitability, the aquatic food base, and energetic conditions for rainbow trout than in the past 

should enhance management capabilities. 
Humpback Chub Annotated Bibliography 92 September 2009

 

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

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

of Fisheries Management 19(4):984–991. 

We examined influences of 3 d of reduced flows on biotic assemblages in the Colorado 

River below Glen Canyon Dam, Arizona. Exposure in the varial zone reduced standing crops of 

periphyton, pondweed Potamogeton pectinatus, and benthic macroinvertebrates, and losses 

following the drawdown were not explained by expected seasonal trends. Losses in 

macroinvertebrate densities and mass and in periphyton mass and chlorophyll a suggest that 

effects of a sudden reduction in dam discharge of moderate duration and magnitude are 

comparable with losses associated with the varial zone of fluctuating daily flows. Compared with 

expected seasonal changes, abundance of rainbow trout Oncorhynchus mykiss increased during 

and following reduced flows. Proportional composition of fish less than 152 mm TL was greater 

after the drawdown, whereas the percentage of trout 406-558 mm declined. Relative condition 

factor before, during, and after the drawdown did not differ significantly for all fish combined, 

following a long-term pattern. However, among length-classes, condition of fish 305-405 mm 

TL declined following reduced flows. Feeding and composition of dietary items generally 

followed expected patterns of seasonal change and failed to correspond with changes in 

periphyton, macrophyte, and macroinvertebrate benthic densities after the drawdown. However, 

fewer rainbow trout ate Cladophora glomerata, and they ate less of this alga. In comparison, fish 

ate more gastropods following the drawdown than accounted for by long-term patterns, but 

frequency of occurrence was unchanged. Sudden reduction in flows of moderate duration and 

magnitude, although significantly reducing benthic assemblages, had little apparent negative 

short-term consequence for rainbow trout. 

Rogers, R.S., W.R. Persons and T. McKinney. 2003. Effects of a 31,000-cfs spike flow and 

low steady flow on benthic biomass and drift composition in the Lees Ferry tailwater. 

Cooperative Agreement 1425-98-FC-40-22690 (mod3). Arizona Game and Fish 

Department, Flagstaff, Arizona. Abstract excerpted from study discussion. 

McKinney et al. (1999a) reported that a controlled flood of brief duration and moderate 

magnitude (1,278 m3

/s[45,000 cfs]) in March 1996 influenced phytobenthic dynamics in the 

Lee’s Ferry tailwater by producing short-term reduction in macrophyte densities and distribution 

and reducing chlorophyll a concentrations in periphyton. We observed no short-term reduction in 

relative macrophyte distribution or effects on macrophyte densities or periphyton chlorophyll a 

after the 878 m3

/s spike flow in early May 2000. However, we were unable to sample periphyton 

in the permanently inundated zone until two months after the spike flow. 

It is likely that any short-term reduction in chlorophyll a had recovered within two 

months of the spike flow. An acceleration or pulse of regrowth following release of persistent 

individuals or new immigrants from competitive constraint is common in many post-disturbance 

recovery sequences in lotic algal communities (Peterson and Stevenson 1992). Shannon et al. 

(2001) observed recovery of phytobenthos on hard substrata on some sites within one month 

after the 1996 test flood. 
Humpback Chub Annotated Bibliography 93 September 2009

 

Lack of change in macrophyte density and distribution in the present study is probably 

because the 2000 spike flow was of lower magnitude than the 1996 flood. Changes in the 

macrophye community of the Lee’s Ferry tailwater between 1996 and 2000 may also have 

influenced its vulnerability during spike flows in 2000. The macrophyte community in 1996 was 

dominated by Chara spp. (McKinney et al. 1999a) and is presently dominated by Potamogeton 

spp. and Egeria densa (Benenati and Shannon 2000). Chara spp., a predominantly fall and 

winter species in the Lee’s Ferry tailwater, was largely senescent at the onset of the 1996 spike 

flow. Potamogeton spp. and Egeria densa are both predominant spring and summer species 

(Barrat-Segretain and Amoros 1995) and were in the early stages of development during the 

2000 spike flow. 

Although periphyton ash-free dry mass (AFDM) was similar in both seasonal trend and 

magnitude to that observed from 1991 to 1997, macrophyte AFDM peaked in the summer during 

2000 but peaked in the fall each year from 1994 to 1997. This change in seasonal pattern is best 

explained by the change in species composition from one dominated by Chara spp. in 1994 and 

1995 to that currently dominated by Potamogeton spp. and Egeria densa. Macrophyte AFDM 

was much higher and distribution more extensive in 2000 than in 1994-1997. It is likely that the 

stable flows increased the amount of suitable shoreline for macrophytes in 2000. 

Our results were consistent with Shannon et al. (1996) and showed that organic drift was 

reduced by steady flows. Although benthic densities of macroinvertebrates, periphyton, and 

macrophytes were not diminished by the spike flow in early May, total drift AFDM, which was 

dominated by filamentous algae, was significantly reduced and did not recover until mid-July. 

Schmidt, J.C., S.J. Topping, D.M. Rubin, J.E. Hazel and M. Kaplinski. 2007. Streamflow 

and sediment data collected to determine the effects of low summer steady flows and 

habitat maintenance flows in 2000 on the Colorado River between Lees Ferry and Bright 

Angel Creek, Arizona. U.S. Geological Survey, Reston, Virginia. 

The low summer steady flows (LSSFs) experiment of 2000 further demonstrated that 

spike flows released from Glen Canyon Dam redistribute sand from the channel bed and lower 

elevation parts of eddy sandbars to channel-margin deposits and the higher elevation parts of 

eddy sandbars. Unfortunately, summer 2000 was a period of unusually low tributary influx of 

sediment and there was little fine sediment (i.e., sand and finer material) available for 

redistribution. Nevertheless, the low steady flows, which held releases from the dam steady at 

230 m3

/s (8,100 ft3/s), during the summer of 2000 effectively retained on the channel bed the 

little sediment that was supplied by tributaries, and a subsequent 4-day, 870 m3/s (30,700 ft3/s) 

spike flow caused modest increases in the area of the mid-elevation zone of eddy sandbars. 

Speas, D W. 2004. Effects of low steady summer flows on rainbow trout in the Lee’s Ferry 

tailwater, 2000. Report to U.S. Geological Survey, Grand Canyon Monitoring and 

Research Center, Flagstaff, Arizona. 

To improve survival and growth of native fishes, an experimental combination of flows 

simulating seasonal floods and low steady summer flows were conducted during marchSeptember of 2000 in the Colorado River below the Glen Canyon Dam, Arizona. Diel flow 

fluctuations were essentially zero and mean daily discharge was 8,000 cfs from occasions during 
Humpback Chub Annotated Bibliography 94 September 2009

 

2000 to assess impacts of the steady flow experiment on CPUE, size structure, and condition 

factor of rainbow trout. Mean catch-per-unit-effort, condition, growth rates, and proportional 

stock density values for 2000 show no significant departure from those observed in recent years 

(1997-1999), but seasonal peaks in condition and appearance of YOY in the catch occurred 

several months earlier during 2000 than during previous year (1991-1999). Previous studies and 

stock assessment models predicted enhanced survival of wild spawned age < 1 fish under low 

daily flow fluctuations, but CPUE of age < fish during 2000 did not deviate significantly from 

those observed during the preceding 3 to 5 years. This lack of change may be attributed to both 

positive (stabilized flows) and negative (low flows) hydrologic forces acting simultaneously on 

early life history of trout, or it simply may be an artifact of low sample statistical power. We 

recommend that long-term monitoring sample sizes be increased in part to enhance statistical 

power for short-term experiments, and that future flow experiments consist of fewer hydrological 

treatments than those applied during 2000. 

Speas, D.W., W.R. Persons, R.S. Rogers, D.L. Ward, A.S. Makinster and J.E. Slaughter, 

IV. 2004. 2001 Fish Investigations in the Lee’s Ferry Tailwater. Report to U.S. Geological 

Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona. 

We present results of rainbow trout monitoring activities in the Lee’s Ferry tailwater 

(Colorado River below Glen Canyon Dam, AZ) during 2001. We also describe modifications 

made to monitoring strategies and techniques which were implemented to improve long-term 

monitoring programs. Objectives and subsequent findings are as follows: 

Objective 1: Monitor the trout fishery in the Lee’s Ferry reach to determine status and 

trends in abundance (population size and CPUE), population structure (size composition and 

proportional stock density, PSD), growth rate and relative condition (Kn). 

Data collected during 2001 indicate the Lee’s Ferry fishery is in a state of decline. High 

relative abundance of juvenile fish (< 305 mm) since 1997 coincide with declines in fish growth 

rates and proportional stock density [PSD; (# fish ≥ 406 mm TL/# fish ≥ 305 mm TL)*100]. 

Relative condition reached low levels unobserved since 1991. Over-recruitment, resource 

limitation (food, space) and density dependent growth have become problematic aspects of the 

fishery, particularly in relation to declining dam discharge since 1997. Flexibility in management 

objectives is needed to allow for maintenance of fish densities that will permit objectives for 

relative condition, growth and PSD to be attained over a range of flow regimes. Modifying flow 

regimes to limit rainbow trout recruitment should be evaluated as a means of making progress 

toward size structure, growth and condition objectives. 

Objective 2: Determine the relationship between Coffelt and Achilles electrofishing (EF) 

boats, measuring CPUE, Kn, PSD and catch size distribution so that linkages between the historic 

data (Coffelt) and data collected with the new gear type (Achilles) can be established. 

Despite conflicting results among three paired gear comparison trials, we can infer that 

catchability of the Achilles electrofishing boat is higher than that of the Coffelt boat. Regression 

analysis indicates that CPUE values obtained with the Coffelt boat are 72-83% of those collected 

by the Achilles, although there is much unexplained variation in this relationship. Uncertainties 
Humpback Chub Annotated Bibliography 95 September 2009

 

surrounding catchability of the two boats remain, particularly in relation to performance under 

various environmental conditions (flow regimen, weather, moon phase, food base elevation, etc.) 

and new EF output regulators. Alternative sampling strategies may need to be implemented to 

ensure continuity of the old (Coffelt-based) data series. For example, a single trip could be 

conducted annually with the Coffelt boat at the nine fixed sites to allow continuity of the old 

(pre-2002) data series. The remaining two or three trips per year could consist of sampling (N=9 

fixed and N=27 random sample sites per trip) sampling trips conducted with the Achilles 

electrofishing boats. 

Objective 3: Divide existing sample sites into smaller units that are representative of the 

larger sites for permanent inclusion in an augmented, serially alternating sampling design. 

Evaluate sample power gained by increasing sample size and predictive capability of habitat 

classifications. 

Most sub-sites were representative of their parent sample sites in that sub-site mean 

CPUE values were of similar magnitude as grand means and 95% confidence intervals always 

overlapped substantially with those of grand means. We recommend moving forward during 

2002 with selection of 27 random transects to augment the nine fixed sub-sites. 

Sample power increased two to three-fold with increasing sample size from nine to 33 

transects per trip during 2001. The present design appears capable of detecting moderate changes 

in CPE over the course of a single year. 

Hydrologic unit, substrate type, shoreline type, and surface velocity were often 

correlated. Shoreline type (talus, cobble bars, cliff faces, sand bars) is the most useful variable, 

because it can be used to stratify catch rates for random site selection and is a surrogate variable 

for substrate type and hydrologic units. Extensive geographic coverage of shoreline type is also 

available in electronic format (GCMRC GIS database). 

Objective 4: Develop and refine a repeatable, efficient and precise snorkel survey 

protocol for quantifying fish observations along the longitudinal axis of the shoreline for use in 

monitoring of trout relative density. Develop a method to measure fish distribution along the 

cross-sectional axis of the river. 

Compared with previous surveys (1998-2000), protocols developed during 2001 provide 

a balance between repeatability, precision, efficiency, standardization of area surveyed, and 

agreement with electrofishing. However, the utility of snorkeling as a monitoring tool for fish 

abundance depends on its ability to reflect changes in the fish population over time with the same 

level of confidence demonstrated by electrofishing and AGFD creel surveys. It is apparent that 

we should expect some seasonal discrepancy between electrofishing and snorkeling trends. We 

recommend that snorkel surveys (longitudinal surveys of EF transects, cross-section surveys, and 

visibility tests) be continued during 2002, with emphasis placed on variables that affect 

catchability of snorkeling (diel and seasonal variance in visibility, turbidity, light availability, 

fish behavior). 
Humpback Chub Annotated Bibliography 96 September 2009

 

CPE data from 2001 shows signs of saturation at or above 4.2 fish/min. At these 

densities more fish can be counted visually than can be captured by netting. Mechanisms that 

cause this saturation appear to vary by habitat type. On cobble bars, fish are stunned effectively 

but there are often too many to bring into the boat during a sample; on sand bars, fish are not 

stunned effectively, but can be counted easily by snorkeling. 

While snorkel/EF data comparisons during 2001 were not entirely conclusive, it is 

evident that catchabilities of both techniques vary among habitat type. For electrofishing, 

literature suggests that large particle substrate types generally favor electrofishing, whereas 

visibility tests in the present study suggests that fish are less visible in such areas, particularly 

over talus. Both hypotheses suggest that apparent trends in fish abundance among habitat types 

may be in part be caused by variable catchability coefficients. The extent to which these biases 

affect population estimates is unknown, and quantifying them would require additional 

electrofishing depletion experiments and more visibility tests. Surveys of fish distribution across 

the river channel take little time to complete and are essential for accurate population estimates. 

Objective 5: Estimate size of rainbow trout population in the Lee’s Ferry tailwater using 

electrofishing CPE and snorkel count data; compare magnitude and variability of the two 

estimates. 

Using habitat-stratified population models, there are an estimated 91,000 RBT > 

152 mm (95% CI = 55,000 – 149,000) in the Lees Ferry fishery based on near-shore estimates 

from electrofishing CPE. Use of abundance estimates from snorkel surveys in a similar model 

returns an estimate of 78,000 fish (95% CI = 54,000 – 114,000). Confidence intervals of the 

latter (snorkel-based) estimate are narrower than those from electrofishing, perhaps reflecting the 

ability to control sample error during individual transect snorkel surveys. Fish density modeled 

in relation to river mileage returns an estimate of 77,000 fish (95% CI = 44,000 – 110,000) based 

on electrofishing data, and 60,000 fish (95% CI = 31,000 – 93,000) based on snorkel data. 

Similarity of population estimates based on EF and snorkeling is likely coincidental, and 

further emphasizes the need to understand variance components (of a seasonal nature, in this 

case) of snorkel surveys. Had the population estimates been calculated from the October data, for 

example, estimates from electrofishing would have undoubtedly been greater than estimates from 

snorkeling because the latter data series suggested a 70% decline in trout abundance, whereas EF 

data showed no change. 

The accuracy of tailwater-scale population estimates depends heavily on accurate 

estimates of what proportion of fish along the cross-channel axis of the river is represented by 

densities in areas surveyed (either by snorkel or EF). Direct extrapolation—which makes the 

assumption that fish densities are uniform across the river channel—results in three to eight-fold 

overestimate of fish per river mile. The 1991 population estimate (which lacked cross-sectional 

fish density information) was used to formulate management recommendations, which state that 

a population consisting of 100,000 age 2+ rainbow trout should be maintained in the tailwater. 

Evidence from the present study indicates that this objective should be approximating 20,000 

fish. The population of RBT in the tailwater today exceeds this objective by a factor of 3 to 4.5. 
Humpback Chub Annotated Bibliography 97 September 2009

 

Declining growth, size structure and condition indices coincide with increased trout abundance 

over the past decade and supports the conclusion that the system is overpopulated. 

Existing objectives for growth, PSD and condition need to be reassessed for their 

attainability in relation to a given target population size. To ensure flexibility in management of 

the Lee’s Ferry fishery, we should establish objectives for population size that are specific to a 

range of discharge regimes and favorable for attaining population size structure (i.e., PSD) and 

Kn objectives. 

Trammell, M., R. Valdez, S. Carothers and R. Ryel. 2002. Effects of a low steady summer 

flow experiment on native fishes of the Colorado River in Grand Canyon, Arizona. SWCA 

Environmental Consultants. Final report to U.S. Geological Survey, Grand Canyon 

Monitoring and Research Center, Flagstaff, Arizona. 

Canyon Dam down the Colorado River through Marble Canyon and Grand Canyon. The 

purpose of the LSSF was to determine if low steady flows in summer would stabilize habitat and 

allow the Colorado River to warm sufficiently for increased growth and survival of the 

endangered humpback chub (Gila cypha) and other native fishes. The LSSF consisted of a high 

steady release of 17,000 cfs from April through May, with a 4-day spike of 30,000 cfs in early 

May, followed by steady releases of 8,000 cfs from June through September, with a 4-day spike 

of 30,000 cfs in early September. Data on species composition, relative abundance and 

distribution of fishes were gathered to provide a baseline for long-term monitoring and an 

evaluation of short-term response to the experimental flows. Systematic shoreline electrofishing 

and extensive mark-recapture efforts were used to gather data for stock-recruitment models to 

understand population dynamics as part of long-term monitoring. Concurrent periodic sampling 

with seines, hoop nets, and trammel nets was used to monitor short-term fish responses 

undetected by sampling schemes designed for long-term monitoring. The following is a 

summary of findings: 

 Distribution and relative abundance of native and nonnative fish species in eight 

longitudinal reaches of the Colorado River through Grand Canyon were described using a 

variety of gear types. Rainbow trout (Oncorhynchus mykiss) were the most abundant 

species in the upper reaches and dominated the catch by electrofishing and netting. 

Fathead minnow (Pimephales promelas) and speckled dace (Rhinichthys osculus) were 

the most abundant species in the lower reaches and dominated the catch by seining. Adult 

humpback chub, bluehead sucker (Catostomus discobolus), flannelmouth sucker 

(Catostomus latipinnis), and brown trout (Salmo trutta) were locally abundant at 

aggregations. YOY native sucker were distributed throughout the study area. 

 Efforts to calibrate trammel net catch rates of native fishes by comparing these to 

simultaneous removal estimators failed. Removal of native fishes from given habitats 

(e.g., large eddies) was ineffective because of our inability to block and sample the entire 

habitat. Fish moved to deep swift water, which could not be sampled. Mark-recapture 

estimates on a small scale were also ineffective because movement of fish to and from 

the sample area violated the assumptions of sample population closure. Calibration of 

trammel net catches of native fishes, using short-term abundance estimators, does not 
Humpback Chub Annotated Bibliography 98 September 2009

 

appear possible. However, it may be possible to calibrate catch rates with long-term 

mark-recapture estimates. 

 The humpback chub aggregation near 30-Mile was not found during the LSSF of 2000. 

In 1993, 26 adults were captured and this aggregation was estimated at 52 adults (95% 

CI=28–136), which was the 4th largest aggregation identified in the Colorado River 

through Grand Canyon. Also, 14 YOY (18–31 mm TL) humpback chub were collected 

and preserved from a school of approximately 100 at a warm shoreline spring at RM 30.8 

on July 14, 1994, indicating successful reproduction by this aggregation. Failure to locate 

this aggregation is cause for concern over loss of a unique stock of mainstem fish. 

Sampling should continue in this area to determine if the aggregation has been lost or has 

relocated to other suitable habitat, possibly in one of the other nearby warm springs 

associated with Fence Fault and Eminence Grabens. 

 Mark-recapture population estimates of humpback chub in Middle Granite Gorge (MGG) 

in 2000 derived an estimated 107.7 fish/mile, compared to a density of 31.1 fish/mile in 

1993. These estimates indicate a three-fold increase in numbers of humpback chub at the 

MGG aggregation in the past 8 years. Average length and range in length were similar for 

the two sample periods, and estimated maximum age of these fish was 7–9 years, 

indicating ongoing recruitment to this aggregation. The source of this recruitment is not 

known, but could be from local mainstem reproduction or downstream drift from the 

LCR. There are no known warm mainstem springs near or immediately upstream of 

MGG, and the possibility of these fish originating from thermal springs is discounted. 

 Size of humpback chub at the time of transition from the LCR to the mainstem was 

determined from temperature checks and first annuli on scales. Average size at transition 

was 83 mm TL, with a minimum of 69 mm TL (compared to mean of 74 mm TL and 

minimum of 52 mm TL reported in 1995). Current data suggest that fish smaller than 

about 69 mm TL do not survive the transition from the warm LCR to the cold mainstem. 

Similar growth checks in fish captured from the LCR suggest stress-related growth 

checks resulting from summer flooding. Similar lengths at first annuli and circuli 

disruptions suggest that fish successfully recruiting in the mainstem likely remained in 

the LCR until age 1. 

 Growth patterns of YOY flannelmouth sucker and bluehead sucker were inconclusive 

during the LSSF because protracted spawning infused newly-hatched larvae into samples 

and kept average YOY lengths depressed. 

 Mean mainstem temperatures were 1.4–3.0°C warmer than under previous dam 

operations (MLFF), and mean backwater temperatures were 0.3–5.3°C warmer; hence, a 

marked warming effect was observed. Longitudinal downstream warming greater than 

that during MLFF was observed. 

 Catch-Per-Effort (CPE) of bluehead sucker, and flannelmouth sucker was significantly 

higher in August 2000 than in July/August from 1991–1997. Fathead minnow CPE was 

much higher than previous levels but the differences were not significant due to greater 
Humpback Chub Annotated Bibliography 99 September 2009

 

variation in CPE. The increase in abundance was likely a result of the warmer, more 

suitable temperatures, which may have affected reproduction and survival. Following the 

September flow spike, CPE of all species declined. However, fathead minnow CPE was 

nearly identical with previous years while CPE of native fishes remained significantly 

higher, suggesting the flow spike was disproportionately detrimental to fathead minnow. 

 No population estimate or depletion of channel catfish (Ictalurus punctatus) in the LCR 

confluence area could be made. Few channel catfish and several humpback chub were 

caught. This effort should be repeated and timed to correspond with catfish spawning 

times, which probably occurred after the sample period of May 31 to June 5. 

Valdez, R.A. 1994. Effects of interim flows from Glen Canyon Dam on the aquatic 

resources of the lower Colorado River from Diamond Creek to Lake Mead: Phase I. 

Bio/West, Inc., Final report to Glen Canyon Environmental Studies. 

An investigation of the aquatic resources of the Colorado River from Diamond Creek 

(RM 226) to below Pearce Ferry (RM 286) in Lake Mead, was initiated in May of 1992 by the 

Hualapai Wildlife Management Department, with technical assistance from BIO/WEST, Inc. 

The purpose of this investigation was to determine the effects of interim flow releases from Glen 

Canyon Dam, located about 240 miles upstream of the upper end of the study reach. Seven 

research trips were conducted from June 1992 to December 1993 to sample fishes, 

macroinvertebrates, water quality, and to monitor variability in river stage associated with flow 

changes. 

 River stage changes recorded each sampling trip showed maximum daily changes of 

about 60 cm, and 90 cm over a 3-day period. Most daily changes in narrow canyon reaches were 

40 to 60 cm. and 20–30 cm in more alluvial downstream reaches where stage changes was 

ameliorated by Lake Mead. River fluctuations in the study area were regular and cyclic, with 

lows of 8,000–10,000 cfs between 2:00 am and 4:00 am, and highs of 13,000–15,000 cfs 

between 11:00 am and 1:00 pm. As measured at the Diamond Creek gage. 

 Conductivity, water temperature, pH, and dissolved oxygen concentrations were 

measured in the mainstem and in some tributaries with a constant recording Hydrolab Surveyor 

II or Datasonde with datalogger. Turbidity was measured in the mainstem with a secchi disk. 

Maximum mainstem water temperature change through the study area in 1992 was 3°C, from 

17°C at Travertine Canyon (RM 229.0) on June 24 to 20°C at Grand Wash Cliffs (RM 276.0) on 

July 1. Surface temperature at Pearce Ferry was 24.5 to 26.0°C on July 1. Water temperature 

ranged from 15.0°C at Bridge Canyon (RM 235.0) on September 27, to 23.0°C at Pearce Ferry 

(RM 280.0) on October 7. December water temperatures ranged from 8.6°C at Bridge Canyon 

on December 1, to 10.2°C at Scorpion Island (RM 277.5) on December 11. 1992. Mainstem 

temperature in 1993 was similar and varied from about 8.5°C in December to about 20°C in 

September. Temperature of Spencer Creek varied from about 14°C in December to about 29°C 

in June. 

 Benthic and drifting macroinvertebrates sampled in the Colorado River and tributaries 

showed relatively low drift densities in the mainstem, and high benthic and drift densities in 
Humpback Chub Annotated Bibliography 100 September 2009

 

Spencer Creek. Densities of drifting macroinvertebrates in Spencer Creek were 40 to 200 times 

those of the mainstem. Terrestrial and other aquatic forms of macroinvertebrates were dominant, 

and when compared to more upstream samples show that drift changes longitudinally 

downstream. Chironomids, simulids, and Gammarus lacustris were less common than in 

upstream reaches. 

 Fish sampling was conducted in the Colorado River as well as the following tributaries: 

Diamond Creek, Travertine Falls, Spencer Creek, Surprise Canyon, Lost Creek, and 

Quartermaster Canyon. Fish were collected with seven primary gear types including 

electrofishing, gill nets, trammel nests, hoop nets, minnow traps, seines, and angling. Nineteen 

species of fish were captured representing 10 families. Only four of these species, humpback 

chub (Gila cypha), speckled dace (Rhinichthys osculus) flannelmouth sucker (Catostomus 

latipinnis), and bluehead sucker (Catostomus discobolus), are native to the Colorado River 

Basin. Carp and channel catfish were the most common species in the Colorado River, moving 

into the study area in large numbers in spring. Red shiners, fathead minnows, and mosquitofish 

were consistently most common in tributaries, and plains killifish were found in local 

aggregations. Striped bass, largemouth bass, green sunfish, black crappie, bluegill, threadfin 

shad, and walleye were lake species that were found in small numbers in tributaries or Separation 

Canyon in spring. The endangered species, razorback sucker (Xyrauchen texanus), Colorado 

squawfish (Ptychocheilus lucius), and bonytail (Gila elegans), were not seen or captured, and 

only one humpback chub was captured at RM 253.2. 

 Few studies have been conducted on the aquatic resources of this lower reach of the 

Colorado River in Grand Canyon. Fish species composition showed that the reach below Bridge 

Canyon was dominated by nonnative species, with a large influence from the Lake Mead 

ichthyofauna. Densities of fish upstream of Bridge Canyon were relatively low. Young 

flannelmouth suckers and bluehead suckers in tributaries indicate that these may be the only 

suitable locations for successful reproduction by native species in the area. Mainstem habitats 

may be too altered by sediment deposits or temperature modifications to provide suitable 

conditions, and the large number of nonnative species limits the chances for survival of young 

native fishes. 

 Sampling in Spencer Creek indicated that a series of waterfalls about 2 miles upstream of 

the outflow was a barrier to upstream movement, and the only species found above these falls 

was the native speckled dace. Perennial flow, good water quality, and good stream habitat make 

this tributary a suitable candidate as an introduction site for young razorback suckers, 

particularly above this fish barrier, since the area downstream is dominated by predaceous 

nonnatives and invaded in spring by channel catfish and carp. Young fish released above the 

water falls and allowed to grow past the size of predator susceptibility could use the Lake Mead 

inflow as adult habitat. The chances for successful reproduction and recruitment by these stocks 

cannot be assessed at this time but would be greatly reduced below fish barriers by large 

numbers of nonnative fishes in the region. 

 This investigation revealed that interim flows continue to be manifested as fluctuating 

river stages of as much as 90 cm just above the Lake Mead inflow, about 250 miles of Glen 

Canyon Dam. While these changes may destabilized shoreline habitats and periodically affect 
Humpback Chub Annotated Bibliography 101 September 2009

 

fish access to tributaries, no direct relationships have been identified to current fish population 

distributions and levels. Although this region of the Colorado River is far enough downstream 

from the dam to allow for longitudinal warming of river temperatures, effects of cold releases on 

primary and secondary production extend into this region, limiting food resources for fish. The 

preliminary determination from this investigation is that interim flows alone do not appear to 

detrimentally impact aquatic resources of the area. Instead, the synergistic effect of fluctuating 

flows, low temperatures, absence of spring runoff, and particularly nonnative fishes, has affected 

the riverine ecosystem throughout Grand Canyon. Effects of interim flows to the lower 45 miles 

of the study area, downstream of Bridge Canyon, are overwhelmed by fluctuating levels of Lake 

Mead, massive sediment deposits that have altered channel geomorphology, and the abundance 

nonnative fishes residing in the reservoir. 

Valdez, R.A. and S.W. Carothers. 1998. The aquatic ecosystem of the Colorado River in 

Grand Canyon. Final report of SWCA, Inc., Flagstaff, Arizona, to U.S. Bureau of 

Reclamation, Upper Colorado Region, Salt Lake City, Utah. 

Introduction- The U.S. Fish and Wildlife Service’s 1995 Biological Opinion on the 

operation of Glen Canyon Dam found that current and proposed dam operations continue to 

jeopardize two endangered species within Grand Canyon: razorback sucker and humpback chub. 

Existing data on the population status of these two species indicate that the razorback sucker is 

virtually extinct in Grand Canyon and the humpback chub- although reproducing in the Little 

Colorado River- has been declining in number over a 35 year period of record. 

 In their Biological Opinion, the U.S. Fish and Wildlife Service identified a “Reasonable 

and Prudent Alternative” to the preferred alternative of the Environmental Impact Statement on 

the operation of Glen Canyon Dam. The preferred alternative was a regime of modified low 

fluctuating flows (MLFF). The Reasonable and Prudent Alternative recommends a seasonally 

adjusted steady flow experiment within the context of the MLFF and undertaken through the 

Adaptive Management Program. 

 The steady flow experiment would consist of sustained high releases during the period of 

April-May, followed by low steady releases during June–October. The high releases would be 

designed to pond tributary inflows and provide warm nursery habitats for young native fish 

descending from tributaries. The low releases would be designed to enhance habitat conditions 

for native fishes by stabilizing and warming mainstem and nearshore habitats, including 

backwaters (i.e., eddy return-current channels). Experimental steady flows would be released 

only during low-release years (i.e., <8.23 million acre feet) over “a sufficient period of time to 

allow for experimental design, biological processes to function and for variability inherent in 

riverine ecosystems to be expressed. The number of years is, therefore, indeterminate.” As a 

preliminary step toward the design of such an experiment, SWCA, Inc. Environmental 

Consultants was retained by the Bureau of Reclamation to summarize and evaluate known 

information about native and non-native fishes in Glen and Grand Canyons with the following 

objectives: 

 Summarize known information that would help predict responses by endangered and 

other native fishes to steady flows; 
Humpback Chub Annotated Bibliography 102 September 2009

 

 Identify information that is still needed to understand the relationship of fish and dam 

release patterns (data gaps); and 

 Frame testable hypotheses for research designed to acquire the needed information. 

To this end, we reviewed the existing knowledge on aquatic ecosystems in Glen and 

Grand Canyons and synthesized that information so the following questions could be addressed: 

 Do sufficient baseline data exist to evaluate the influence of the steady flow experiment 

described in RPA? 

 Do existing data indicate that the steady flow experiment will likely have an overall 

positive influence on endangered and other native fishes in Grand Canyon? 

Results- The best available scientific information indicates that primary and secondary 

production have been highest under short-term steady or low fluctuating flows, and lowest under 

high fluctuating releases. However, drift of algae and macroinvertebrates, a major food source 

of fishes, has generally been higher during fluctuating flows than during short-term steady flows, 

but the effect of long-term steady flows on drift, water clarity, and temperature, such as proposed 

in the experiment, have not been evaluated or modeled. Available data also indicate that, 

although cold mainstem temperatures and fluctuating flows have limited reproduction and 

perhaps survival of endangered and other native fishes, these flow variables have also limited 

invasion and proliferation of warm-water nonnative competing and predaceous fishes. Cold 

mainstem water temperatures have also limited the spread of recently introduced parasites, 

particularly the potentially lethal Asian tapeworm (Bothriocephalus acheilognathi), which has 

become prevalent in cyprinid fishes of the LCR. 

Except for temperature and possibly turbidity, water quality parameters currently found 

in the Colorado River in Grand Canyon are not limiting to native fishes. Availability of suitable 

food for each life stage of fish has been considered a potentially important limiting factor; 

however, clear evidence of food limitations in Grand Canyon is lacking. Most studies of fish 

diet report few empty stomachs, and potential food supplies appear to be fairly abundant from 

drift and benthic macroinvertebrate studies. Nonetheless, a few observations have been made of 

possible food shortages for specific life stages of some species. Because of cold mainstem 

temperatures, the only known spawning habitats of native fishes in Grand Canyon are tributaries 

or warm springs. We believe that most larval flannelmouth suckers, bluehead suckers, and 

humpback chub descending from warm natal tributaries into the cold mainstem die of thermal 

shock or from predation elicited by erratic swimming behavior. For those fish old enough to 

survive the transition, swimming ability may be reduced by as much as 98% by cold mainstem 

temperatures. This reduced swimming ability, combined with reduced turbidity for cover, 

greatly advantage cold-water sight predators, such as rainbow trout and brown trout. Juvenile 

native along sheltered shoreline habitats are often forced to move to alternative locations by 

changing river stage, increasing exposure to predators and needless energy expenditure. 
Humpback Chub Annotated Bibliography 103 September 2009

 

The degree to which nonnative fish species have negatively affected native fish 

population in Grand Canyon through predation and competition has been clearly demonstrated. 

Nonnative fishes do prey on native fishes in Grand Canyon. Brown trout, channel catfish, 

rainbow trout, and black bullheads are the principle predators of native fish. The extent of this 

predation is not known, but predator-prey models suggest it is substantial. Competition between 

native fishes and nonnative fishes is implied by extensive overlap in diet and sympatry in many 

habitats for all life stages; however, data on abundances, distribution, and habitat use by 

nonnative species in Grand Canyon is patchy because life history studies of these fishes have not 

been conducted in the canyon. 

Without knowing more about native/nonnative interactions under existing flow 

conditions (i.e., low fluctuating flows), it is difficult to predict which, if either group of fishes 

would benefit more from steady flows. We cannot predict the outcome for endangered and other 

native fishes if, indeed, nonnative predators and competitors increase in abundance, but all 

available evidence suggests a detrimental effect on native species unless these species receive 

substantially disproportionate benefits from the flows. By their nature, nonnative fishes have a 

more variable range of life history requirements that tends to make them more tolerant and 

resilient to disturbances that the native fishes in Grand Canyon. Hence, flow modifications, even 

if they resemble historic regimes, may directly benefit native fishes, but may also benefit 

nonnative forms. This could result in overall, long-term negative effects on the native species. 

Valdez, R.A., B.R. Cowdell and E. Pratts. 1995. Effects of interim flows from Glen 

Canyon Dam on the aquatic resources of the lower Colorado River from Diamond Creek to 

Lake Mead: Phase II, Bio/West, Inc., Final report to Glen Canyon Environmental Studies. 

An investigation of the aquatic resources of the Colorado River from Diamond Creek 

(RM 226) to below Pearce Ferry (RM 286) in Lake Mead, was initiated in May of 1992 by the 

Hualapai Wildlife Management Department, with technical assistance from BIO/WEST, Inc. 

The purpose of this investigation was to determine the effects of interim flow releases from Glen 

Canyon Dam on aquatic resources of the region of the Colorado River bordered by the Hualapai 

Indian Reservation. Eleven research trips were conducted from June 1992 through January 1995 

to sample fishes, macroinvertebrates, water quality, and to monitor variability in river stage 

associated with flow changes. The first nine trips were conducted from Diamond Creek to 

Pearce Ferry, and the last two trips extended sampling upstream to National Canyon. The 

Colorado River forms 109 miles of the northern boundary of the Hualapai Indian Reservation 

from near National Canyon (RM 164.5) to near Emery Falls Canyon (RM 273.5). A Phase I 

Report (Valdez 1994) presented findings for the first seven trips. This Phase II Report presents 

the integration of data from all 11 trips. 

 River stage recorded each sampling trip showed a maximum vertical change of about 60 

cm for 24 hours, and a net change of about 90 cm over a 3-day period. Most daily changes were 

40 to 60 cm in narrow canyon reaches, and 20-30 cm in more alluvial downstream reaches where 

stage changes was ameliorated by Lake Mead. River fluctuations in the study area were regular 

and cyclic, with lows of 8,000 to 10,000 cfs between 2:00 am and 4:00 am, and highs of 13,000 

to 15,000 cfs between 11:00 am and 1:00 pm, as measured at the Diamond Creek gage. 
Humpback Chub Annotated Bibliography 104 September 2009

 

 Conductivity, water temperature, pH, and dissolved oxygen concentrations were 

measured in the mainstem and in some tributaries with a constant recording Hydrolab Surveyor 

II or Datasonde with datalogger. Turbidity was measured in the mainstem with a secchi disk. 

Maximum mainstem water temperature change in summer was about 3°C, from 17°C at 

Travertine Canyon (RM 229.0) on June 24, 1992 to 20°C at Grand Wash Cliffs (RM 276.0) on 

July 1. Maximum surface temperature at Pearce Ferry was 24.5 to 26.0°C on July 1. Water 

temperature in fall (September-October) was typically isothermal at about 13.0°C to 16°C from 

the river to Pearce Ferry, while December temperature was usually warmer, from 8°C to 10°C, 

and January temperature was usually colder near Pearce Ferry, from 10°C to 8°C. Temperature 

of Spencer Creek varied from about 14°C in December to about 29°C in June. 

 Benthic and drifting macroinvertebrates sampled in the Colorado River and tributaries 

showed relatively low drift densities in the mainstem, and high benthic and drift densities in 

Spencer Creek. Densities of drifting macroinvertebrates in Spencer Creek were 40 to 200 times 

those of the mainstem. Terrestrial and other aquatic forms of macroinvertebrates were dominant, 

and when compared to more upstream samples show that drift changes longitudinally 

downstream. Chironomids, simuliids, and Gammarus lacustris were less common than in 

upstream reaches. 

 Fish sampling was conducted in the Colorado River as well as the following tributaries: 

Diamond Creek, Travertine Falls, Spencer Creek, Surprise Canyon, Lost Creek, and 

Quartermaster Canyon. Fish were collected with seven primary gear types including 

electrofishing, gill nets, trammel nests, hoop nets, minnow traps, seines, and angling. Nineteen 

species of fish were captured representing 10 families. Only four of these species, humpback 

chub (Gila cypha), speckled dace (Rhinichthys osculus) flannelmouth sucker (Catostomus 

latipinnis), and bluehead sucker (Catostomus discobolus), are native to the Colorado River 

Basin. Carp and channel catfish were the most common species in the Colorado River, moving 

into the study area in large numbers in spring. Red shiners, fathead minnows, and mosquitofish 

were consistently most common in tributaries, and plains killifish were found in local 

aggregations. Striped bass, largemouth bass, green sunfish, black crappie, bluegill, threadfin 

shad, and walleye were lake species that were found in small numbers in tributaries or Separation 

Canyon in spring. The endangered species, razorback sucker (Xyrauchen texanus), Colorado 

squawfish (Ptychocheilus lucius), and bonytail (Gila elegans), were not seen or captured, and 

only one humpback chub was captured at RM 253.2; the fish probably dispersed downstream 

from a central population at the Little Colorado River inflow about 19.1.9 miles upstream. 

 Few studies have been conducted on the aquatic resources of this lower reach of the 

Colorado River in Grand Canyon. Fish species composition showed that the reach below Bridge 

Canyon was dominated by nonnative species, with a large influence from the Lake Mead 

ichthyofauna. Densities of fish upstream of Bridge Canyon were relatively low. Young 

flannelmouth suckers and bluehead suckers in tributaries indicate that these may be the only 

suitable locations for successful reproduction by native species in the area. Mainstem habitats 

may be too altered by sediment deposits or temperature modifications to provide suitable 

conditions, and the large number of nonnative species limits the chances for survival of young 

native fishes. 
Humpback Chub Annotated Bibliography 105 September 2009

 

 Sampling in Spencer Creek indicated that a series of waterfalls about 2 miles upstream of 

the outflow was a barrier to upstream movement, and the only species found above these falls 

was the native speckled dace. Perennial flow, good water quality, and good stream habitat make 

this tributary a suitable candidate as an introduction site for young razorback suckers, 

particularly above this fish barrier, since the area downstream is dominated by predaceous 

nonnatives and invaded in spring by channel catfish and carp. Young razorback suckers released 

above the water falls and allowed to grow past the size of predator susceptibility could use the 

Lake Mead inflow as adult habitat. The chances for successful reproduction and recruitment by 

these stocks cannot be assessed at this time but would be greatly reduced below fish barriers by 

large numbers of nonnative fishes in the region. 

 This investigation revealed that interim flows continue to be manifested as fluctuating 

river stages of as much as 90 cm just above the Lake Mead inflow, about 250 miles of Glen 

Canyon Dam. While these changes may destabilized shoreline habitats and periodically affect 

fish access to tributaries, no direct relationships have been identified to current fish population 

distributions and levels. Although this region of the Colorado River is far enough downstream 

from the dam to allow for longitudinal warming of river temperatures, effects of cold releases on 

primary and secondary production extend into this region, limiting food resources for fish. The 

preliminary determination from this investigation is that interim flows alone do not appear to 

detrimentally impact aquatic resources of the area. Instead, the synergistic effect of fluctuating 

flows, low temperatures, absence of spring runoff, and particularly nonnative fishes, has affected 

the riverine ecosystem throughout Grand Canyon. Effects of interim flows to the lower 45 miles 

of the study area, downstream of Bridge Canyon, are overwhelmed by fluctuating levels of Lake 

Mead, massive sediment deposits that have altered channel geomorphology, and the abundance 

nonnative fishes residing in the reservoir. Commercial motorized boat traffic (i.e., large jet 

boats) that transport rafters across flatwater areas (Bridge Canyon to Pearce Ferry) generate 

sudden and fast-moving waves that may erode banks and destabilize shorelines to a greater 

degree than dam operations. 

Valdez, R.A., T.L. Hoffnagle, C.D. McIvor, T. McKinney and W.C. Liebfried. 2001. Effects 

of a test flood on fishes of the Colorado River in Grand Canyon, Arizona. Ecological 

Applications 11:686-700. 

A beach/habitat-building flow (i.e., test flood) of 1,274 m3

/s, released from 

Glen Canyon Dam down the Colorado River through Grand Canyon, had little effect on 

distribution, abundance, or movement of native fishes, and only short-term effects on densities of 

some nonnative species. Shoreline and backwater catch rates of native fishes, including juvenile 

humpback chub (Gila cypha), flannelmouth suckers (Catostomus latipinnis), and bluehead 

suckers (C. discobolus), and all ages of speckled dace (Rhinichthys osculus), were not 

significantly different before and after the flood. Annual spring spawning migrations of 

flannelmouth suckers into the Paria River and endangered humpback chub into the LCR took 

place during and after the flood, indicating no impediment to fish migrations. Pre-spawning 

adults staged in large slack water pools formed at the mouths of these tributaries during the 

flood. Net movement and habitat used by nine radio-tagged adult humpback chub during the 

flood were not significantly different from prior observations. Diet composition of adult 

humpback chub varied, but total biomass did not differ significantly before, during, and after the 
Humpback Chub Annotated Bibliography 106 September 2009

 

flood, indicating opportunistic feeding for a larger array of available food items displaced by the 

flood. Numbers of nonnative rainbow trout (Oncorhynchus mykiss) ,152 mm total length 

decreased by 8% in electrofishing samples from the dam tailwaters (0–25 km downstream of the 

dam) during the flood. Increased catch rates in the vicinity of the LCR (125 km downstream of 

the dam) and Hell’s Hollow (314 km downstream of the dam) suggest that these young trout 

were displaced downstream by the flood, although displacement distance was unknown since 

some fish could have originated from local populations associated with intervening tributaries. 

Abundance, catch rate, body condition, and diet of adult rainbow trout in the dam tailwaters were 

not significantly affected by the flood, and the flood did not detrimentally affect spawning 

success; catch of YOY increased by 20% in summer following the flood. Post-flood catch rates 

of nonnative fathead minnows (Pimephales promelas) in shorelines and backwaters, and plains 

killifish (Fundulus zebrinus) in backwaters decreased in the vicinity of the LCR, and fathead 

minnows increased near Hell’s Hollow, suggesting that the flood displaced this nonnative 

species. Densities of rainbow trout and fathead minnows recovered to pre-flood levels eight 

months after the flood by reinvasion from tributaries and reproduction in backwaters. We 

concluded that the flood was of insufficient magnitude to substantially reduce populations of 

nonnative fishes, but that similar managed floods can disadvantage alien predators and 

competitors and enhance survival of native fishes. 

Weiss, J. 1992. The relationship between flow and backwater fish habitat of the Colorado 

River in Grand Canyon. Draft report. Glen Canyon Environmental Studies, Bureau of 

Reclamation, Flagstaff. pp 13. Abstract excerpted from study introduction and results. 

The purpose of this study was to assess the size and number of backwaters at different 

flow levels in order that a recommendation might be made on a flow level that would optimize 

conditions for native fishes. 

Colorado River backwaters are an important nursery and resting area for both native and 

introduced fishes. Since the construction of Glen Canyon Dam, backwaters are the only portion 

of the mainstem offering warm water for successful rearing, higher productivity, lower current, 

refugia from predatory fishes, and other characteristics needed for optimum growth. 

In 1991, backwater numbers decreased from 36 at 5,000 cfs to 9 at 15,000 cfs. The total 

area of backwaters at 5,000 cfs was 32,301 m2

, and decreased to 5,708 m2 at 15,000 cfs, (18% of 

the backwaters at 5000 cfs). The total number of backwaters decreases with an increase in 

discharge. At 15,000 cfs, there were 8 connected backwaters and 1 isolated backwater. There 

were 32 return channels at 5,000 cfs, and at 15,000 cfs there were 8 return channels. 

 There was a four-fold increase in the number of backwaters at 4,800 cfs (130) as 

compared with the backwaters present at 28,000 cfs (20) in 1985. When availability of 

backwaters was examined at 28,000 cfs, RM 61.5–77 contained only 4 connected backwaters 

(2.1% of all backwaters). At 4,800 cfs, there were 78 connected backwaters (15.7%), a twentyfold increase. 

 A comparison of backwaters with the 11 geomorphic reaches as defined by Schmidt and 

Graf (1988) was performed. The reaches are based on the types of bedrock exposed at river 
Humpback Chub Annotated Bibliography 107 September 2009

 

level. Because channel characteristics of the Colorado River vary with the types of bedrock that 

are exposed, these reaches may reflect backwater size and abundance. The analysis showed that 

the most numerous numbers of backwaters occurred in the widest reaches, which are reaches 4.5 

and 10. This occurred in the 1985 4,800 cfs flow and the 1991 5,000 cfs flow. The 1991 data at 

15,000 cfs flow and the 1992 8000 cfs flow showed the highest number of backwaters remaining 

in reaches: 4 and 10, respectively. 

4.2 EFFECTS ON SEDIMENT AND DEBRIS DEPOSITION 

Benenati, E.P., J.P. Shannon, J.S. Hagan and D.W. Blinn. 2001. Drifting fine particulate 

organic matter below Glen Canyon Dam in the Colorado River, Arizona. Journal of 

Freshwater Ecology 16(2):235–248. 

The concentration and composition of drifting fine particulate organic matter (FPOM) in 

regulated rivers may be influenced by dam operations and site of collection within the river 

channel. The authors examined FPOM composition and biomass in the Colorado River, Arizona 

below Glen Canyon Dam along a 350 km reach during 15 collection trips over four years. Lotic 

zooplankton and detritus components were positively correlated with distance downriver from 

the dam, increased discharge, and near-shore habitats versus mid-channel locations. Lentic 

zooplankton also increased at higher discharges and in near-shore habitats but was negatively 

correlated with distance downriver. There is evidence that the near-shore habitat provides a more 

stable environment than the mainstem for invertebrates which may enhance rearing and 

development of lentic zooplankton. 

Dexter, L.R. and B.L. Cluer. 1999. Cyclic erosional instability of sandbars along the 

Colorado River, Grand Canyon, Arizona. Annals of the Association of American 

Geographers 89(2):238-266. 

The study and management of regulated rivers have become important issues. A prime 

example is Glen Canyon Dam and its operational impacts on the downstream environment in 

Grand Canyon National Park, Arizona. We present an overview of the Glen Canyon Dam 

environmental issue, a novel methodology for monitoring dam impacts on alluvial sediments, 

and three years of study relating to the stability of alluvial deposits along the Colorado River. 

This research uses oblique photographs taken daily, automatically, from twenty-one fixedposition programmable cameras. Digital image-processing techniques created planimetric 

models of sandbar area from the photos for the period of March 1993 through May 1995. The 

technique allowed daily tracking of sandbar areas for detection of rapid erosional events. We 

demonstrated that rapid erosional events occur commonly on Grand Canyon sandbars. Sandbars 

are unstable over the study period, especially the first two years. Most of the rapid erosional 

events are associated with weekend or seasonal reduction in flow. Sandbar area frequency is 

bimodal with negative kurtosis, indicating that measurements taken at long time-steps are not 

likely to document mean area but rather minima or maxima. Time-series analysis suggests that 

periods of relative stability occur between rapid area-reducing events. Sandbars appear to adjust 

in two modes, a short-term adjustment mode occurring over hours and a long-term adjustment 

mode over days to weeks. The understanding and minimization of rapid-failure events should be 
Humpback Chub Annotated Bibliography 108 September 2009

 

increased, and the phenomenon needs to be addressed in any comprehensive sediment 

management plan. 

Grams, P.E., J.C. Schmidt and D.J. Topping. 2007. The rate and pattern of bed incision 

and bank adjustment on the Colorado River in Glen Canyon downstream from Glen 

Canyon Dam, 1956-2000. Bulletin of the Geological Society of America 119(5):556–575. 

Closure of Glen Canyon Dam in 1963 transformed the Colorado River by reducing the 

magnitude and duration of spring floods, increasing the magnitude of base flows, and trapping 

fine sediment delivered from the upper watershed. These changes caused the channel 

downstream in Glen Canyon to incise, armor, and narrow. This study synthesizes over 45 yr of 

channel-change measurements and demonstrates that the rate and style of channel adjustment are 

directly related to both natural processes associated with sediment deficit and human decisions 

about dam operations. Although bed lowering in lower Glen Canyon began when the first 

cofferdam was installed in 1959, most incision occurred in 1965 in conjunction with 14 pulsed 

high flows that scoured an average of 2.6 m of sediment from the center of the channel. The 

average grain size of bed material has increased from 0.25 mm in 1956 to over 20 mm in 1999. 

The magnitude of incision at riffles decreases with distance downstream from the dam, while the 

magnitude of sediment evacuation from pools is spatially variable and extends farther 

downstream. Analysis of bed-material mobility indicates that the increase in bed-material grain 

size and reduction in reach-average gradient are consistent with the transformation of an 

adjustable-bed alluvial river to a channel with a stable bed that is rarely mobilized. Decreased 

magnitude of peak discharges in the post-dam regime coupled with channel incision and the 

associated downward shifts of stage-discharge relations have caused sandbar and terrace erosion 

and the transformation of previously active sand-bars and gravel bars to abandoned deposits that 

are no longer inundated. Erosion has been concentrated in a few pre-dam terraces that eroded 

rapidly for brief periods and have since stabilized. The abundance of abandoned deposits 

decreases downstream in conjunction with decreasing magnitude of shift in the stage-discharge 

relations. In the downstream part of the study area where riffles controlling channel elevation 

have not incised, channel narrowing has resulted from decreased magnitude of peak discharges 

and minor post-dam deposition. These physical changes to the aquatic and riparian systems have 

supported the establishment and success of an artifact ecosystem dominated by non-native 

species. Models for the channel response downstream from large dams typically consider factors 

such as the degree of sediment deficit, the pre-dam surface and subsurface grain size, and the 

magnitude of post-dam average flows. These results suggest that it is also necessary to consider 

(1) the possibility of variable responses among different channel elements and (2) the potential 

importance of exceptional flows resulting from management decisions. 

Howard, A. and R. Dolan. 1981. Geomorphology of the Colorado River in the Grand 

Canyon. Journal of Geology 89:269–298. 

Sediment supplied to the Colorado River within the Grand Canyon has been sorted into 

distinct deposits of three grain size ranges. The major rapids are formed by boulder deposits 

from side-canyon tributaries. As a result of a fourfold reduction in peak discharge when Glen 

Canyon Dam was closed in 1963, new fan debris may increase the gradient through some of the 

rapids by a factor of 1.8. Cobbles and gravel, transported only during flood stages, are 
Humpback Chub Annotated Bibliography 109 September 2009

 

preferentially deposited in the wider sections of the river as bars and riffles and are, for the most 

part, inactive during post-dam discharges. Fine-grain (largely sandy) terraces occur throughout 

the canyon, especially along the banks of the large reverse eddies above and below the rapids. 

The lower terraces are being reworked into beach-like shores by diurnally-varying, post-dam 

discharges. A slight net lateral erosion of the terraces has resulted. Prior to construction of the 

dam, sandy bed deposits underwent scour averaging about 1 m during spring floods, balanced by 

deposition from tributary sources during the summer. Downstream from rapids, decreased 

turbulence due to lower discharges has resulted in deposition averaging 2.2 m on the bed within 

the upper portions of the canyon. Difference in rock types along the river determine overall 

channel morphology. Rocks of low resistance result in a wide valley, a meandering channel, and 

abundant cobble bars and sand terraces. Narrow channels with rapids and deep pools are most 

frequent within the sections of the canyon where Precambrian crystalline rocks dominate. 

LaGory, K.E., J.W. Hayse, and D. Tomasko. 2003. Recommended priorities for 

geomorphology research in endangered fish habitats of the Upper Colorado River Basin. 

Final report of Argonne National Laboratory to Upper Colorado River Endangered Fish 

Recovery Program, Lakewood, Colorado. 

Activities of the Upper Colorado River Endangered Fish Recovery Program (Recovery 

Program) include habitat improvement and management (e.g., restoration of flooded 

bottomlands, provision of fish passage) and flow management to provide suitable habitat 

conditions for the four species of endangered fishes in the Upper Colorado River Basin — 

Colorado pikeminnow (Ptychocheilus lucius), humpback chub (Gila cypha), bonytail (Gila 

elegans), and razorback sucker (Xyrauchen texanus). In this report, we identify and apply an 

approach for prioritizing river reaches and habitats for geomorphic research in the Upper 

Colorado River Basin. 

The goal of this project was to identify priorities for geomorphology research in 

endangered fish habitats of the Upper Colorado River Basin. These recommended priorities 

provide input to the Recovery Program as it develops a comprehensive research and monitoring 

program for endangered fish habitats. Project objectives included: 

 Review and consolidate geomorphic, habitat, and flow information; 

 Identify relationships among flow regimes, habitats, fish needs, and recovery goals; 

and 

 Identify data gaps and rank their importance to recovery. 

The report focuses on the reaches and habitats used by life stages (larvae, juveniles, 

subadults, adults, and spawning) of three of the four species — the Colorado pikeminnow, 

humpback chub, and razorback sucker. Insufficient information was available on the bonytail to 

permit a meaningful evaluation. The evaluation includes the Green River between Flaming 

Gorge Dam and its confluence with the Colorado River and the upper Colorado River upstream 

of the headwaters of Lake Powell. Major tributaries of these two rivers, up to the point of 

occupation by endangered fishes, also were included. 
Humpback Chub Annotated Bibliography 110 September 2009

 

We developed a linked-matrix approach to systematically and objectively identify overall 

priorities for research. Spreadsheets were developed that contained scores (0, 1, 2, or 3) to 

represent relative importance of (1) existing reach use for species and life stages, (2) habitat use 

for species and life stages, (3) habitat occurrence within planform types, and (4) dependencies 

between habitat characteristics and hydrologic and geomorphic parameters. Scores also were 

assigned to life stages and species on the basis of sensitivity to environmental variability and 

population status, respectively. These scores enabled weighting of life stages and species when 

scores were combined to determine overall priorities. Weights were applied in a phased manner 

that enabled consideration of priorities at various levels, including (1) species-life stage, 

(2) species, and (3) all species combined. Scores were developed during two workshops attended 

by researchers from various agencies, consulting firms, and universities. 

The Upper Colorado River Basin was subdivided into the Green River subbasin and the 

upper Colorado River subbasin. Each major river was divided into reaches based on the 

dominant geomorphic planform (restricted meander, fixed meander, and canyon). These 

planforms describe various levels of confinement of the river channel within the surrounding 

geology, which in turn affects habitat characteristics relevant to endangered fishes. Restricted 

meanders occur in broad alluvial terraces that are bounded by relatively more resistant geology. 

Fixed meanders are confined by resistant geology on both outside and inside bends of the main 

channel. Canyons consist of relatively straight sections of river with resistant geology on both 

sides of the river. Habitat types considered included pools, runs, riffles/rapids, connected 

backwaters, side channels, eddies, flooded tributary mouths, and flooded bottomlands. 

 Consideration also was given to potential use of reaches, assuming improvements in 

conditions in response to implementation of flow recommendations, planned removal of existing 

barriers to passage, and successful establishment of populations through augmentation. 

Consideration of potential reach use was considered especially important for the razorback 

sucker in the upper Colorado River subbasin, because existing levels of use are so low and so 

few larvae and juveniles exist in the system. 

Once we computed reach-habitat scores and scored the dependence of habitat 

characteristics on hydrology and geomorphology, we searched the available literature for studies 

that addressed important parameters in the highest scoring reaches and habitats. Remaining 

information needs were those important relationships in priority reaches and habitats that had not 

been addressed by previous studies. 

In the Green River subbasin, the highest overall reach-habitat scores for species and life 

stages combined are in the Split Mountain Canyon to Desolation Canyon reach. Habitats with 

high scores in this restricted-meander reach include connected backwaters, side channels, 

flooded tributary mouths, and flooded bottomlands. All are low-velocity habitats that serve as 

critical nursery areas for Colorado pikeminnow and razorback suckers. 

The extremely dynamic nature of backwater and side-channel habitats demands a greater 

understanding of the geomorphic processes that form and maintain those habitats. Additional 

research is needed to verify the existing conceptual model of backwater formation and more fully 

understand underlying geomorphic processes, including the effects of antecedent conditions. 
Humpback Chub Annotated Bibliography 111 September 2009

 

Studies are also needed to address the effects of base-flow variability (inter-annual, intra-annual, 

and within day) on backwater and side-channel habitat availability and conditions. 

Scores were high for spawning bar complexes in the Desolation and Gray Canyons reach 

and in the Yampa Canyon reach because several species spawn in each. Studies are needed of 

spawning bars in the Split Mountain Canyon to Desolation Canyon reach and in Desolation and 

Gray Canyons to determine the effects of peak flow, base flow, and sediment characteristics on 

the formation and maintenance of suitable spawning habitats. Although several studies have 

examined geomorphic properties of the razorback spawning bar in the Split Mountain Canyon to 

Desolation Canyon reach, additional study is needed to verify the existing conceptual model for 

this bar and better understand the effects of peak-flow magnitude, peak-flow duration, peak-flow 

frequency, peak-flow timing, and sediment on habitat conditions during the spawning period. 

Several studies have examined the underlying geomorphic processes that affect the 

formation and characteristics of backwaters and side channels in the upper Colorado River 

upstream of Westwater Canyon, and focused on the effects of a few high-water years in the 

1990s. It is important to study flow-habitat relationships in more years and to determine the role 

of peak-flow magnitude, duration, frequency, and variability on habitat maintenance. In addition, 

geomorphic processes affecting backwaters in the Moab Bridge to Green River reach have not 

been studied, and the processes identified for the gravel-bedded upper river would not apply to 

this sand-bedded reach. As for the Green River, additional studies of backwater availability need 

to be conducted because of the dynamic nature of this habitat. 

No studies have been conducted of spawning habitat in any reach in the upper Colorado 

River subbasin because spawning apparently is not concentrated in a few areas as it is in the 

Green River subbasin. However, studies of spawning habitat and the underlying geomorphic 

processes that affect availability and characteristics during the spawning season are critically 

needed. Studies should focus on identifying suitable spawning habitats and determining the 

effects of peak flow, base flow, and sediment characteristics on spawning habitat. 

We suggest that reach-habitat priorities based on existing levels of reach use be used 

wherever possible to avoid the uncertainties associated with potential use. However, the 

population status of razorback suckers in the upper Colorado River subbasin and barriers to fish 

passage in the upper river reduces the value of using existing use patterns in developing priorities 

for geomorphic research. Consequently, we recommend basing prioritization on potential reach 

use for the upper Colorado River subbasin. As the status of populations change in response to 

management actions, including stocking, habitat improvements, and reconnection to historic 

habitat, priorities for the upper Colorado River subbasin should be reconsidered. 

 We recommend a phased, integrated approach to implementation of the research 

priorities identified in this report. Primary information needs for overall reach-habitat priorities 

should be considered the highest priorities for research because research on these topics and 

reaches has the potential to have the largest benefit to recovery of the endangered fishes. 

Consideration should also be given to those primary species-specific information needs. Primary 

information needs for overall reach-habitat priorities in the Green River and upper Colorado 

River subbasins include: 
Humpback Chub Annotated Bibliography 112 September 2009

 

Green River Subbasin (based on existing conditions in the subbasin)

1. Connected backwaters and side channels (Split Mountain Canyon to Desolation 

Canyon and Labyrinth and Stillwater Canyons) 

 Role of peak flow (magnitude, duration, and frequency) and sediment on 

formation and maintenance of habitats. 

 Effects of antecedent conditions (flow and sediment) and base-flow magnitude on 

habitat availability. 

 Effects of base-flow variability on inter-annual availability, intra-annual stability, 

and within-day stability. 

2. Flooded bottomlands (Split Mountain Canyon to Desolation Canyon) 

 Effects of peak flow (magnitude, duration, and frequency), sediment, and 

configuration of connection to main channel on maintenance of connection and 

sediment deposition effects. 

3. Spawning bar complexes (Desolation and Gray Canyons) 

 Effects of peak flow (magnitude, duration, frequency, and timing), base flow 

(magnitude and duration), and sediment on habitat conditions during the 

spawning period. 

 Upper Colorado River Subbasin (based on potential conditions in the subbasin) 

1. Connected backwaters and side channels (Moab Bridge to Green River) 

 Same as those identified for Split Mountain Canyon to Desolation Canyon reach 

of the Green River. 

2. Flooded bottomlands (Palisade to Gunnison River and Gunnison River to Loma) 

 The relationship of habitat availability to peak-flow and base-flow magnitude. 

 Effects of peak flow (magnitude, duration, and frequency), sediment, and 

configuration of connection to main channel on maintenance of connection and 

sediment deposition effects. 

3. Flooded bottomlands (Gunnison River—Hartland Dam to Roubideau Creek) 

 Effects of peak flow (magnitude, duration, and frequency), sediment, and 

configuration of connection to main channel on maintenance of connection and 

sediment deposition effects. 

4. Spawning bar complexes in the Colorado River (Palisade to Gunnison River, 

Gunnison River to Loma, and Loma to Westwater) and Gunnison River (Hartland 

Dam to Roubideau Creek, Roubideau Creek to Colorado River) 

 Location and characteristics of spawning habitats. 
Humpback Chub Annotated Bibliography 113 September 2009

 

 Effects of peak flow (magnitude, duration, frequency, and timing), base flow 

(magnitude and duration), and sediment on habitat conditions during the 

spawning period. 

Primary information needs to address species-specific reach-habitat priorities include: 

Green River Subbasin (based on existing conditions in the subbasin) 

1. Colorado Pikeminnow 

a. Connected backwaters and side channels (Split Mountain Canyon to Desolation 

Canyon, Gray Canyon to Labyrinth Canyon, Labyrinth and Stillwater Canyons) 

 Same as those identified for Split Mountain Canyon to Desolation Canyon 

reach under overall reach-habitat priorities above. 

b. Spawning bar complexes (Desolation and Gray Canyons) 

 Same as those identified for Desolation and Gray Canyons reach under overall 

reach-habitat priorities above. 

2. Humpback Chub 

a. Spawning bar complexes (Desolation and Gray Canyons) 

 Same as those identified for Desolation and Gray Canyons reach under overall 

reach-habitat priorities above. 

3. Razorback Sucker 

a. Spawning bar complexes (Split Mountain Canyon to Desolation Canyon) 

 Same as those identified for Desolation and Gray Canyons under overall 

reach-habitat priorities above. 

 Location of additional potential spawning areas in reach. 

b. Flooded bottomlands (Split Mountain Canyon to Desolation Canyon) 

 Same as those identified for Split Mountain Canyon to Desolation Canyon 

reach under overall reach-habitat priorities above. 

 Upper Colorado River Subbasin (based on potential conditions in the subbasin) 

1. Colorado Pikeminnow 

a. Connected backwaters and side channels (Cottonwood Wash to Dewey Bridge, 

Jackass Canyon to Moab Bridge, Moab Bridge to Green River) 

 Same as those identified for connected backwaters in Split Mountain Canyon 

to Desolation Canyon reach of the Green River under overall reach-habitat 

priorities above. 

b. Spawning bar complexes in the Colorado River (Palisade to Gunnison River, 

Gunnison River to Loma, Loma to Westwater, Cottonwood Wash to Dewey 

Bridge) and Gunnison River (Hartland Dam to Roubideau Creek, Roubideau 

Creek to Colorado River) 
Humpback Chub Annotated Bibliography 114 September 2009

 

 Same as those identified for spawning bar complexes in upper Colorado River 

subbasin under overall reach-habitat priorities. 

2. Humpback Chub 

a. Spawning bar complexes (Loma to Westwater Canyon—Black Rocks portion, 

Westwater Canyon) 

 Same as those identified for spawning bar complexes in upper Colorado River 

subbasin under overall reach-habitat priorities. 

3. Razorback Sucker 

a. Flooded bottomlands (Palisade to Gunnison River, Gunnison River to Loma, 

Gunnison River—Hartland Dam to Roubideau Creek) 

 Same as those identified for flooded bottomlands in upper Colorado River 

subbasin under overall reach-habitat priorities above. 

b. Spawning bar complexes in the Colorado River (Palisade to Gunnison River, 

Gunnison River to Loma, Moab Bridge to Green River) and Gunnison River 

(Hartland Dam to Roubideau Creek). 

 Same as those identified for spawning bar complexes in upper Colorado River 

subbasin under overall reach-habitat priorities. 

c. Connected backwaters and side channels (Moab Bridge to Green River) 

 Same as those identified for connected backwaters in Split Mountain Canyon 

to Desolation Canyon reach of the Green River under overall reach-habitat 

priorities above. 

One aspect of a phased, integrated approach is selection among the identified information 

needs. For instance, rather than attempting to determine the geomorphic basis of spawning 

habitats in all nine of the identified high-priority reaches of the upper Colorado River subbasin 

simultaneously, research should focus on a limited subset of representative spawning areas in 

one or a few of these reaches. Reaches should be selected for further study on the basis of the 

results of initial studies to identify and characterize spawning habitats in the subbasin. As 

relationships among flow, geomorphology, and habitat characteristics are determined in 

representative study reaches, results can be verified in other high priority reaches. 

 All research of geomorphic processes and habitats should be based on hypothesis testing. 

We recommend that, whenever possible, studies incorporate experimental manipulations and the 

testing of predicted responses. We also recommend standardization of research protocols and 

data collection techniques. It is important to recognize that these recommendations are based on 

current understanding of habitat requirements and geomorphic processes. It is likely that 

adjustments to research priorities will be necessary as the research proceeds, and, indeed, the 

success of the effort will require such adaptation as new information is obtained and inferences 

are drawn. The research priorities identified in the report are recommendations based on data 

needs and their importance to recovery. Ultimately, the Recovery Program will determine the 

direction of future research, and multiple factors (including, but not limited to those considered 

in this report) will be considered in those determinations. 
Humpback Chub Annotated Bibliography 115 September 2009

 

Powell, K. 2002. Open the floodgates!--A second attempt to restore the altered 

environment of the Grand Canyon, by letting the Colorado River run free. Nature 

420(6914):356–358. 

On 27 March 1996, the Colorado River ran three meters higher than the previous day. 

The flood continued for seven days, as 1,290 cubic meters of water per second flowed through 

the bypass tubes of the Glen Canyon Dam, more than 160 kilometers upstream. The goal was to 

rebuild sandbars and beaches that had been eroded since the dam was completed in 1963. The 

flood should have liberated years of accumulated sand, silt and clay from the river channel and 

deposit it onto the eroded beaches. A chronic lack of sediment in the river downstream of the 

dam doomed the flood to fail in its goal of restoring the Grand Canyon’s beaches to a more 

natural state. Hydrologists are now planning to flood the canyon once more, timing the deluge to 

coincide with an abundance of fresh sediment. 

Rubin, D.M., D.J. Topping, J.C. Schmidt, J. Hazel, M. Kaplinski and T.S. Melis. 2002. 

Recent sediment studies refute Glen Canyon Dam hypothesis. Transactions American 

Geophysical Union 83(25):273. 

Recent studies of sedimentology, hydrology, and geomorphology indicate that releases 

from Glen Canyon Dam are continuing to erode sandbars and beaches in the Colorado River in 

Grand Canyon National Park, despite attempts to restore these resources. The current strategy for 

dam operations is based on the hypothesis that sand supplied by tributaries of the Colorado River 

downstream from the dam will accumulate in the channel during normal dam operations and 

remain available for restoration floods. Recent work has shown that this hypothesis is false, and 

that tributary sand inputs are exported downstream rapidly, typically within weeks or months 

under the current flow regime. 

Rubin, D.M., J.M. Nelson and D.J. Topping. 1998. Relation of inversely graded deposits to 

suspended-sediment grain-size evolution during the 1996 flood experiment in Grand 

Canyon. Geology 2692):99–102. 

Before Glen Canyon Dam was completed upstream from Grand Canyon, floods scoured 

sand from the channel bed and deposited sand on bars within recirculating eddies. After 

completion of Glen Canyon Dam in 1963, peak discharge of the mean annual floods dropped 

from about 2600 to 900 m3

/s, and 85% of the sediment supply was eliminated. Under the postdam flow regime, sand bars in eddies have degraded. In an experiment to study, in part, the 

effects of floods in rebuilding these bars, a controlled flood was released from Glen Canyon Dam 

in late March and early April 1996. Although fluvial sequences characteristically fine upward, 

the deposits of the experimental flood systematically coarsen upward. Measurements of 

suspended-sediment concentration and grain size and of bed-material grain size suggest that the 

upward coarsening results from the channel becoming relatively depleted of fine-grained 

sediment during the seven days of the high-flow experiment. Pre-dam flood beds of the Colorado 

River also coarsen upward, indicating that supply-limitation and grain-size evolution are natural 

processes that do not require the presence of a dam. 
Humpback Chub Annotated Bibliography 116 September 2009

 

Schmidt, J.C. 1994. Compilation of historic hydrologic and geomorphic data for the upper 

Colorado River basin. Annual report of Utah State University Department of Geography 

and Earth Resources to Upper Colorado River Endangered Fish Recovery Program, 

Lakewood, Colorado. Abstract excerpted from results and conclusions. 

Preliminary results of ongoing investigations of the geomorphology and hydrology 

records of the Green River Basin are: (1) The magnitude of the annual peak discharge of the 

Green River upstream from the Yampa River has decreased about 60% from the 1923–1962 

period to the period following closure of Flaming Gorge Dam. At Jensen and Green River, Utah, 

the changes have been about 25%, depending on the recurrence of the flood being evaluated. 

Floods on the Yampa River were unchanged during the same periods. (2) The highest floods of 

this century occurred in the early part of the century. Instantaneous peak discharge at Green 

River, Utah, exceeded 60,000 ft3/s (1,698 m3/s) in 1897, 1909, 1917, and 1921. Peak flows at 

Greendale are estimated to have exceeded 20,000 ft3

/s (566 m3/s) in 1899, 1918, and 1921. These 

floods are unprecedented; the fact that floods of this magnitude do not occur at present may be 

related to climatic change and be unrelated to the existence of dams. The effects of these floods 

on habitat availability have not been evaluated. (3) The bed at the Greendale gage aggraded 0.3 

ft between 1961 and 1987. (4) The bed at the Jensen gage has not changed in elevation since 

1948. Speculation about channel degradation in the Razorback Bar and Escalante Bottoms area is 

not supported by these findings. (5) Degradation of about 0.3 ft of the channel bed at Ouray 

occurred between 1951 and 1966. It is unlikely that these changes are related to the Flaming 

Gorge Dam. (6) Prior to closure of the Flaming Gorge Dam, the Green River near Greendale, 

Utah, was covered by ice between 3 and 5 months per year. The last year that ice cover was 

reported at this gage was 1958. (7) Between the winters of 1946–47 and 1960–67, the average 

duration of ice cover was 3.6 months near Jensen. Since that time, the duration has decreased to 

0.8 months. At Ouray, the average duration of ice cover was 3 months between 1951 and 1965. 

(8) A new floodplain, in apparent equilibrium with reduced floods, has developed in the Uinta 

Basin, especially in the Ouray National Wildlife Refuge. This floodplain is regularly inundated, 

but the areal extent of these surfaces is an order of magnitude less than the pre-dam floodplain. It 

appears that significant inundation of the alluvial valley of the Green River may not have 

regularly occurred since the 1920s. (9) Significant channel narrowing in Lodore Canyon has 

occurred since closure of Flaming Gorge Dam. Numerous eddy bars have been vegetated, and 

backwater habitats may have been lost. 

Schmidt, J.C. and D.M. Rubin. 1995. Regulated streamflow, fine-grained deposits, and 

effective discharge in canyons with abundant debris fans. Pages 177–195 in J. E. Costa, A. 

J. Miller, K. W. Potter and P. R. Wilcock, editors. Natural and anthropogenic influences in 

fluvial geomorphology. AGU Geophysical Monograph 89. Abstract excerpted from results 

and conclusions. 

The debris fan-eddy complex is the fundamental geomorphic channel unit in canyons 

with abundant debris fans. This assemblage includes, in a downstream direction, a river segment 

of ponded flow that has a low downstream velocity and that is controlled by a downstream 

channel constriction, a constricting debris fan, eddies and eddy bars, and a gravel bar. This 

assemblage occurs at nearly every tributary mouth where debris fans constrict the river. Such 

tributaries exist along many, but not all, of the narrow canyons of the Green and Colorado 
Humpback Chub Annotated Bibliography 117 September 2009

 

Rivers. Reaches affected by debris fans are steeper, have higher stream power per unit bed area, 

and have coarser beds than other narrow canyons of the same river system. The extent of each 

channel element varies from site to site. 

Schmidt, J.C., D.J. Topping, P.E. Grams and J.E. Hazel. 2004. System wide changes in the 

distribution of fine sediment in the Colorado River corridor between Glen Canyon Dam 

and Bright Angel Creek, Arizona. Final report of the Fluvial Geomorphology Laboratory, 

Utah State University, Logan, Utah. 99 p. 

The riverine ecosystem of the Colorado River between Glen Canyon Dam and Bright 

Angel Creek had less fine sediment on its bed, in eddies, and as channel-margin deposits in 2001 

than it did prior to completion of the dam. Changes in dam operations in the 1990s did not arrest 

this trend. 

The decrease in fine sediment storage is documented by comparison of historical oblique 

photographs, analysis of historical aerial photographs, and field surveys since 1990. The 

magnitude of the decrease is uncertain. The loss of sand is probably about 25% of the area 

typically exposed at base flow in pre-dam photographs, but estimates range between 0 and -55%, 

depending on study reach and method of analysis. There is no indication that the magnitude of 

decrease is less in the downstream part of the study area. The cumulative loss of eddy sand is 

about 1 m in thickness but also varies greatly. 

Eddies are now the primary storage site of fine sediment. Eddies have always been a very 

large storage site for fine sediment, but the bed once played a more important role than it does 

today. The bed has been significantly lowered in Glen Canyon, but the bed has only degraded in 

pools and ponded backwaters in Marble and Upper Grand Canyons. There is no evidence that 

fine sediment aggrades on the main channel bed or in the deep parts of eddies for longer than a 

few weeks to a few months, and these parts of the river respond quickly to changes in flow and 

sediment transport. These areas evacuate fine sediment during flows typical of the 1990s. Postdam flood deposits have a longer response time and adjust over a period of years to decades to 

changes in dam operations. These deposits are only constructed by dam releases that exceed 

power plant capacity. They are subject to large erosion rates during the first months following 

flood recession, but erosion rates thereafter decrease. The area of these deposits caused by the 

1996 Controlled Flood lasted about 5 years, although some individual deposits remain large 

today. 

Topping, D.J., D.M. Rubin and L.E. Vierra, Jr. 2000. Colorado River sediment transport 

1. Natural sediment supply limitation and the influence of Glen Canyon Dam. Water 

Resources Research 36:515–542. 

Analyses of flow, sediment-transport, bed-topographic, and sedimentologic data suggest 

that before the closure of Glen Canyon Dam in 1963, the Colorado River in Marble and Grand 

Canyons was annually supply-limited with respect to fine sediment (i.e., sand and finer material). 

Furthermore, these analyses suggest that the predam river in Glen Canyon was not supplylimited to the same degree and that the degree of annual supply limitation increased near the 

head of Marble Canyon. The pre-dam Colorado River in Grand Canyon displays evidence of 
Humpback Chub Annotated Bibliography 118 September 2009

 

four effects of supply limitation: (1) seasonal hysteresis in sediment concentration, (2) seasonal 

hysteresis in sediment grain size coupled to the seasonal hysteresis in sediment concentration, 

(3) production of inversely graded flood deposits, and (4) development or modification of a lag 

between the time of a flood peak and the time of either maximum or minimum (depending on 

reach geometry) bed elevation. Analyses of sediment budgets provide additional support for the 

interpretation that the pre-dam river was annually supply-limited with respect to fine sediment, 

but it was not supply-limited with respect to fine sediment during all seasons. In the average predam year, sand would accumulate and be stored in Marble Canyon and upper Grand Canyon for 

9 months of the year (from July through March) when flows were dominantly below 200–

300 m3/s; this stored sand was then eroded during April through June when flows were typically 

higher. After closure of Glen Canyon Dam, because of the large magnitudes of the uncertainties 

in the sediment budget, no season of substantial sand accumulation is evident. Because most 

flows in the post-dam river exceed 200–300 m3/s, substantial sand accumulation in the post-dam 

river is unlikely. 

Topping, D.J., D.M. Rubin and T.S. Melis. 2007. Coupled changes in sand grain size and 

sand transport driven by changes in the upstream supply of sand in the Colorado River: 

relative importance of changes in bed-sand grain size and bed-sand area. Sedimentary 

Geology 202(3):538–561. 

Sand transport in the Colorado River in Marble and Grand canyons was naturally limited 

by the upstream supply of sand. Prior to the 1963 closure of Glen Canyon Dam, the river 

exhibited the following four effects of sand supply limitation: (1) hysteresis in sediment 

concentration, (2) hysteresis in sediment grain size coupled to the hysteresis in sediment 

concentration, (3) production of inversely graded flood deposits, and (4) development or 

modification of a lag between the time of a flood peak and the time of either maximum or 

minimum (depending on reach geometry) bed elevation. Construction and operation of the dam 

has enhanced the degree to which the first two of these four effects are evident, and has not 

affected the degree to which the last two effects of sand supply limitation are evident in the 

Colorado River in Marble and Grand canyons. The first three of the effects involve coupled 

changes in suspended-sand concentration and grain size that are controlled by changes in the 

upstream supply of sand. During tributary floods, sand on the bed of the Colorado River fines; 

this causes the suspended sand to fine and the suspended-sand concentration to increase, even 

when the discharge of water remains constant. Subsequently, the bed is winnowed of finer sand, 

the suspended sand coarsens, and the suspended-sand concentration decreases independently of 

discharge. Also associated with these changes in sand supply are changes in the fraction of the 

bed that is covered by sand. Thus, suspended-sand concentration in the Colorado River is likely 

regulated by both changes in the bed-sand grain size and changes in the bed-sand area. A 

physically based flow and suspended-sediment transport model is developed, tested, and applied 

to data from the Colorado River to evaluate the relative importance of changes in the bed-sand 

grain size and changes in the bed-sand area in regulating suspended-sand concentration. 

Although the model was developed using approximations for steady, uniform flow, and other 

simplifications that are not met in the Colorado River, the results nevertheless support the idea 

that changes in bed-sand grain size are much more important than changes in bed-sand area in 

regulating the concentration of suspended sand. 
Humpback Chub Annotated Bibliography 119 September 2009

 

Webb, R.H., D.L. Wegner, E.D. Andrews, R.A. Valdez and D.T. Patten. 1999. 

Downstream effects of Glen Canyon dam on the Colorado River in Grand Canyon: a 

review. Geophysical Monograph 110:1–21. 

 Glen Canyon Dam, completed in 1963, has altered geomorphic and ecological processes 

and resources of the Colorado River in Grand Canyon. Before the dam was completed, the river 

transported large quantities of sediment during spring floods as large as 8500 m3/s. After 1963, 

dam releases typically were less than 900 m3/s with large diurnal fluctuations and little sediment. 

The 2-yr peak discharge decreased by a factor of 2.5, resulting in aggraded rapids and a large 

increase in riparian vegetation. The clearwater releases from the dam eroded sand deposited on 

the bed and banks. Although pre-dam water temperatures varied seasonally, darn releases 

typically are about 8°C year round. Because of the clear, cold water and reduced flooding, postdam aquatic productivity is considerably higher in the tailwater. Rainbow trout and other nonnative fishes are now common, 3 native species have been extirpated, and the remaining species, 

including the endangered humpback chub, cannot successfully reproduce in the river. 

Webb, R.H., P.G. Griffiths, C.S. Magirl and T.C. Hanks. 2005. Debris flows in Grand 

Canyon and the rapids of the Colorado River. Pages 139-152 in Gloss, S.P., J.E. Lovich and 

T.S. Melis, eds., The state of the Colorado River ecosystem in Grand Canyon. A report of 

the Grand Canyon Monitoring and Research Center 1991-2004. USGS Circular 1282. U.S. 

Geological Survey, Flagstaff, Arizona. 

Debris flows transport poorly sorted sediment onto debris fans in the Colorado River at a 

frequency that varies through Grand Canyon. Historically, an average of 5.0 debris flows per 

year has occurred in Grand Canyon. The occurrence of these debris flows does not appear to be 

related to seasonal precipitation amounts. Modeling debris-flow frequency in Grand Canyon 

based on the interpretation of 1,365 photographs of the river corridor yielded frequency 

information in 167 of 740 tributaries (23%). Of the 167 tributaries, 98 (59%) had debris flows 

during the last 100 yr. 

Frequency estimates indicate that 57% of the tributaries had at least one debris flow per 

century, while about 10% of the tributaries had a frequency of more than two debris flows per 

century. Estimates of sediment yield to the Colorado River in Grand Canyon by debris flow are 

as high as 3.3 million tons (3.0 million Mg) of sediment per decade, of which 452,000 tons 

(410,000 Mg) are boulders larger than 10 inches (>256 mm) in diameter. Distributed evenly 

throughout the river corridor, these boulders would raise the bed in Grand Canyon by 2.3 ft per 

thousand years (0.72 m per thousand years). If deposition is limited to existing debris fans at 

tributary mouths, these boulders would raise the bed by an average of 8.66 ft (2.64 m) per 

thousand years at each confluence. 

By combining the frequency model with relations for debris-flow volume and particlesize distribution, debris-flow sediment yields were calculated for several time periods. On 

average, debris flows deliver between 0.15.106 and 0.33.106 tons/yr (0.14.106 and 0.30.106 Mg/ 

yr) of sediment to the main channel. Although debris flows deliver only 23,142 to 48,488 tons/yr 

(21,000 to 44,000 Mg/yr) of boulders to the river, these boulders control the longitudinal profile 

and geomorphic framework of the river, defining debris fans, rapids, and related sandbars, and 
Humpback Chub Annotated Bibliography 120 September 2009

 

are unlikely to be removed by regulated flows. Moreover, the effects of debris flows are shown 

to affect the river on several length and temporal scales. 

Comparison of the two water-surface profiles (one surveyed in 1923 and one in 2000) 

showed a change in 80 rapids. The average elevation of pools at the heads of rapids was 0.85 ft 

(0.26 m) higher between 1923 and 2000, indicating net aggradation of the coarse-grained 

sediment forming the rapids throughout Grand Canyon. Furthermore, comparison of the two 

water-surface profiles showed enhanced pool-and-rapid structure; while 50% of the total drop of 

the river occurred in just 9% of the river distance in 1923, that figure increased to 66% by 2000. 

Reconstruction of water-surface profiles showed that debris-flow deposition can also have large 

upstream effects, particularly in the cases of reducing gradients between rapids and reducing the 

fall in the upstream rapid. 

Analysis of the entire longitudinal profile through Grand Canyon reveals convexities that 

reflect sustained debris-flow deposition. Specifically, there are two long wavelength (about 62 

mi (about 100 km)), large-amplitude (49 to 98 ft (15 to 30 m)) river-profile convexities: the 

eastern canyon convexity between RM 30 and RM 80 and the western canyon convexity between 

RM 160 and RM 250. These large amplitude convexities have strong spatial correlations with 

high probabilities of debris-flow occurrence, high densities of debris fans, and the largest debris 

fans along the river. These convexities appear to be maintained by debris-flow activity in Grand 

Canyon, presumably for all of the Holocene. In this period, the Colorado River has been 

expending its energy transporting sediment within Grand Canyon and integrating shortwavelength convexities into long-wavelength convexities, with little or no bedrock incision. 

Coarse-sediment fill in the channel of the Colorado River at any wavelength has its 

origins in the rapids, which result from the tributary debris flows and fans that feed them. In 

contrast, the amount of fill in the rapids, either individually or collectively, is a small volume 

compared to the fill that creates the longer wavelength convexities. Periodic channel 

maintenance floods are not likely to perform the transport necessary to create the longwavelength convexities, although reworking of locally aggraded debris fans is clearly feasible. 

The river reworking processes by which point-source contributions of debris-flow sediment are 

aggregated into longer wavelength convexities are as yet unknown and certainly involve a more 

detailed understanding of the flood dynamics of the pre-dam river. Nevertheless, the close spatial 

associations of the longer wavelength convexities with the locations and sizes of debris fans and 

with the frequency of debris flows lead to the conclusion that unusual accumulations of debris 

fill in the channel are their principal cause, just as they are for the rapids. 

In terms of adaptive management and operations of Glen Canyon Dam, reworking of 

aggraded debris fans has been shown to be feasible. Reworking has been documented during 

modified low fluctuating flow releases, maximum powerplant releases, and flood releases up to 

47,500 cfs. Both reworking and transport capacity increase with increasing discharge, which 

suggests that flood releases larger than powerplant capacity of about 33,500 cfs are more 

efficient than smaller events. Because reworking mostly occurred in the rising limb of flood 

hydrographs, large-magnitude floods designed for debris-fan reworking do not have to have 

significant duration. As shown in figure 13, a flood designed to rework debris fans could have a 

peak discharge of 100,000 cfs for only 1 min at Diamond Creek then drop rapidly to a beach-
Humpback Chub Annotated Bibliography 121 September 2009

 

building discharge for several days. This type of management prescription may be only used 

every 5 to 10 yr, with smaller intervening releases. 

Webb, R.H., P.G. Griffiths, T.S. Melis and D.R. Hartley. 2000. Sediment delivery by 

ungaged tributaries of the Colorado River in Grand Canyon, Arizona. Water Resources 

Investigations Report, U.S. Geological Survey no. 4055, pp 78. 

The purpose of this report is to estimate the total sediment yield and sand delivery from 

ungaged tributaries in each of six reaches between Glen Canyon Dam and upper Lake Mead 

reservoir at the Grand Wash Cliffs. This includes the entire drainage area between Glen Canyon 

Dam and upper Lake Mead reservoir except for the four largest tributaries. These estimates are 

based on an evaluation of both the debris-flow and streamflow components of sediment yield by 

multiple techniques. As a secondary objective, the authors evaluate the potential influence of 

climatic variability on sediment input in the light of historical climatic fluctuations. This study 

was funded in cooperation with the Bureau of Reclamation, as part of the Glen Canyon 

Environmental Studies Program, and the Grand Canyon Monitoring and Research Center. 

Wiele, S.M., J.B. Graf and J.D. Smith. 1996. Sand deposition in the Colorado River in the 

Grand Canyon from flooding of the Little Colorado River. Water Resources Research 

32:3579–96. 

A model of flow, sand transport, and bed evolution is used to examine processes during 

the 1996 controlled flood and to examine the effect of low and high sand concentrations on 

depositional rate, magnitude, and location. During a flood on the Little Colorado River in 

January 1993, water discharge in the main stem was increased to about 950 m3

/s and a sand 

volume sufficient to increase sand concentrations to about twice the sand concentration measured 

on the first day of the controlled flood was delivered to the main stem and redistributed 

downstream. This influx of sand led to large deposits in depressions in main channel pools and 

deposition in recirculation zones that the model predicts originated as separation deposits and 

spread downstream and into the recirculation zone. In contrast, during the controlled flood at a 

discharge of 1270 m3

/s sand was eroded from the main channel and the delivery of suspended 

sand from the main channel to the recirculation zones was focused at the reattachment point. 

Similar depositional patterns were predicted by the model using sand inputs at the upper and 

lower bounds of measured sand transport at the controlled flood water discharge. Rates of 

deposition and deposit volume were proportional to the sand input to the reach.

Wright, S.A., T.S. Melis, D.J. Topping and D.M. Rubin. 2005. Influence of Glen Canyon 

Dam operations on downstream sand resources of the Colorado River in Grand Canyon. 

Pages 17-31 in Gloss, S.P., J.E. Lovich and T.S. Melis, eds., The state of the Colorado River 

ecosystem in Grand Canyon. A report of the Grand Canyon Monitoring and Research 

Center 1991-2004. USGS Circular 1282. U.S. Geological Survey, Flagstaff, Arizona. 

Extensive research and monitoring of fine-sediment transport and sandbars since the 

completion of the EIS have resulted in a better understanding of the geomorphology of the 

Colorado River in Marble and Grand Canyons and of the effects of the operations of Glen 

Canyon Dam on the river’s downstream resources. Probably the single most important finding of 
Humpback Chub Annotated Bibliography 122 September 2009

 

this research and monitoring is that post-dam mainstem sand transport exceeds the post-dam 

supply of sand from tributaries on a seasonal to annual basis, such that the post-dam river is in an 

annual fine-sediment deficit (i.e., export exceeds input). This sediment deficit has resulted in a 

consistent downstream pattern of erosion of channel and sandbar deposits from Marble and 

Grand Canyons despite restrictions on daily power plant fluctuations required by the 

implementation of the MLFF alternative. 

The finding of an annual sediment deficit directly contradicts the critical EIS assumption 

that sand will accumulate on the bed of the Colorado River over multiple years under the MLFF 

operating alternative (and minimum annual volume releases) and has important implications for 

the potential success of managing tributary sediment inputs. It is also worth noting that the EIS 

conclusion resulted fundamentally from a lack of long-term records for tributary sand supply and 

mainstem sand-transport rates, illustrating the importance of long-term data sets in river 

management. A continuous sediment budget for the Colorado River in Grand Canyon since 

construction of Glen Canyon Dam, based on high-frequency measurements, likely would have 

resulted in a different EIS conclusion about fine sediment dynamics below the dam, one that may 

have prevented the continued erosion of sandbars between 1991 and 2004. 

A second important finding of recent research and monitoring efforts is that during the 

1996 BHBF the primary source of sand for building high-elevation sandbars was the lowelevation portion of the sandbars instead of the channel bed as hypothesized in the EIS. This 

scenario of building high-elevation sandbars at the expense of the low-elevation portions was 

repeated during the powerplant capacity flow in September 2000. This process of sandbar 

building is supported by the finding of an absence of multiyear accumulation on the channel bed: 

sand cannot be transported from the bed to high-elevation sandbars because there is typically 

little sand available on the channel bed. 

Neither of these two findings supports the EIS hypotheses, but they have led scientists 

and managers to reassess the management strategy for sand resources within Grand Canyon. An 

emerging paradigm is the need to strategically time high-flow releases in order to take advantage 

of sporadic tributary sediment inputs, a scenario that requires greater flexibility in the annual 

operating plan for the dam with respect to both hydroelectric power generation and economic 

cost. Only immediately after these inputs are significant sand available on the channel bed for 

transfer to high-elevation sandbars through high-flow releases. Alternatively, dam releases may 

be constrained following inputs for a period of time until a high flow can be released from the 

dam; however, during extended periods of above-average upper Colorado River Basin hydrology 

and high storage in Lake Powell, constraining daily operations may not be possible. In the 

absence of high-flow releases strategically timed to redistribute tributary inputs to high-elevation 

sandbars, the inputs are exported from Grand Canyon in a period of weeks or months under 

normal dam operations, leading to continued long-term erosion of sandbars. 

In November 2004, this paradigm of strategically timed, high-flow releases was tested for 

the first time on the Colorado River. Scientists are in the process of evaluating the results of this 

experiment. The findings will be critical for the long-term management of fine sediment 

resources and sandbars in Grand Canyon. If a management approach of strategically timed, highflow releases, triggered by tributary inputs, is to be followed, then further research will be 
Humpback Chub Annotated Bibliography 123 September 2009

 

required to define the appropriate triggering criteria and to develop high-flow hydrographs 

(peaks and durations) that may optimize deposition of tributary sand inputs within eddies while 

minimizing export during controlled flood peaks. 

If strategically timed, high-flow releases are deemed inadequate for meeting the 

management objectives for Grand Canyon sandbars, then alternative approaches must be 

considered, such as further restraints on daily powerplant operations, changes in monthly volume 

release patterns, or sediment augmentation. 

4.3 EFFECTS ON TEMPERATURE 

Clarkson, R.W. and M.R. Childs. 2000. Temperature effects of hypolimnial-release dams 

on early life stages of Colorado River Basin big-river fishes. Copeia 402–412. 

Declines of native big-river fishes of the Colorado River Basin, southwestern United 

States, have been attributed in part to emplacement of hypolimnial-release dams. 

Lowered spring-summer tailwater temperatures inhibit spawning and embryonic development, 

depress swimming performance and growth, and reduce survival of early life stages. We 

examined effects of three temperatures (10°C, 14°C, 20°C) on aspects of growth, development, 

and physiology of larval and early juvenile life stages of Xyrauchen texanus (Razorback Sucker), 

Catostomus latipinnis (Flannelmouth Sucker), Gila cypha (Humpback Chub), and Ptychocheilus 

lucius (Colorado Squawfish) in the laboratory. Lengths, weights, and specific growth rates of all 

species were significantly lower at 10°C and 14°C than at 20°C, and time to transformation from 

larval to juvenile life stage was delayed at colder temperatures. Transfer of fishes from 20°C to 

10°C (simulating transport from warm tributaries to cold tailwaters) caused loss of equilibrium in 

youngest life stages. All these effects increase exposure of larvae to existing sources of mortality. 

Conservation of the big-river species in hypolimnial-release tailwaters will require thermal 

modification of dam discharges to lessen detrimental effects of cold water temperatures. Because 

such action may also benefit nonindigenous biota, recovery of the native fauna may ultimately 

depend upon implementation of comprehensive (and likely expensive) control measures against 

nonnative species. 

Paukert, C.P. and J.H. Petersen. 2007. Comparative growth and consumption potential of 

rainbow trout and humpback chub in the Colorado River, Grand Canyon, Arizona, under 

different temperature scenarios. The Southwestern Naturalist 52(2):234-242. 

 We used bioenergetics models for humpback chub, Gila cypha, and rainbow trout, 

Oncorhynchus mykiss, to examine how warmer water temperatures in the Colorado River, Grand 

Canyon, Arizona, through a proposed selective withdrawal system (SWS) at Glen Canyon Dam, 

would affect growth, consumption, and predation rates. Consumption by the rainbow trout 

population was at least 10 times higher than by the smaller humpback chub population. Water 

temperature increases of 6°C during autumn increased growth of humpback chub and likely 

increased their survival by reducing the time vulnerable to predation. Water temperature 

increases caused by drought in 2005 did not alter humpback chub growth as much as the SWS. 

Increased temperatures might cause changes to the invertebrate community and the distribution 
Humpback Chub Annotated Bibliography 124 September 2009

 

and abundance of other warmwater nonnative fishes. The implications on the entire aquatic 

community need to be considered before any management action that includes increasing water 

temperatures is implemented. 

Vernieu, W.S., S.J. Hueffle and S.P. Gloss. 2005. Water quality in the Lake Powell and the 

Colorado River. Pages 1991-2004 in Gloss, S.P., J.E. Lovich and T.S. Melis, eds., The state 

of the Colorado River ecosystem in Grand Canyon. A report of the Grand Canyon 

Monitoring and Research Center 1991-2004. USGS Circular 1282. U.S. Geological Survey, 

Flagstaff, Arizona. 

Water temperature, nutrient concentrations, turbidity, and other water-quality parameters 

are of interest to managers and scientists because these parameters influence a range of 

ecosystem components, from support of aquatic microorganisms and invertebrates to the 

behavior of native and nonnative fishes. For example, declines of Colorado River Basin native 

fishes and changes in their condition have been attributed, in part, to low water temperatures 

downstream from dams, such as Glen Canyon Dam, that release water from deeper portions of 

the reservoir. Similarly, water quality is an important determinant of food-web structure in 

aquatic habitats and abundance of consumers like fish in those food webs. 

4.4 EFFECTS ON FOOD AVAILABILITY 

Benenati, E.P., J.P. Shannon, D.W. Blinn, K.P. Wilson, and S.J. Hueftle. 2000. Reservoirriver linkages: Lake Powell and the Colordao River, Arizona. Journal of the North 

American Benthological Society 19(4):742–755. 

The effect of lotic-lentic interactions on the phytobenthic community was studied in the 

Colorado River below Glen Canyon Dam (GCD), Arizona. Major compositional changes in river 

phytobenthos occurred following high snowmelt inflows that filled the Lake Powell reservoir 

and resulted in high, steady discharges from GCD. Cladophora glomerata, the previously 

dominant alga, was partly displaced by a mixed mucilaginous phytobenthic assemblage 

consisting of miscellaneous algae, macrophytes, and bryophytes (MAMB). Relationships 

between abiotic parameters (discharge, conductivity, nutrient concentration, and season) and 

biotic responses (composition and biomass of filamentous and epiphytic algae, and invertebrate 

biomass) were analyzed from 1995 to 1998. In addition, the response of the phytobenthos to an 

experimental flood (1275 m super (3)/s) was examined in the tailwaters below GCD. Significant 

compositional changes occurred within 3 mo of lake filling and the onset of elevated discharges 

in June 1995. Relative phytobenthic composition by biomass prior to June 1995 was: 

Cladophora glomerata = 91.5%, MAMB = 3.5%, and cyanobacteria = 5.0%, compared to 49.6, 

47.9, and 2.5%, respectively, after the initiation of high discharges. Cladophora and MAMB had 

an inverse relationship that fluctuated seasonally. Cladophora was positively associated with 

increased nutrient concentrations and lower discharge during summer-autumn, whereas MAMB 

was positively correlated with decreased nutrients and higher discharge during winter-spring. 

Cladophora was positively associated with invertebrate biomass and also had greater epiphyton 

biomass and density than MAMB. The 1996 experimental flood resulted in a significant loss of 

MAMB biomass, in contrast to a minimal decrease in Cladophora and invertebrates. Interactions 
Humpback Chub Annotated Bibliography 125 September 2009

 

between inflow patterns, reservoir chemistry, and discharge regime have an important effect on 

benthic community structure below dams. Resource managers need to consider these 

relationships and regard water resources above and below impoundments as a connected system 

when making management decisions. 

Blinn, D.W. and G.A. Cole. 1991. Algal and invertebrate biota in the Colorado River: 

Comparison of pre-and post-dam conditions. Pages 102-123 in Colorado River Ecology and 

Dam Management, Proceedings of a symposium, May 24-25, 1990. National Academy 

Press, Washington, DC. 

Few reports exist on the physicochemical conditions of the pre-impounded Colorado 

River that relate to the growth and development of algal and aquatic invertebrate communities. 

Post-impoundment studies indicate that Cladophora glomerata is the dominant attached 

filamentous green algal species. Two hundred-thirty-five diatom taxa from the Colorado River 

and tributaries and from springs in the Glen and Grand Canyon systems have been reported. 

Ephemeropterans, snails, leeches, species from at least 10 insect families, and crayfish were 

intentionally introduced into the Colorado River after the Glen Canyon dam was closed. 

Zooplankters show a richness of faunas in backwaters along the borders of the river channel and 

at the mouths of tributaries. The macroinvertebrates occurring in the Colorado River consist of 

only a few species. The amphipod Gammarus lacustris constitutes an important food for most of 

the fishes of the Colorado River. Exotic and unusual species such as Craspedacusta sowerbyi, 

Branchiura sowerbyi, and the parasite Lernaea cyprinacea have also been reported in the 

Colorado River. Damming of the river has caused stranding of some plant and animal 

communities during periods of low flow. Some species have shown adaptations to fluctuating 

flow regimens caused by dams. Regulated flow can increase the standing crops of both attached 

algae and aquatic macrophytes, as well as aquatic mosses. Creation of reservoirs may cause 

enrichment of some nutrients that affect algal growth. The most common effect of impounded 

rivers on the macroinvertebrate community is reduced species diversity accompanied by high 

density and biomass. Modifications in thermal conditions also contribute to the compositional 

changes in macroinvertebrates below reservoirs. Research priorities recommended are: seasonal 

studies of Cladophora glomerata, studies on optimal flow rates for Cladophora glomerata

population growth, food web studies in tailwaters of Glen Canyon Dam, phenological studies of 

invertebrates in the Colorado River ecosystem, and model development to study the effects of 

physicochemical parameters on plant and animal communities in regulated rivers.

Blinn, 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 

14(2):233–248. 

 We used five in situ experiments to test the influence of fluctuations in river discharge on 

the structure and function of the tailwaters benthos associated with cobble substrate in the 

Colorado River downstream from Glen Canyon Dam, Arizona, U.S.A. Periods of daily 

desiccation and freezing during river fluctuation significantly limited community biomass and 

energy. The permanently submerged channel supported 4-fold higher macroinvertebrate mass 

than the varial zone. Daily harvest of benthos showed a 50% reduction in mass of Cladophora 

glomerata after 2 d of repeated 12-h summer exposure. Five days of repeated exposure resulted 
Humpback Chub Annotated Bibliography 126 September 2009

 

in >70% reduction in macroinvertebrate mass after only one 12-h summer exposure. One night 

time exposure to subzero winter air temperatures resulted in >50% loss of chlorophyll a and 

mass of C. glomerata and >90% loss in macroinvertebrate mass. Gastropod densities on resubmerged cobbles that were subjected to long-term desiccation (~6 mo) equaled submerged 

control cobbles within 1 wk, whereas recolonization by C. glomerata, Gammarus lacustris, and 

chironomid larvae was significantly slower; i.e. <30% of controls after 4 mo. Hence, our data 

showed that two 12-h exposure periods may require >4 mo for recovery to achieve the mass of 

permanently submerged benthos. Incremental increases in benthic energy (joules/m2

) over 

increased base discharge from 142 to 793 m3

/s may result in an increase in trout mass of 

approximately 42.5 kg/ha in the tailwaters of Lees Ferry.

Dresser, Jr., T.J. 1996. Diet of adult humpback chub. Pages 59-65. In The effects of an 

experimental flood on the aquatic biota and their habitats in the Colorado River, Grand 

Canyon, Arizona. Arizona Game and Fish Department, Phoenix. Abstract excerpted from 

study discussion. 

The null hypothesis being tested is that there is no difference in the stomach contents of 

adult humpback chub before, during, or after the high river discharge. We anticipate that 

scouring caused by the flood will alter food availability, which will alter the diet of these 

opportunistic feeders. 

 Humpback chub in the Colorado River, Grand Canyon, consumed a variety of aquatic 

and terrestrial invertebrates during the study period. Simuliids were the most common aquatic 

invertebrates ingested by humpback chub during all phases of the experiment. Chironomids and 

Gammarus lacustris were next in occurrence. The bulk of the terrestrial invertebrates found in 

the stomach contents of humpback chub were primarily Coleoptera. During the pre-flood phase, 

simuliids and chironomids comprised the bulk of the diet by ash-free dry weight. The observed 

increases in Gammarus in the stomach contents of humpback chub during the flood and postflood phases may be attributed to increased stream flow. High flows that scoured the backwaters 

and margins of the Colorado River transported Gammarus downstream making them more 

accessible to the chub. 

 Based on ash-free dry weights, simuliids and chironomids in the stomach contents of 

humpback chub decreased significantly during the flood. This decrease in simuliid and 

chironomid biomass may be attributed to increased turbidity, which may have made these 

organisms less visible to the chub. Decreases in simuliid and chironomid biomass may also be 

related to changes in benthic community structure because of high discharges. 

 Increases in the occurrence and percent (AFDM) of terrestrial invertebrates in the 

stomach contents of humpback chub were observed during this study. Increases in terrestrial 

invertebrates can be attributed to increased flows washing them into the river. 

 Based on the findings of this study, we conclude that humpback chub are very 

opportunistic in their feeding habits and can use food sources as they become available. Our 

findings indicate no significant changes in mean total biomass or mean number of invertebrates 
Humpback Chub Annotated Bibliography 127 September 2009

 

in the stomach contents of chub. Therefore, we conclude that the effects of the 1996 

Experimental Flood on the feeding behavior of the adult humpback chub were minimal. 

Haden, G.A., D.W. Blinn, J.P. Shannon and K.P. Wilson. 1999. Driftwood: an alternative 

habitat for macroinvertebrates in a large desert river. Hydrobiologia 397:179–186. 

Driftwood was an important substratum for macroinvertebrates in the Colorado River, a 

desert river in southwestern U.S.A. with high suspended sediments and limited cobble substrate. 

Higher light availability and reduced abrasion on driftwood substrata resulted in a significantly 

higher ash-free dry mass (AFDM) of biofilm when compared to cobbles. Overall mean mass of 

biofilm on driftwood was 3.76 g m-2 AFDM (SE ±0.19) compared to 2.45 g m-2 AFDM (SE 

±0.15) on cobbles. Total macroinvertebrates AFDM was not significantly different between 

cobble and driftwood substrate. However, there were differences in the Ephemeroptera 

assemblage on the two substrata which were attributed to the type of food resources available in 

each habitat. Driftwood was dominated by the scraper/collector Heptagenia elegantula (Eaton), 

while the filter/collector, Traverella albertana (McDunnough) dominated cobbles. Twenty taxa 

were found on driftwood substrata. This habitat expands the type of niches available to 

macroinvertebrates in lotic systems with high suspended sediments. We calculated that 4.4 m2

 of 

driftwood substratum passed our sample station each minute during a 12-h sampling period on 

the rising limb of the hydrograph. River impoundments limit the supply and transport of 

driftwood, which may have negative implication on macroinvertebrate communities in desert 

rivers with high suspended sediment. Studies in turbid desert rivers that do not sample driftwood 

may underestimate both the total standing mass/energy of the system and taxon richness. 

Kennedy, T.A. and S.P. Gloss. 2005. Aquatic ecology: the role of organic matter and 

invertebrates. Pages 87-102 in Gloss, S.P., J.E. Lovich and T.S. Melis, eds., The state of the 

Colorado River ecosystem in Grand Canyon. A report of the Grand Canyon Monitoring 

and Research Center 1991-2004. USGS Circular 1282. U.S. Geological Survey, Flagstaff, 

Arizona. 

Closure of Glen Canyon Dam and the beginning of flow regulation of the Colorado River 

through Grand Canyon in 1963 changed the river through the canyon considerably. The river 

changed from having highly variable discharge rates and temperatures and high suspendedsediment loads to having a relatively constant flow regime, cold and constant water 

temperatures, and suspended-sediment loads that are dramatically reduced relative to pre-dam 

levels. These changes in the physical environment, coupled with changes in the quantity and 

types of organic matter present in the Colorado River and intentional introductions of aquatic 

invertebrates that occurred shortly after Glen Canyon Dam was closed, have led to substantial 

changes in the kinds of aquatic invertebrates present in the Grand Canyon ecosystem. Since the 

closure of the dam, considerable effort has been directed toward understanding the aquatic 

ecology of this altered ecosystem. This chapter describes the results of the research and 

monitoring activities that have investigated the kinds of organic matter and invertebrate 

communities in the Colorado River below Glen Canyon Dam. Collectively, organic matter and 

the aquatic invertebrates that consume it largely constitute the food base for fish in the Colorado 

River ecosystem. This chapter focuses on patterns, trends, and important controls on the amount 

and sources of organic matter and invertebrates that are primary food resources for humpback 
Humpback Chub Annotated Bibliography 128 September 2009

 

chub (Gila cypha) and rainbow trout (Oncorhynchus mykiss) in an effort to understand the role 

that food plays in determining the distribution, population density, and growth of these fish in 

this ecosystem. Furthermore, most of the research and monitoring that have been conducted on 

organic matter and invertebrates in this ecosystem have centered on the food items that are 

important for these two species. This chapter also addresses how organic matter and 

invertebrates are affected by the timing and magnitude of water releases from Glen Canyon 

Dam, including the modified low fluctuating flow (MLFF) alternative, which was implemented 

in 1996 and continues as the operating regime for Glen Canyon Dam today. Finally, this chapter 

concludes with a brief discussion of recommended research directions and management actions. 

Shannon, J.P., D.W. Blinn, T. McKinney, E.P. Benenati, K.P. Wilson and C. O’Brien. 

2001. Aquatic food base response to the 1996 test flood below Glen Canyon Dam, Colorado 

River, Arizona. Ecological Applications 11(3): 672–685. 

We examined the impact of the 1996 test flood released from Glen Canyon Dam (GCD) 

on the aquatic food base in the Colorado River through Grand Canyon National Park, Arizona, 

USA. Benthic scour and entrainment of both primary and secondary producers occurred at all 

study sites along the 385-km river corridor. The majority of the organic drift occurred within the 

first 48 h of the test flood with the arrival of the hydrostatic wave. Recent macrophyte colonizers 

(Chara, Potamogeton, and Elodea) of fine sediment in the tailwaters were scoured from the 

channel bottom, with recovery to pre-flood estimates within 1-7 months depending on taxa. 

Macroinvertebrates and filamentous algae recovered within three months depending on taxa. The 

test flood removed suspended particles from the water column and increased water clarity, which 

enhanced benthic recovery. The test-flood hydrograph was designed primarily as an experiment 

in sand transport and occurred during a period of sustained high releases from GCD starting in 

June 1995 due to above-average inflow into Lake Powell. We discuss the implications of the 

hydrograph shape, pre- and post-riverine conditions, and the slow response time of biological 

resources for design of aquatic ecosystem experiments. 

Shannon, J.P., D.W. Blinn, P.L. Benenati and K.P. Wilson. 1996. Organic drift in a 

regulated desert river. Canadian Journal of Fisheries and Aquatic Sciences 53(6):1360–

1369. 

Coarse particulate organic mass varied seasonally and changed from autochthonous to 

allochthonous organic matter along a 386-km section of the Colorado River below Glen Canyon 

Dam, Arizona. Dam operations influenced drift components selectively throughout the 

hydrograph; however, ramping rate had no effect on drift mass. Eddies and pools collected 

approximately 50% of the mainstem drift with only detritus retained long enough to settle in 

pools. Coarse particulate organic drift mass was negatively correlated with stream gradient in the 

Colorado River. Cladophora drift packets were pulverized by rapids, which subsequently 

increased fine particulate organic matter at downriver sites. Tributary type (spring stream or 

large desert watershed river) significantly altered the mass and composition of tributary drift; 

however, tributaries contributed <0.1% of the total organic matter to main-stem drift. Terrestrial 

insects represented <0.001% of the total invertebrate mass in main-stem drift. As a result of 

hydraulics and suspended sediment, organic drift mass throughout the river corridor is reach 

specific. Longitudinal change in drift composition corresponds with a shift in fish species. 
Humpback Chub Annotated Bibliography 129 September 2009

 

Shaver, M.L., J.P. Shannon, K.P. Wilson, P.L. Benenati and D.W. Blinn. 1997. Effects of 

suspended sediment and desiccation on the benthic tailwater community in the Colorado 

River, USA. Hydrobiologia 357(1-3):63–72. 

We demonstrated that differences in habitat requirements by C. glomerata and 

Oscillatoria have a profound bottom-up influence on the foodweb in the tailwaters below Glen 

Canyon Dam in the Colorado River through Grand Canyon National Park, USA. We examined 

the effects of suspended sediment and desiccation on the colonization sequence of Cladophora 

glomerata and Oscillatoria spp. and the consequent effects on macroinvertebrates in each algal 

community in a series of reciprocal transplants in the regulated Colorado River, AZ. Our 

experiments showed that C. glomerata grows best in continuously submerged, clear-water, stable 

habitats, whereas Oscillatoria forms dense mat-like matrices of trichomes and sand in varial 

zones and habitats with high suspended sediments typical of many southwestern USA streams. 

Varial zone conditions have a stronger influence on community structure than habitats with high 

suspended sediments. Recruitment by chironomid larvae was less dependent on C. glomerata

and less affected by suspended sediment and periodic desiccation than Gammarus lacustris. We 

estimated the energy from macroinvertebrate biomass associated with tufts of C. glomerata to be 

an order of magnitude higher than that in Oscillatoria matrices. Therefore, loss of C. glomerata 

and replacement of habitat more suitable for Oscillatoria as a result of regulated flows indirectly 

reduces potential energy flow in the Colorado River foodweb. 

4.5 SUPPORTING ARTICLES 

Bestgen, K. and L.W. Crist. 2000. Response of the Green River fish community to 

construction and re-regulation of Flaming Gorge Dam, 1962–1996. Final report of 

Colorado State University Larval Fish Laboratory to Upper Colorado River Endangered 

Fish Recovery Program, Lakewood, Colorado. 

We evaluated aspects of the protocol offered by Stanford et al. (1996) for restoration of 

biota in regulated rivers. The chronology of river regulation events and associated biotic 

evaluations that occurred in the regulated reach of the Green River upstream of the Yampa River 

from 1962 to 1996 offered an opportunity to determine the effectiveness of thermal enhancement 

and discharge re-regulation to restore native fishes. Prior to closure of Flaming Gorge Dam, the 

Green River supported an intact native fish assemblage and few non-native fishes occurred there. 

Closure and operation of Flaming Gorge Dam eliminated most native fishes in the regulated 

reach of the Green River from 1967 to 1978 because low water temperatures inhibited 

reproduction. The hydrograph was flat with no spring peak, high summer base flow, and 

sediment load was reduced. Thermal enhancement of the regulated reach in 1978, via dam 

penstock modification, had an immediate effect because reproduction by most resident native 

fishes was restored. The regulated reach supported nine native fishes, and only rare Colorado 

pikeminnow and razorback sucker did not reproduce. Discharge re-regulation begun in 1992 

partially restored spring peaks and lowered early summer base flows. Sampling conducted 

during the period 1994 to 1996 demonstrated that native fishes were numerically dominant in 

electrofishing samples collected in Lodore Canyon. Native fishes were dominant in seine 
Humpback Chub Annotated Bibliography 130 September 2009

 

samples collected in upstream Lodore Canyon low-velocity habitats. Roundtail chub was very 

rare in the reach and may be declining in abundance. Non-native fishes dominated in backwaters 

in lower Lodore and in Island -Rainbow Park. Populations of other native fishes were stable and 

abundance of Colorado pikeminnow increased since 1980, perhaps in response to flow reregulation and subsequent changes in the thermal environment. Abundance of cold water fishes 

has declined since 1980, and abundance of cool or warm-water fishes increased. Diversity and 

abundance of non-native fishes increased since 1980, especially in lower Lodore Canyon. 

Especially problematic may be piscivorous channel catfish, smallmouth bass, and northern pike. 

A strong water temperature gradient played a large role in controlling distribution and abundance 

of fishes in the regulated reach during the period 1994-1996. Relatively cool upstream 

temperatures may have limited the distribution and abundance of several warm-water fishes to 

reaches of the Green River downstream of lower Lodore Canyon. Limited backwater habitat in 

the upper reaches of Lodore Canyon may have restricted occurrence of obligate backwater 

species such as red and sand shiner, fathead minnow, and redside shiner. Abundance of several 

combinations of hybrid suckers was high and much increased since 1980. Particularly common 

were hybrids that had white sucker as one parental type. Occurrence of cool water white suckers 

and hybrids declined in a downstream direction in Lodore Canyon, presumably in response to 

warmer water temperatures. Drift net sampling captured few fish of any kind, and reproduction 

by Colorado pikeminnow was not detected. A moderate-sized population of Colorado 

pikeminnow inhabited Lodore Canyon and were captured there in spring, summer, and fall. 

Length changes of recaptured fish and length-mass relationships indicated that resident fish had 

high growth rates. Minimally, Lodore Canyon provided important habitat for adult feeding. 

Water temperature of the Green River downstream of Flaming Gorge Dam was reliably 

predicted by ambient air temperature and discharge level. Water temperatures suitable for 

reproduction by Colorado pikeminnow were present early in the summer in some years. 

However, mid- and late-summer warming associated with reproduction by Colorado 

pikeminnow in the unregulated Yampa River was negated in the regulated reach of the Green 

River by increased discharge from Flaming Gorge Dam. Increased discharge was mandated by 

the 1992 Biological Opinion on operation of Flaming Gorge Dam. Further restoration of the fish 

community and habitat in the regulated reach of the Green River requires re-establishment of 

more natural discharge and temperature regimes, similar in pattern to those which occur in the 

unregulated Yampa River and the historical Green River. More natural flow and temperature 

patterns may also benefit native fishes in Green River reaches downstream of the Yampa River. 

Distribution and abundance of non-native fish populations will also likely expand if summer 

water temperatures of the regulated reach of the Green River are enhanced. 

Bowen, Z.K., M.C. Freeman and K.D. Bovee. 1998. Evaluation of generalized habitat 

criteria for assessing impacts of altered flow regimes on warmwater fishes. Transactions of 

the American Fisheries Society 127:455–468. 

 Our study investigated relationships between availability and temporal persistence of key 

habitats and fish assemblage structure at regulated and unregulated sites in the Tallapoosa River 

system. Fish assemblage characteristics at seven sites were quantified based on 1,400 

electrofishing samples collected during 1994 and 1995. Physical Habitat Simulation (PHABSIM) 

programs were used to model availability and persistence of key habitats at regulated and 

unregulated sites. Associations between fish assemblages and availability or persistence of key 
Humpback Chub Annotated Bibliography 131 September 2009

 

habitats were identified via regression and analysis of variance. We found that hydropeaking 

dam operation reduced the average length of time that shallow-water habitats persisted and also 

reduced year-to-year variation in the persistence of shallow-water habitats compared with 

unregulated sites. Across sites and years, proportional representation of catostomids was 

positively correlated with persistence of shallow and slow-water habitats during spring. 

Proportion of individuals as cyprinids was positively correlated with median availability of 

deep–fast habitat whereas proportion of percids was inversely related to median availability of 

deep–fast habitat. Mean fish density was positively correlated with the persistence of shallow 

and slow-water habitats. Comparisons of key-habitat measures and fish abundances between 

1994 and 1995 at each site indicated that higher abundances of percids, catostomids, and 

cyprinids were associated with increased availability and persistence of shallow and slow-water 

habitats in 1995. These findings demonstrate that the temporal and spatial availability of key 

habitats could serve as useful measures of the potential effects of flow alteration on lotic fish 

assemblages and suggest that both short-term persistence of key habitats as well as annual 

variation in key-habitat availability are important for maintaining diverse fish assemblages. 

Casagrandi, R. and M. Gatto. 1999. A mesoscale approach to extinction risk in 

fragmented habitats. Nature 400: 560–562. 

 Assessing the fate of species endangered by habitat fragmentation 1±3 using spatially 

explicit and individual-based models4±7 can be cumbersome and requires detailed ecological 

information that is often unavailable. Conversely, Levins-like8 macroscale models neglect data 

on the distribution of local numbers, which are frequently collected by field ecologists11±13. 

Here we present an alternative, mesoscale approach for metapopulations that are subject to 

demographic stochasticity, environmental catastrophes and habitat loss. Starting from a model 

that accounts for discrete individuals in each patch and assumes a birth-death stochastic process 

with global dispersal14,15, we use a negative binomial approximation16 to derive equations for 

the probability of patch occupancy and the mean and variance of abundance in each occupied 

patch17. A simple bifurcation analysis18 can be run to assess extinction risk. Comparison with 

both the original model and a spatially explicit model with local dispersal proves that our 

approximation is very satisfactory. We determine the sensitivity of metapopulation persistence to 

patch size, catastrophe frequency and habitat loss, and show that good dispersers are affected 

more by habitat destruction than by environmental disasters. 

Johnson, J.E. and R.T. Hines. 1999. Effect of suspended sediment on vulnerability of 

young razorback suckers to predation. Transactions of the American Fisheries Society 

128:648–655. 

The decline of native fishes in North America is principally a result of altered habitats, 

and the impact of mainstream dams has accounted for many of the habitat changes. Diminished 

turbidity, and introduced nonnative predators were investigated as possible reasons for the 

decline of endangered razorback suckers Xyrauchen texanus in the Colorado River. In laboratory 

tests, young razorback suckers selected clear water over two water samples with higher 

concentrations of suspended sediment. In clear water, however, young razorback suckers were 

extremely susceptible to predation; native Colorado squawfish Ptychocheilus lucius consumed 

90% of test razorback suckers, and nonnative green sunfish Lepomis cyanellus consumed 99.6%. 
Humpback Chub Annotated Bibliography 132 September 2009

 

As turbidity increased, razorback sucker predator avoidance improved and differences in 

predator success disappeared. Winter–spring spawning by razorback suckers in Lake Mohave, 

along with the extreme susceptibility of larvae to predation in clear water, may account for total 

recruitment failure in that lake. However, in upper basin rivers, suspended sediments remain high 

enough to limit predation by fishes tested, suggesting that other impacts, including contaminants 

and lack of floodplain habitat, may be thwarting recruitment in those rivers. 

Junk, W.J., P.B. Bailey and R.E. Sparks. 1989. The flood pulse concept in river-floodplain 

systems. Canadian Special Publication of Fisheries and Aquatic Sciences 106:110–127. 

The principal driving force responsible for the existence, productivity, and interactions of 

the major biota in river-floodplain systems is the flood pulse. A spectrum of geomorphological 

and hydrological conditions produces flood pulses, which range from unpredictable to 

predictable and from short to long duration. The flood pulse is a "batch" process and is distinct 

from concepts that emphasize the continuous processes in flowing water environments, such as 

the river continuum concept. Floodplains are distinct because they do not depend on upstream 

processing inefficiencies of organic matter, although their nutrient pool is influenced by periodic 

lateral exchange of water and sediments with the main channel. 

Papoulias, D. and W.L. Minckley. 1990. Food limited survival of larval razorback sucker, 

Xyrauchen texanus, in the laboratory. Environmental Biology of Fishes 29:73–78. 

Razorback suckers in Lake Mohave, Arizona-Nevada, are suffering recruitment failure. 

Concomitantly, lake zooplankton levels are low and variable. We test, under laboratory 

conditions, the possibility that starvation is a cause of low recruitment. Razorback sucker larvae 

that were starved, received food too late, or were provided with insufficient food died between 

20 and 30 d after hatching. Yolk absorption was at 8d after hatching, the critical period during 

which larvae must feed or most will die lies between 8 and 19d, and the point of irreversible 

starvation for individuals is between 19 and 23 d after hatching. Results support food-related 

mortality as a contributor to year-class failure of razorback sucker in Lake Mohave. 

Stevens, L.E., J.C. Schmidt, J.C. Ayers, T.J. Brown and T. Bryan. 1995. Flow regulation, 

geomorphology, and Colorado River marsh development in the Grand Canyon, Arizona. 

New, productive fluvial marshes may develop along regulated canyon rivers through 

reduction in flood frequency, thereby increasing diversity, production, and wildlife habitat 

availability. Few fluvial marshes occurred along the eddy-dominated Colorado River in the 

Grand Canyon prior to construction of Glen Canyon Dam in 1963. Reduction of flooding after 

1963 permitted widespread marsh development. Fluvial marshes exhibited low stability but high 

resilience, quickly redeveloping after scouring by high flows between 1983 and 1986. In 1991, 

253 fluvial wet marshes (cattail/reed and horseweed/Bermuda grass) and 850 dry marshes 

(horsetail/willow) occupied 25.0 ha (1%) of the 363 km mainstream riparian corridor between 

Lees Ferry and Diamond Creek, Arizona. Fluvial marsh development and composition varied in 

relation to local and reach-based geomorphology, and microsite gradients in inundation 

frequency and soil texture. Colorado River marsh density (number/km2

) increased with distance 

downstream, and marshes were larger and more abundant in wide reaches. Wet marsh 
Humpback Chub Annotated Bibliography 133 September 2009

 

cattail/reed stands developed on silty loam soils in low velocity depositional environments that 

were inundated 54% of the days from 1986 to 1991, whereas dry horsetail/willow marshes 

occupied less frequently inundated sites with sandy soils. Mean marsh standing mass (641 g 

C/m2

) was comparable with values from regulated alluvial river marshes, but litter retention 

appeared limited by flow variability in both regulated and unregulated fluvial marshes. We 

discuss implications of flow management on the four marsh assemblages, and the need for 

consensus on priorities for management of regulated fluvial wetlands. 

Ward, D.L. and S.A. Bonar. 2003. Effects of cold water on susceptibility of age-0 

flannelmouth sucker predation by rainbow trout. Southwestern Naturalist 48:43–46. 

We conducted laboratory tests to evaluate the effects of an abrupt 10°C decrease in water 

temperature on ability of age-0 flannelmouth suckers (Catostomus latipinnis) to escape predation 

by rainbow trout (Oncorhynchus mykiss). Juvenile flannelmouth suckers (58 mm mean total 

length) were maintained at 20°C and introduced individually, without acclimation, into tanks 

containing a single adult rainbow trout (246 mm mean total length) at 10 or 20°C. Rainbow trout 

attacked suckers more often at 20°C, but were more likely to capture them at 10°C. Age-0 

flannelmouth suckers experience an abrupt temperature decrease when they exit warm tributaries 

and enter cold hypolimnetic water released from Glen Canyon Dam on the Colorado River. This 

temperature change might increase susceptibility of young flannelmouth suckers to predation by 

rainbow trout, which are abundant in the Colorado River in Glen, Marble, and Grand canyons. 

Ward, J.V. and J.A. Stanford. 1995. Ecological connectivity in alluvial river ecosystems 

and its disruption by flow regulation. Regulated Rivers: Research & Management 

11(1):105–119. 

The ecological integrity of dynamic floodplain river systems was maintained by 

ecological connectivity operating across a range of time scales through dynamic interactions 

between hydrological, geomorphological and successional processes. During seasonal inundation 

of the floodplain the flood pulse formed a ‘moving littoral’ that traversed the aquatic/terrestrial 

transition zone increasing productivity and enhancing connectivity. Spatiotemporal heterogeneity 

of floodplain river systems structured biotic communities and natural levels of disturbance 

maintained the floodplain ecological integrity. Flow regulation decreased the frequency and 

extent of floodplain inundation, reduced channel migration and altered the temporal pattern of 

flooding, while truncation of sediment transport resulted in channel degradation and channel 

deepening affected riparian vegetation dynamics. Connectivity between the river channel and 

floodplain was decreased and habitat heterogeneity declined. Regulation tended to accelerate the 

successional trend towards terrestrialization and reduce the formation of floodplain water bodies 

but the ecological integrity of river-floodplain ecosystems could be restored by re-establishing 

dynamic connectivity between the channel and floodplain water bodies. 
Humpback Chub Annotated Bibliography 134 September 2009

 

Ward, D.L., O.E. Maughan, S.A. Bonar and W.J. Matter. 2002. Effects of temperature, 

fish length and exercise on swimming performance of age-0 flannelmouth sucker. 

Transaction of the American Fisheries Society 131:492–497. 

 The flannelmouth sucker Catostomus latipinnis is one of the few native fish that persists 

in the lower Colorado River basin. Little is known about the effects of hypolimnetic releases of 

cold, swift water from Colorado River dams on flannelmouth sucker populations. We conducted 

fatigue velocity tests on age-0 flannelmouth suckers in the laboratory to evaluate the effects of 

water temperature and fish size on swimming ability. Fish of 25-114 mm total length (TL) were 

subjected to incremental increases in water velocity until the upper limit of their swimming 

ability was reached. Swimming tests were conducted at 10, 14, and 20°C. Swimming ability 

increased with fish length and was directly related to water temperature at all fish sizes. A 

decrease in water temperature from 20°C to 10°C resulted in an average decrease in swimming 

ability of 40%. Mean swimming ability of wild-caught flannelmouth suckers was 7 cm/s higher 

than that of captive-reared flannelmouth suckers of similar size at 20°C and 14°C. Flannelmouth 

suckers subjected to an abrupt 10°C temperature drop did not have significantly different 

swimming ability than flannelmouth suckers acclimated to 10°C over 4 d. 

5 OTHER IMPACTS 

5.1 NONNATIVE SPECIES 

Douglas, M.E. and P.C. Marsh. 1996. Endangered humpback chub (Gila cypha) as prey of 

introduced fishes in the Little Colorado River, Arizona. Section 2 in M.E. Douglas and P.C. 

Marsh, eds. Ecology and Conservation Biology of Humpback Chub (Gila cypha) in the 

Little Colorado River. Bureau of Reclamation, Salt Lake City, Utah. 

 Endangered humpback chub and other native fishes were a significant dietary component 

(13.5% of 408 stomachs) of five predatory, non-native fishes from the Little Colorado River, 

Arizona. Stomach contents varied among species, were low in diversity, and predominated by 

detritus, algae (primarily Cladophora), and aquatic insects. Twenty-one introduced species occur 

n Grand Canyon, and more than 25.8 million fish have been stocked there and in reservoirs 

immediately up- and downstream. Interaction between non-native and native fishes predation, 

resource competition, displacement) may constitute a significant impact on the latte. 

Kennedy, T.A. 2007. A Dreissena risk assessment for the Colorado River ecosystem. U.S. 

Geological Survey open file report 2007–1085. 

Nonnative zebra and quagga mussels (Dreissena polymorpha and Dreissena bugensis, 

respectively; fig. 1) were accidentally introduced to the Great Lakes in the 1980s and 

subsequently spread to watersheds of the Eastern United States (Strayer and others, 1999). The 

introduction of Dreissena mussels has been economically costly and has had large and farreaching ecological impacts on these systems. Quagga mussels were found in Lakes Mead and 

Havasu in January 2007. Given the likelihood that quagga mussels and, eventually, zebra 
Humpback Chub Annotated Bibliography 135 September 2009

 

mussels will be introduced to Lake Powell and the Colorado River at Lees Ferry, it is important 

to assess the risks that introduction of Dreissena mussels pose to the Colorado River ecosystem 

(here defined as the segment of river from just below Glen Canyon Dam to Diamond Creek; 

hereafter CRE). In this report, I assess three different types of risks associated with Dreissena 

and the CRE: (1) the risk that Dreissena will establish at high densities in the CRE, (2) the risk 

of ecological impacts should Dreissena establish at high densities in the CRE or in Lake Powell, 

and (3) the risk that Dreissena will be introduced to tributaries of the CRE. 

The risk of Dreissena establishing within the CRE is low, except for the Lees Ferry 

tailwater reach where the risk appears high. Dreissena are unlikely to establish at high densities 

within the CRE or its tributaries because of high suspended sediment, high ratios of suspended 

inorganic:organic material, and high water velocities, all of which interfere with the ability of 

Dreissena to effectively filter feed. The rapids of Grand Canyon may represent a large source of 

mortality to larval Dreissena, which would limit their ability to disperse and colonize 

downstream reaches of the CRE. In contrast, conditions within the Lees Ferry tailwater generally 

appear suitable for Dreissena establishment, with the exception of high average water velocity. 

If Dreissena establish within the CRE, the risks of negative ecological impacts appear 

low. If Dreissena are able to attain moderate densities in Lees Ferry, estimates of filtration 

capacity indicate they are unlikely to substantially alter the composition (e.g., nutrient 

concentrations, suspended organic matter concentrations) of water exported from Lees Ferry. 

Further, a moderate density of Dreissena within Lees Ferry may actually increase food available 

to fishes by increasing habitat complexity and stimulating benthic production. If Dreissena attain 

moderate densities in the CRE mainstem, which seems unlikely, ecological impacts will 

probably be comparable to Lees Ferry—an increase in benthic production. Dreissena may have 

ecological impacts on the CRE, if they become established in Lake Powell and substantially alter 

the composition of water released from Glen Canyon Dam; however, it is unclear whether 

changes in the composition of water released from Glen Canyon Dam will have a net positive or 

negative impact on food availability in the CRE mainstem. 

 The risk of Dreissena introduction to tributaries appears low. None of the tributaries have 

upstream lakes or reservoirs that could actually serve as a source population for Dreissena; 

reservoirs on the Little Colorado River may eventually support Dreissena, but they are far up in 

the watershed and the segment of river connecting them with the mainstem CRE is intermittent. 

If the CRE mainstem is colonized by Dreissena, there are no significant vectors for transporting 

them upstream into the tributaries. In addition, lethally high summer water temperatures make it 

unlikely that Dreissena will establish in many tributaries. 

Lake Powell is a logical focus for management and research efforts, given that 

maintenance of Dreissena populations within the CRE will require an upriver source population 

and the uncertainty associated with the downstream impact of changes in Lake Powell water 

quality. 
Humpback Chub Annotated Bibliography 136 September 2009

 

Marsh, P.C. 2005. Immiscibility of native and nonnative species. Pages 59-63 in 

Proceedings of two symposia: restoring native fish to the lower Colorado River: interaction 

of native and non-native fishes. July 13-14, 1999. Las Vegas, Nevada. U.S. Fish and Wildlife 

Service, Southwest Region, Albuquerque, New Mexico. 

Native and non-native fishes in the lower Colorado River overlap broadly in their 

physical habitat and resource uses, and no attribute of either use-category favors one group of 

fishes over another. The presence of nonnative fishes alone precludes life-cycle completion by 

the natives. In the absence of non-natives, however, the natives thrive even in severely altered 

habitats. Compelling evidence supports a recommendation of segregated management of native 

and non-native fishes. Unabated declines of the imperiled native fish fauna demands expedient 

action by responsible parties to plan and implement appropriate strategies. 

Marsh, P.C. and M.E. Douglas. 1995. Humpback chub as food of non-native fishes in the 

Little Colorado River. Proceedings of the Desert Fishes Council, Flagstaff, Arizona. 

 We examined foods of non-native rainbow and brown trout, channel catfish, and yellow 

and black bullhead in monthly samples from the Little Colorado River, Arizona, from June 1991 

to July 1994. Food items varied among species, were low in diversity, and dominated by detritus, 

algae, and aquatic insects. Endangered humpback chub and other native fishes appeared minor 

components (5% frequency of occurrence in 315 guts). However, non-native fish are abundant, 

and even modest predation rates could result in consumption of substantial numbers of native 

fish. For example, if 5% of predators each eat 2 fish a week (the average number per stomach), 

then as few as 1,000 predators would consume 5,200 fish a year. Consumed chubs that we were 

able to measure (N=11) averaged 121 mm TL and were mostly yearlings. We have not quantified 

age/size specific mortality, but recaptures of PIT-tagged individuals >150 mm TL suggest rates 

are low. Thus, annual loss to non-native predators of several thousand young chub could 

significantly impact the native population, even to the point of limiting or reducing population 

size by curtailing recruitment. 

Marsh, P.C. and M.E. Douglas. 1997. Predation by introduced fishes on endangered 

humpback chub and other native species in the Little Colorado River, 

Arizona. Transactions of the American Fisheries Society (Bethesda) 126(2):343-346. 

Fishes in the Little Colorado River in the Grand Canyon, Arizona, were sampled monthly 

from July 1991 to June 1995 as part of a study of the ecology of endangered humpback chub 

Gila cypha. Diets of five introduced predatory fish species were examined. Stomach contents 

varied among species and were low in diversity and dominated by algae (primarily Cladophora), 

aquatic insects, and fishes. Humpback chub plus other native species were a significant 

component of the diet (13.7% frequency of occurrence among 219 of 408 stomachs that 

contained food). Predation mortality from introduced fishes may significantly affect the native 

species by depleting numbers and reducing recruitment. 
Humpback Chub Annotated Bibliography 137 September 2009

 

Marsh, P.C., C.A. Pacey and W.L. Minckley. 1999. Resource use attributes of Colorado 

River fishes and implication for management of native and non-native species. Proceedings 

of the Desert Fishes Council 30:24. 

 The Colorado River is physically altered and hydrologically regulated. New habitats 

created by dams include impoundments and thermally depressed tailwaters, which differ 

dramatically from the stream before dams. Nonetheless, evidence from case studies argues that 

these altered places should be occupied by self-sustaining native fish communities. Instead, an 

introduced ichthyofauna overwhelmingly dominates the lower river, and native fishes are 

reduced to a few imperiled species in isolated reaches. The array of non-native fishes has 

feeding, behavioral, and reproductive attributes that allow it to displace, replace, or exclude the 

natives independent of physical habitat features. We therefore recommend segregated 

management of native and non- native fishes as the only means of attaining the maintenance of 

self-perpetuating populations of indigenous species. 

Mueller, G.A. 2005. Predatory fish removal and native fish recovery in the Colorado 

River mainstem: what have we learned? Fisheries 30(9):10–19. 

 Mechanical predator removal programs have gained popularity in the United States and 

have benefited the recovery of several native trout and spring fish. These successes have been 

limited to headwater streams and small, isolated ponds or springs. Nevertheless, these same 

approaches are being applied to large river systems on the belief that any degree of predator 

removal will somehow benefit natives. This attitude is prevalent in the Colorado River mainstem 

where recovery and conservation programs are struggling to reverse the decline of four 

endangered fish species. Predator removal and prevention are major thrusts of that work but 

unfortunately, after 10 years and the removal of >1.5 million predators, we have yet to see a 

positive response from the native fish community. This leads to the obvious question: is 

mechanical removal or control in large (>100 cfs base flow) western streams technically or 

politically feasible? If not, recovery for some mainstem fishes may not be practical in the 

conventional sense, but require innovative management strategies to prevent their extirpation or 

possible extinction. This article examines (1) what has been attempted, (2) what has worked, and 

(3) what has not worked in the Colorado River mainstem and provides recommendations for 

future efforts in this critical management area. 

Ruppert, J.B., R.T. Muth, and T.P. Nesler. 1993. Predation on fish larvae by adult red 

shiner, Yampa and Green Rivers, Colorado. Southwestern Naturalist 38:397–399. Abstract 

excerpted from results and conclusions. 

The objective of this study was to document predation on fish larvae, particularly larvae 

of native fishes, by nonnative adult cyprinids or juvenile centrarchids or ictalurids collected from 

ephemeral shoreline embayments near the confluence of the Green and Yampa Rivers, Colorado, 

in early summer. Collections with fine-mesh seines (1.6-mm-square mesh) were made on June 

30 and July 2, 14, 19, and 25, 1991. Sampling on June 30 was at 1600–1800 hours, and on other 

dates at 0000–0200, 0400–0600, 1200–1400, 1600–1800, and 2000–2200 hours. Nonnative 

fishes collected and analyzed were yearling channel catfish Ictalurus punctatus (N=17; 51–

144 mm TL) and adult red shiners Cyprinella lutrensis (N=184; 36–79 mm TL), sand shiners 
Humpback Chub Annotated Bibliography 138 September 2009

 

Notropis stramineus (N=47; 30–65 mm TL), fathead minnows Pimephales promelas (N=42; 32–

60 mm TL), and redside shiners Richardsonius balteatus (N=176; 36–77 mm TL). Fish larvae 

(N=58; 1–9 per digestive tract) were found in 15% of the red shiners collected during daylight or 

dusk on June 30 and July 2 and 14; no larvae were detected in digestive tracts of the other 

species. Most of the fish larvae found were too digested for species identification or accurate 

length measurements, but all were cypriniforms (mostly catostomids) and probably less than 

16 mm TL. Seven fish larvae, 11–13 mm TL, were identified as native bluehead sucker 

Catostomus discobolus. The high incidence of fish larvae ingested by red shiners suggests that 

this widespread and abundant species may be an important predator on native fishes in the 

Colorado River system. The degree of predation may be influenced by the abundance of 

alternative invertebrate prey and may be especially severe during spring and early summer in 

ephemeral nursery habitats with fluctuating water levels. 

Stone, D.M. and O.T. Gorman. 2005. Ontogenesis of endangered humpback chub (Gila 

cypha) in the Little Colorado River, Arizona. The American Midland Naturalist 155:123–

135. 

The largest population of endangered humpback chub Gila cypha inhabits the Colorado 

River below Glen Canyon Dam and the lower 14 km of the Little Colorado River (LCR), 

Arizona. Currently, adults from both rivers spawn and their progenies grow and recruit to 

adulthood primarily within the LCR, where we studied G. cypha’s life history using hoop net 

capture data. Humpback chub undergo an ontogenesis from diurnally active, vulnerable, 

nearshore-reliant YOY (30–90 mm total length) into nocturnally active, large-bodied adults 

(≥180 mm TL). During the day, adults primarily resided in deep midchannel pools; however, at 

night they dispersed inshore amongst the higher densities of YOY conspecifics. Many YOY G. 

cypha shifted to nocturnal habitats that provided greater cover, possibly, to avoid inshore 

invading adults. These findings mirror predator-prey scenarios described in other freshwater 

assemblages, but do not refute other plausible hypotheses. Gila cypha piscivorous activity may 

escalate in hoop nets, which can confine fish of disparate sizes together; adults were significantly 

associated with YOY conspecifics and small dead fish in hoop nets at night and eight G. cypha

(156–372 mm TL) regurgitated and/or defecated other fish body parts during handling following 

capture. Gila cypha can definitely be piscivorous given the opportunity, but the magnitude of 

their piscivorous activity in the wild is debatable. 

Stone, D.M., D.R. Van Haverbeke, D.L. Ward and T.A. Hunt. 2007. Dispersal of 

nonnative fishes and parasites in the intermittent Little Colorado River, Arizona. 

Southwestern Naturalist 52(1):130–137. 

We sampled nonnative fishes stranded in isolated pools near Grand Falls in the Little 

Colorado River (LCR), Arizona, after the river ceased flowing (21 June and 12 July 2005) to 

evaluate whether nonnative fishes can invade the perennial, lower 21 km of the LCR from 

upriver sources. The encroachment of nonnative fishes could jeopardize resident populations of 

endangered humpback chub, Gila cypha, and other native fishes in the lower LCR. We captured 

red shiner, Cyprinella lutrensis; common carp, Cyprinus carpio; fathead minnow, Pimephales 

promelas; black bullhead, Ameiurus melas; and plains killifish, Fundulus zebrinus, all of which 

have been captured 0.132 km downriver in the lower LCR and 0.127 km upriver in the closest 
Humpback Chub Annotated Bibliography 139 September 2009

 

perennial sources. Moreover, we detected Asian tapeworm, Bothriocephalus acheilognathi, in 9 

of 30 common carp examined. Our findings suggest that nonnative fishes, including those 

hosting parasites, can invade the lower LCR from upriver sources 0.250 km away during freshets 

and provide a mechanism for the dispersal of invasive aquatic species in intermittent river 

systems. 

Tyus, H.M. and J.F. Saunders. 1996. Nonnative fishes in the Upper Colorado River Basin 

and a strategic plan for their control. Final report of University of Colorado Center for 

Limnology to Upper Colorado River Endangered Fish Recovery Program, Lakewood, 

Colorado. 

Native freshwater fish populations are declining in North America and more than 100 

fishes are federally listed as threatened or endangered. The Colorado River system in the 

southwestern United States has been especially affected. Most of its native fish populations are 

in decline, including four “big river” fishes, Colorado pikeminnow (Ptychocheilus lucius), 

humpback chub (Gila cypha), bonytail (G. elegans), and razorback sucker (Xyrauchen texanus), 

whose populations have declined so precipitously that they are endangered. Physical habitat 

alteration caused native fish declines, but nonnative fishes pose a more serious threat to native 

fishes than previously thought. Nonnative fish control measures needed in the upper Colorado 

River system, identified in part by a workshop of experts, include: (1) preventing movements of 

game fishes out of impoundments and curtailing future stockings, (2) reducing numbers of small, 

nonnative cyprinids in shoreline habitat used as rearing areas by young native fishes, and 

(3) increasing the harvest of channel catfish (Ictalurus punctatus) and common carp (Cyprinus 

carpio) in the mainstream. Large-scale implementation of these nonnative fish control measures 

has proven difficult. Recovery efforts have identified the need for developing nonnative fish 

control strategies and testing methodologies, but no solutions have emerged. A holistic approach, 

including ecosystem recovery plans, should be used in systems where more than one species 

share common problems, such as interactions with nonnative fishes. Nonnative fish interactions 

should be suspected as a potential cause of declining native fish populations.

5.2 PARASITISM 

Brouder, M.J. and T.L. Hoffnagle. 1997. Distribution and prevalence of the Asian fish 

tapeworm, Bothriocephalus acheilognathi, in the Colorado River and tributaries, Grand 

Canyon, Arizona, including two new host records. Journal of the Helminthological Society 

of Washington 64(2):219-226. 

 The Asian tapeworm, Bothriocephalus acheilognathi, was introduced into the United 

States via imported grass carp in the early 1970's. It has since become well established in the 

southeast and mid-south and has been recently found in the southwest. The definitive host in the 

life cycle of B. acheilognathi is cyprinid fishes and therefore, is a potential threat to the federally 

endangered humpback chub, Gila cypha, in the Colorado River, Grand Canyon. In past studies, 

Arizona Game and Fish Department has found that humpback chub in the LCR were infested 

with the Asian tapeworm. However, the cold water of the mainstem Colorado River may be 

limiting their expansion beyond the LCR. This study was conducted to determine the prevalence 
Humpback Chub Annotated Bibliography 140 September 2009

 

of B. acheilognathi in two cyprinid fishes, fathead minnows, Pimephales promelas, and speckled 

dace, Rhinichthys osculus, and determine if it has expanded its distribution to sites outside of the 

LCR. Preliminary data from 1994 show that 54% of the humpback chub, 27% of the speckled 

dace, and 6% of the fathead minnows that were caught were infested with the Asian tapeworm. 

All infested humpback chub were caught in a 15-mile stretch of the Colorado River just 

downstream from the mouth of the LCR, the likely source of their infestation. 

Choudhoury, A., T.L. Hoffnagle and R.A. Cole. 2001. Parasites of native and nonnative 

fishes of the Little Colorado River, Grand Canyon, Arizona. Journal of Parasitology 90: 

1042–1053. 

A 2-yr, seasonal, parasitological study of 1,435 fish, belonging to 4 species of native 

fishes and 7 species of nonnative fishes from the lower Little Colorado River (LCR) and 

tributary creeks, Grand Canyon, Arizona, yielded 17 species of parasites. These comprised 

1 myxozoan (Henneguya exilis), 2 copepods (Ergasilus arthrosis and Lernaea cyprinacea), 

1 acarine (Oribatida gen. sp.), 1 piscicolid leech (Myzobdella lugubris), 4 monogeneans 

(Gyrodactylus hoffmani, Gyrodactylus sp., Dactylogyrus extensus, and Ligictaluridus 

floridanus), 4 nematodes (Contracaecum sp., Eustrongylides sp., Rhabdochona sp., and 

Truttaedacnitis truttae), 3 cestodes (Bothriocephalus acheilognathi, Corallobothrium 

fimbriatum, and Megathylacoides giganteum), and 2 trematodes (Ornithodiplostomum sp. and 

Posthodiplostomum sp.). Rhabdochona sp. was the only adult parasite native to the LCR. 

Infection intensities of Ornithodiplostomum sp. and B. acheilognathi were positively correlated 

with length of the humpback chub Gila cypha. Adult helminths showed a high degree of host 

specificity, except B. acheilognathi, which was recovered from all fish species examined but was 

most abundant in cyprinids. Abundance of B. acheilognathi in the humpback chub was highest in 

the fall and lowest in the summer in both reaches of the LCR. There was no major taxonomic 

difference in parasite assemblages between the 2 different reaches of the river (LC1 and LC2). 

Parasite community diversity was very similar in humpback chub, regardless of sampling site or 

time. The parasite fauna of the LCR is numerically dominated by B. acheilognathi and 

metacercariae of Ornithodiplostomum sp. The richest and most diverse component community 

occurred in a nonnative species, the channel catfish Ictalurus punctatus, but infra-community 

species richness was highest in a native host, humpback chub. 

Clarkson, R.W., A.T. Robinson and T.L. Hoffnagle. 1997. Asian tapeworm, 

Bothriocephalus acheilognathi, in native fishes from the Little Colorado River, Grand 

Canyon, Arizona. Great Basin Naturalist 57: 66–69. 

 Examination of gastrointestinal tracts of native cyprinids from the Little Colorado River 

(LCR) in Grand Canyon, Arizona, 1990-1994, revealed varying rates of prevalence and 

infrapopulation levels of Asian tapeworm (Bothriocephalus acheilognathi). Mean prevalence 

was 28% (range 0-78%) in humpback chub (Gila cypha) and 8% (range 0-46%) in speckled dace 

(Rhinichthys osculus), with infrapopulation as high as 46 and 28 respectively. We also note 

Asian tapeworm infection of the nonnative carp (Cyprinus carpio), fathead minnow (Pimephales 

promelas), and plains killifish (Fundulus zebrinus) from the LCR. Reported pathogenic and 

chronic effects of this cestode to its definitive hosts add concern for the status of the Grand 

Canyon population of the federally endangered humpback chub. The rapidity with which Asian 
Humpback Chub Annotated Bibliography 141 September 2009

 

tapeworm has spread to different drainages of the Colorado River Basin likely portends an 

eventual cosmopolitan basin distribution in lower elevations suitable to the parasite’s 

thermophilic life history. Such biotic changes must be considered among the most serious 

threats to conservation and recovery of native fish populations. 

Cole, R. 2005. Exotic tapeworm found in endangered desert fishes. U.S. Geological 

Survey, Fisheries and Aquatics Bulletin 4(1):2-3. Abstract excerpted from article contents. 

The Asian fish tapeworm (Bothriocephalus acheilognathi) was introduced into the US in 

the 1970s with the importation of grass carp (Ctenopharyngodon idella) and has become 

established in the endangered humpback chub (Gila cypha) population from the Colorado and 

Little Colorado Rivers in Grand Canyon, AZ. This parasite is known to cause disease and death 

primarily in hatchery raised carp, however, pathogenic effects have also been observed in other 

fish species. At the USGS National Wildlife Health Center in Madison, WI, a series of 

experimental trials were carried out using the closely related bonytail chub (Gila elegans), 

another endangered fish of the southwest US, to study the potential impacts of Asian fish 

tapeworm infections on survival, growth, and physiological condition of humpback chub. While 

older juvenile fish (10 months old and 83 mm long) revealed no negative effects associated with 

infections, subsequent experiments with younger and smaller fish (2.5 months and 22 mm long) 

demonstrated infected fish length was reduced as much as 9% on average compared to control 

fish by the end of the 24-week study. Infected fish were found to have significantly lower 

hematocrit levels and a reduced amount of visceral fat when compared with control fish. 

An experiment was also conducted to examine whether tapeworm infections exacerbate 

the effects of thermal shock that small chub undergo when being swept from the warm waters of 

the Little Colorado River (23.5°C) into the cold waters of the Colorado River (9.5°C) during 

monsoon flooding. Results from this experiment revealed no synergistic effects of cold shock 

and tapeworm infection, with control and infected fish exhibiting similar stress responses to the 

thermal extremes.

Hansen, S.P., A. Choudhury, D.M. Heisey, J.A. Ahumada, T.L. Hoffnagle and R.A. Cole. 

2006. Experimental infection of the endangered bonytail chub (Gila elegans) with the 

Asian fish tapeworm (Bothriocephalus acheilognathi): impacts on survival, growth, and 

condition. Canadian Journal of Zoology 84(10):1383–1394. 

Bothriocephalus acheilognathi Yamaguti, 1934, a tapeworm known to be pathogenic to 

some fish species, has become established in the endangered humpback chub (Gila cypha Miller, 

1964) in Grand Canyon, USA, following the tapeworm’s introduction into the Colorado River 

system. The potential impact of this tapeworm on humpback chub was studied by exposing the 

closely related bonytail chub (Gila elegans Baird and Girard, 1853) to the parasite under a range 

of conditions that included potential stressors of humpback chub in their natal waters, such as 

abrupt temperature change and a limited food base. Survival of infected fish under low food 

rations was considerably lower than that of control fish, and mortality of infected fish began 

20 days earlier. Growth of infected fish was significantly reduced, and negative changes in health 

condition indices were found. No significant negative impacts were revealed from the synergistic 

effects between temperature shock and infection. Bothriocephalus acheilognathi does present a 

potential threat to humpback chub in Grand Canyon and should be considered, along with 
Humpback Chub Annotated Bibliography 142 September 2009

 

conventional concerns involving altered flow regimes and predation, when management 

decisions are made concerning conservation of this endangered species. 

Hoffnagle, T.L., A. Choudhury and R.A. Cole. 2006. Parasitism and body condition in 

humpback chub from the Colorado and Little Colorado rivers, Grand Canyon, Arizona. 

Journal of Aquatic Animal Health 18: 184-193. 

Glen Canyon Dam has greatly altered the Colorado River in Grand Canyon. The Little 

Colorado River (LCR) provides a small refuge of seasonally warm and turbid water that is 

thought to be more suitable than the Colorado River for endangered humpback chub Gila cypha. 

However, the LCR has low productivity and contains nonnative fishes and parasites, which pose 

a threat to humpback chub. The Colorado River hosts a different suite of nonnative fishes and is 

cold and clear but more productive. We compared condition factor (K), abdominal fat index 

(AFI), and presence and number of two introduced pathogenic parasites (Lernaea cyprinacea

and Bothriocephalus acheilognathi) between juvenile (<150 mm total length) humpback chub 

from the LCR and those from the Colorado River during 1996–1999. Both K and AFI were 

lower and L. cyprinacea prevalence and B. acheilognathi prevalence were higher in LCR fish 

than in Colorado River fish for all years. Mean K and AFI were 0.622 and 0.48, respectively, in 

the LCR and 0.735 and 2.02, respectively, in the Colorado River, indicating that fish in the 

Colorado River were more robust. Mean prevalence of L. cyprinacea was 23.9% and mean 

intensity was 1.73 L. cyprinacea/infected fish in the LCR, whereas prevalence was 3.2% and 

intensity was 1.0 L. cyprinacea/infected fish in the Colorado River. Mean prevalence of B. 

acheilognathi was 51.0% and mean intensity was 25.0 B. acheilognathi/infected fish in the LCR, 

whereas prevalence was 15.8% and intensity was 12.0 B. acheilognathi/infected fish in the 

Colorado River. Increased parasitism and poorer body condition in humpback chub from the 

LCR challenge the paradigm that warmer LCR waters are more suitable for humpback chub than 

the colder Colorado River and indicate the need to consider the importance and benefits of all 

available habitats, as well as biotic and abiotic factors, when managing endangered species and 

their environment. 

Ward, D.L. 2007. Removal and quantification of Asian tapeworm from bonytail chub 

using praziquantel. North American Journal of Aquaculture 69(3):207–210. 

The spread of the Asian tapeworm Bothriocephalus acheilognathi has been identified as a 

potential threat to endangered cyprinid fishes, such as bonytail Gila elegans and humpback chub 

G. cypha. Praziquantel is often used to remove Asian tapeworms from these species, but 

little information is available on the effectiveness or side effects of these treatments. I performed 

laboratory experiments using bonytails (110-457 mm total length) to evaluate the dosage and 

time needed to effectively remove 100% of Asian tapeworms using praziquantel. A low dose of 

0.7 mg/L for 24 h was not effective at removing all Asian tapeworms, whereas a 24-h exposure 

at 1.5 mg/L and higher was 100% effective. A bath treatment of 12-h duration only appears 

effective at the highest dose of 36 mg/L, but not all Asian tapeworms are cleared from the host 

within this time frame. No short-term mortality or side effects of praziquantel treatment were 

observed. Praziquantel bath treatments can effectively and safely remove 100% of Asian 

tapeworms from bonytail if dosage and treatment duration are adequate. In some cases, repeated 
Humpback Chub Annotated Bibliography 143 September 2009

 

treatments may be necessary to ensure that Asian tapeworms are not spread into new 

environments. 

5.3 CLIMATE CHANGE 

Christensen, N.S., A.W. Wood, N. Voisin, D.P. Lettenmaier and R.N. Palmer. 2004. The 

effects of climate change on the hydrology and water resources of the Colorado River 

Basin. Climatic Change 62: 337–363. 

The potential effects of climate change on the hydrology and water resources of the 

Colorado River basin are assessed by comparing simulated hydrologic and water resources 

scenarios derived from downscaled climate simulations of the U.S. Department of 

Energy/National Center for Atmospheric Research Parallel Climate Model (PCM) to scenarios 

driven by observed historical (1950–1999) climate. PCM climate scenarios include an ensemble 

of three 105-year future climate simulations based on projected `business-as-usual’ (BAU) 

greenhouse gas emissions and a control climate simulation based on static 1995 greenhouse gas 

concentrations. Downscaled transient temperature and precipitation sequences were extracted 

from PCM simulations, and were used to drive the Variable Infiltration Capacity (VIC) 

macroscale hydrology model to produce corresponding stream flow sequences. Results for the 

BAU scenarios were summarized into Periods 1, 2, and 3 (2010–2039, 2040–2069, and 2070–

2098). Average annual temperature changes for the Colorado River basin were 0.5°C warmer 

for control climate, and 1.0, 1.7, and 2.4°C warmer for Periods 1–3, respectively, relative to the 

historical climate. Basin-average annual precipitation for the control climate was slightly (1%) 

less than for observed historical climate, and 3, 6, and 3% less for future Periods 1–3, 

respectively. Annual runoff in the control run was about 10% lower than for simulated historical 

conditions, and 14, 18, and 17% less for Periods 1–3, respectively. Analysis of water 

management operations using a water management model driven by simulated stream flows 

showed that stream flows associated with control and future BAU climates would significantly 

degrade the performance of the water resources system relative to historical conditions, with 

average total basin storage reduced by 7% for the control climate and 36, 32 and 40% for Periods 

1–3, respectively. Releases from Glen Canyon Dam to the Lower Basin (mandated by the 

Colorado River Compact) were met in 80% of years for the control climate simulation (versus 

92% in the historical climate simulation), and only in 59–75% of years for the future climate 

runs. Annual hydropower output was also significantly reduced for the control and future climate 

simulations. The high sensitivity of reservoir system performance for future climate is a 

reflection of the fragile equilibrium that now exists in operation of the system, with system 

demands only slightly less than long-term mean annual inflow. 

Christensen, N.S. and D.P. Lettenmaier. 2006. A multi-model ensemble approach to 

assessment of climate change impacts on the hydrology and water resources of the 

Colorado River basin. Hydrology and Earth System Sciences Discussions 3: 3727–3770. 

Implications of 21st century climate change on the hydrology and water resources 

of the Colorado River basin were assessed using a multi-model ensemble approach 

in which downscaled and bias corrected output from 11 General Circulation Models (GCMs) 

was used to drive macroscale hydrology and water resources models. Downscaled climate 
Humpback Chub Annotated Bibliography 144 September 2009

 

scenarios (ensembles) were used as forcings to the Variable Infiltration Capacity (VIC) 

macroscale hydrology model, which in turn forced the Colorado River Reservoir Model 

(CRMM). Ensembles of downscaled precipitation and temperature, and derived streamflows and 

reservoir system performance were assessed through comparison with current climate 

simulations for the 1950–1999 historical period. For each of the 11 GCMs, two emissions 

scenarios (IPCC SRES A2 and B1, corresponding to relatively unconstrained growth in 

emissions, and elimination of global emissions increases by 2100) were represented. Results for 

the A2 and B1 climate scenarios were divided into period 1 (2010–2039), period 2 (2040–2069), 

and period 3 (2070–2099). The mean temperature change averaged over the 11 ensembles for 

the Colorado basin for the A2 emission scenario ranged from 1.2 to 4.4°C for periods 1–3, and 

for the B1 scenario from 1.3 to 2.7°C. Precipitation changes were modest, with ensemble mean 

changes ranging from −1 to −2 percent for the A2 scenario, and from +1 to −1 percent for the B1 

scenario. An analysis of seasonal precipitation patterns showed that most GCMs had modest 

reductions in summer precipitation and increases in winter precipitation. Derived 1 April snow 

water equivalent declined for all ensemble members and time periods, with maximum (ensemble 

mean) reductions of 38 percent for the A2 scenario in period 3. Runoff changes were mostly the 

result of a dominance of increased evapotranspiration over the seasonal precipitation shifts, with 

ensemble mean runoff reductions of −1, −6, and −11 percent for the A2 ensembles, and 0, −7, 

and −8 percent for the B1 ensembles. These hydrological changes were reflected in reservoir 

system performance. Average total basin reservoir storage generally declined, however there was 

a large range across the ensembles. Releases from Glen Canyon Dam to the Lower Basin 

(mandated by the Colorado River Compact) were reduced for all periods and both emissions 

scenarios in the ensemble mean. The fraction of years in which shortages occurred increased by 

approximately 20% by period 3 in for both emissions scenarios, and the average shortage 

increased to a maximum of 3.7 BCM/yr for 5 the period 3 A2 ensemble average. Hydropower 

output was reduced in the ensemble mean for all time periods and both emissions scenarios. 

Hoerling, M. and J. Eischeid. 2006. Past peak water in the Southwest. Southwest 

Hydrology 6(1). 

Nobody relishes being "past peak" anything. Whether it’s the prime of our human 

existence or the prime of Nature’s abundance, the notion of having less rather than more is often 

vehemently denied. But demand growth in the face of production and storage decline has severe 

consequences, especially when existing uses already consume the available supply. The lifeblood 

of the Southwest is the Colorado River, which is increasingly impacted by climate forces not 

previously experienced. The recent drought prompts concern among water users and water 

stewards alike, and requires the scientific community to probe whether a sustained threat is rising 

to our already perilous moisture balance. The consensus of the Intergovernmental Panel on 

Climate Change (IPCC, 2001) affirms that Earth’s atmosphere is accumulating unprecedented 

quantities of carbon dioxide that are now causing detectable increases in surface air temperature. 

Seager, R., M. Ting, I. Held, Y. Kushnir, J. Lu, G. Vecchi, H. Huang, N. Harnik, A. 

Leetmaa, N. Lau, C. Li, J. Velez and N. Naik. 2007. Model projections of an imminent 

transition to a more Arid Climate in Southwestern North America. Science.10:1126. 
Humpback Chub Annotated Bibliography 145 September 2009

 

How anthropogenic climate change will affect hydroclimate in the arid regions of 

southwestern North America has implicationsfor the allocation of water resources and the course 

of regional development. Here we show that there is a broad consensus among climate models 

that this region will dry in the 21st century and that the transition to a more arid climate should 

already be under way. If these models are correct, the levels of aridity of the recent multiyear 

drought or the Dust Bowl and the 1950s droughts will become the new climatology of the 

American Southwest within a time frame of years to decades.

5.4 SUPPORTING ARTICLES 

Bulow, F.J., J.R. Winningham and R.C. Hooper. 1979. Occurrence of copepod parasite 

Lernaea cyprinacea in a stream fish population. Transactions of the American Fisheries 

Society 108: 100–102. 

 Although Lernaea cyprinacaea is often an epizootic in lakes, ponds, and hatcheries, its 

occurrence and intensity of infection in a central Tennessee stream system were quite low. Ten 

of the 13 species of fish collected in the Blackburn Fork watershed (Tennessee) were infected 

and intensity of infection was highest during the warmest of the seasons. There was also a 

tendency for the rate of infection to be higher in fish from smaller streams. Adult female L. 

cyprinacaea showed a definite affinity for attachment to the host fish body near the base of a fin. 

Granath, W.O., Jr. and G.W. Esch. 1983. Seasonal dynamics of Bothriocephalus 

acheilognathi in ambient and thermally altered areas of a North Carolina cooling reservoir. 

Proceedings of the Helminthological Society Washington 50: 205–218. 

The seasonal dynamics of Bothriocephalus acheilognathi were studied in three arbitrarily 

established size classes of mosquitofish, Gambusia affinis , from thermally altered and ambienttemperature locations in predator-free areas of Belews Lake, a North Carolina cooling reservoir. 

At both stations, lowest prevalence and densities of the cestode were observed during summer 

months. Densities rose sharply in the fall and peaked by early winter, after which they began to 

decline. Recruitment of the parasite at each site was also seasonal, beginning in late spring and 

continuing into October of both years of the study. However, recruitment at the thermally altered 

site began about 2 wk sooner, lasted about 2 wk longer, and was interrupted for several weeks in 

late summer when water temperatures exceeded 35°C. 

Hamilton, S. J. and B. Waddell. 1994. Selenium in eggs and milt of razorback sucker 

(Xyrauchen texanus) in the middle Green River, Utah. Archives of Environmental 

Contamination and Toxicology 27:195–201. 

Eggs from three females and milt from five male endangered razorback suckers 

(Xyrauchen texanus) were collected from the Razorback Bar (about 20 km upstream of Ashley 

Creek) in the Green River of northeastern Utah. Eggs, but not milt, had concentrations of 

selenium that were above the range of selenium concentrations in control fish from laboratory 

studies or reference fish from field studies. The concentrations, however, were below those 

reported in selenium-exposed fish that had reproductive problems in laboratory studies or field 
Humpback Chub Annotated Bibliography 146 September 2009

 

investigations. Tests with three streamside spawned pairs of razorback suckers, which were 

sampled for eggs and milt in this study, resulted in no hatching of fertilized eggs. Concentrations 

of selenium in eggs and milt were significantly correlated with selenium concentrations in 

muscle plugs taken from the same fish, but egg and milt concentrations were not significantly 

different from muscle plugs. Selenium concentrations in eggs of razorback suckers in the Green 

River may be sufficiently elevated to cause reproductive problems that are contributing to the 

decline of this species in the upper Colorado River basin.

Hamilton, S.J., R.T. Muth, B. Waddell and T.W. May. 1998. Selenium and other trace 

elements in wild larval razorback suckers from the Green River, Utah. Final report of U.S. 

Geological Survey Environmental and Contaminants Research Center to U.S. Bureau of 

Reclamation Irrigation Drainage Program, Denver, Colorado. 

Contaminant investigations of the middle Green River, Utah, have documented selenium 

contamination at sites receiving irrigation drainage. The middle Green River provides critical 

habitat for four endangered fishes including the largest extant riverine population of razorback 

sucker (Xyrauchen texanus). Although 2,175 larval razorback suckers were collected from the 

river between 1992 and 1996, very few juveniles have been captured within recent decades. 

Selenium concentrations were measured in larval razorback suckers collected from five sites in 

the middle Green River to assess the potential for adverse effects on recruitment of larvae to the 

juvenile stage and the adult population. Larvae from all sites contained selenium concentrations 

at or above the proposed toxic threshold of 4 μg/g for adverse biological effects in fish, derived 

from several laboratory and field studies with a wide range of fish species. At two sites, Cliff 

Creek and Stewart Lake Drain, selenium concentrations in larvae increased over time as fish 

grew, whereas selenium concentrations decreased as fish grew at Sportsman’s Drain. Evaluation 

of a 279-larvae composite analyzed for 61 elements demonstrated that selenium, and to lesser 

extent vanadium, were elevated to concentrations reported to be toxic to a wide range of fish 

species. Elevated selenium concentrations in larval razorback suckers from the five sites suggests 

that selenium contamination may be widespread in the middle Green River, and that survival and 

recruitment of larvae to the juvenile stage may be limited due to adverse biological effects. 

Selenium contamination may be adversely affecting the reproductive success of endangered 

razorback sucker. 

Hinck, J.E., V.S. Blazer, N.D. Denslow, K.R. Echols, T.S. Gross, T.W. May, PJ. Anderson, 

L.J. Coyle and D.E. Tillit. 2007. Chemical contaminants, health indicators and 

reproductive biomarker responses in fish from the Colorado River and its tributaries. 

Science of the Total Environment 378: 376–402. 

Common carp (Cyprinus carpio), black bass (Micropterus spp.), and channel catfish 

(Ictalurus punctatus) were collected from 14 sites in the Colorado River Basin (CRB) to 

document spatial trends in accumulative contaminants, health indicators, and reproductive 

biomarkers. Organochlorine residues, 2,3,7,8-tetrachlorodibenzo-p-dioxin-like activity (TCDDEQ), and elemental contaminants were measured in composite samples of whole fish, grouped 

by species and gender, from each site. Selenium (Se) and mercury (Hg) concentrations in fish 

were elevated throughout the CRB, and pesticide concentrations were greatest in fish from 

agricultural areas in the Lower Colorado River and Gila River. Selenium concentrations 
Humpback Chub Annotated Bibliography 147 September 2009

 

exceeded toxicity thresholds for fish (> 1.0 μg/g ww) at all CRB sites except the Gila River at 

Hayden, Arizona. Mercury concentrations were elevated (> 0.1 μg/g ww) in fish from the Yampa 

River at Lay, Colorado; the Green River at Ouray National Wildlife Refuge (NWR), Utah and 

San Rafael, Utah; the San Juan River at Hogback Diversion, New Mexico; and the Colorado 

River at Gold Bar Canyon, Utah, Needles, California, and Imperial Dam, Arizona. 

Concentrations of p,p′-DDE were relatively high in fish from the Gila River at Arlington, 

Arizona (> 1.0 μg/g ww) and Phoenix, Arizona (> 0.5 μg/g ww). Concentrations of other 

formerly used pesticides including toxaphene, total chlordanes, and dieldrin were also greatest at 

these two sites but did not exceed toxicity thresholds. Currently used pesticides such as Dacthal, 

endosulfan, γ-HCH, and methoxychlor were also greatest in fish from the Gila River 

downstream of Phoenix. Total polychlorinated biphenyls (PCBs; > 0.11 μg/g ww) and TCDDEQs (> 5 pg/g ww) exceeded wildlife guidelines in fish from the Gila River at Phoenix. Hepatic 

ethoxyresorufin O-deethylase (EROD) activity was also relatively high in carp from the Gila

River at Phoenix and in bass from the Green River at Ouray NWR. Fish from some sites showed 

evidence of contaminant exposure as indicated by fish health indicators and reproductive 

biomarker results. Multiple health indicators including altered body and organ weights and high 

health assessment index scores may be associated with elevated Se concentrations in fish from 

the Colorado River at Loma, Colorado and Needles. Although grossly visible external or internal 

lesions were found on most fish from some sites, histopathological analysis determined many of 

these to be inflammatory responses associated with parasites. Edema, exophthalmos, and 

cataracts were noted in fish from sites with elevated Se concentrations. Inter-sex fish were found 

at seven of 14 sites and included smallmouth bass (M. dolomieu), largemouth bass (M. 

salmoides), catfish, and carp and may indicate exposure to endocrine disrupting compounds. A 

high proportion of smallmouth bass from the Yampa River at Lay (70%) was intersex but the 

cause of this condition is unknown. Male carp, bass, and catfish with low concentrations of 

vitellogenin were common in the CRB. Comparatively high vitellogenin concentrations 

(> 0.2 mg/mL) were measured in male bass from the Green River at Ouray NWR and the 

Colorado River at Imperial Dam and indicate exposure to estrogenic or anti-androgenic 

chemicals. Anomalous reproductive biomarkers including low GSI and gonadal abnormalities 

(calcifications, edema, and parasites) observed in fish downstream of Phoenix are likely related 

to the poor water-quality of the Gila River in this area. 

Hunt, T.A. 2008. The effects of capture by trammel nets on native Arizona fishes. 

Master’s Thesis. Northern Arizona University, Flagstaff, Arizona. 

Trammel nets are commonly used to sample fish; however, little is known about postcapture effects of this gear type on the fish captured. We conducted experiments to evaluate the 

effects of trammel net sampling on survival and cortisol levels of razorback sucker, Xyrauchen 

texanus, bonytail, Gila elegans, and roundtail chub, Gila robusta, at 15°C, 20°C, and 25°C. Fish 

between 139 mm to 388 mm in total length (TL) were obtained from both captive hatchery stock 

and wild populations, quarantined for two weeks, and acclimated in two 18,000 L tanks for 13 

days. Treatment fish were entangled in a trammel net for two hours and control fish were 

captured with a seine net. After capture, all fish were weighed, measured, PIT tagged. We 

extracted ~ 0.37 mL (between 0.1 mL and 0.5 mL) of blood from the caudal vasculature of 30-

80% of fish in both the treatment and control groups. All fish were placed in a 36,000 L holding 

tank, where they were monitored for delayed mortality for 14 days. 
Humpback Chub Annotated Bibliography 148 September 2009

 

Fish captured in the trammel net experienced up to 94% mortality within the first two 

weeks after capture, whereas seined fish experienced less than 24% mortality. There was little 

immediate net mortality for both control and treatment fish, which is consistent with field 

observations; however, up to two weeks after capture trammel netted fish were still dying. In 

warmer water temperatures, both bonytail and razorback suckers experienced significantly 

increased mortality rates (p < 0.05, Fisher’s Exact Test); however, roundtail chub did not show 

this trend. Even higher levels of mortality may occur in nature, as any increased stress and/or 

physical injury that fish incur during capture and handling may lead to a competitive 

disadvantage and impair foraging ability. Post-capture mortality of wild fish may have gone 

undocumented thus far because of the time delay between capture and death. Our results suggest 

management agencies should re-examine the appropriateness of trammel net sampling for 

imperiled fish populations, especially when water temperatures are above 20°C. 

Although the magnitude of the cortisol response varied among species, cortisol levels 

were higher for fish captured by the trammel net than for fish captured by the seine net (p < 

0.05). Fish captured at the highest temperature (25°C) were more likely to have elevated cortisol 

levels than fish captured in the same way at lower temperatures (p < 0.05). Significantly more 

fish died after capture by trammel net (p < 0.05), and more fish died at the highest experimental 

temperatures: 20°C and 25°C (p < 0.05). For bonytail and razorback suckers, elevated cortisol 

levels were an effective predictor of mortality (p < 0.05); however, roundtail chub did not 

demonstrate a significant association between cortisol levels and subsequent mortality. These 

results suggest that cortisol could be used as a potential index of stress and post-capture 

mortality, at least for some species. 

Mueller, G.A., J. Carpenter and D. Thornbrugh. 2006. Bullfrog tadpole (Rana catesbeina) 

and red swamp crayfish (Procambarus clarkii) predation on early life stages of endangered 

razorback sucker (Xyrauchen texanus). The Southwestern Naturalist 51(2):258-261. 

Bullfrog tadpoles (Rana catesbeiana) and red swamp crayfish (Procambarus clarkii) are 

widespread introduced taxa that are problematic throughout the western United States. Their 

impact on native amphibians and crustaceans is well documented, but less is known regarding 

their influence on native fishes. Predator-prey tank tests showed both species consumed eggs and 

larvae of the endangered razorback sucker (Xyrauchen texanus) in a laboratory setting. Tadpoles 

consumed 2.2 razorback sucker eggs/d and 1.4 razorback sucker larvae/d, while crayfish ate 6.0 

eggs/d and 3.5 larvae/d. Relatively high densities of bullfrog tadpoles and crayfish in razorback 

sucker spawning areas suggest that these nonnative taxa might pose a threat to the recruitment 

success of this and other imperiled native fish. 

Webb, R.H., R. Hereford and G.J. McCabe. 2005. Climatic fluctuations, drought and flow 

in the Colorado River. Pages 57-68 in S.P. Gloss, Lovich, J.E. and Melis, T.S. (eds.). The 

state of the Colorado River ecosystem in the Grand Canyon: U.S. Geological Survey 

Circular 1282. 

From 2000 through 2004, the early 21st century drought caused abnormally low flows in 

the Colorado River and its tributaries upstream from Lake Powell. By using either actual annual 
Humpback Chub Annotated Bibliography 149 September 2009

 

flow data or annual flow records adjusted for consumptive uses in the upper basin, it was found 

that runoff from 2000 through 2004 was the lowest in the period of record (99–110 yr). This low 

flow has caused considerable concern about the ability of the reservoirs on the Colorado River to 

deliver water from upper basin States to lower basin States. Water managers increasingly want to 

know the predictability of climate and its effects on water resources over annual, decadal, and 

longer term spans. 

Climate, drought, and streamflow in the Colorado River are linked in poorly understood 

ways. Initial understanding of flows in the system was based on a relatively short historical 

record that is now believed to be a period of above-average precipitation. Examination of longterm records based on tree-ring analyses suggests that drought magnitude and persistence 

patterns are associated with much broader hemispheric climate patterns; however, these 

correlations are imperfect and do not provide a clear understanding of long-term precipitation 

patterns. 

Currently, there is no reliable way to predict how long the early 21st century drought will 

last in the Colorado River Basin. Components of the climate system, such as sea-surface 

temperature of the Atlantic and Pacific Oceans, provide some context for understanding past 

variations in precipitation and streamflow, but they are insufficient for predicting the fate of the 

ongoing drought. Time series of the relevant climate indices indicate a large amount of year-toyear variability and relatively rapid changes from one regime to another. Above-average 

precipitation for winter 2004–05 and forecasts for above average runoff may signal the end of 

the drought, or the drought conditions may resume after the present El Niño ends. Both outcomes 

underscore the unpredictability of climatic shifts affecting the Colorado River Basin. 

6 CONSERVATION AND MANAGEMENT 

6.1 HABTIAT AND SPECIES MANAGAMENT 

Arizona Game and Fish Department. 1996. Ecology of Grand Canyon backwaters. Final 

report to U.S. Bureau of Reclamation, Upper Colorado Region. Arizona Game and Fish 

Department, Phoenix. Abstract excerpted from report introduction. 

 The closure of Glen Canyon Dam in 1963 turned a river that was characteristically warm 

and muddy into a cold clear one, and greatly affected the biota of the river corridor, particularly 

the native fishes. The controlled daily fluctuations in the relatively clear Colorado River of 

today differ greatly from pre-dam conditions. Prior to impoundment by Glen Canyon Dam, the 

Colorado River, laden with sediment, underwent large, seasonally predictable floods, peaking in 

May and June. These floods probably created and maintained a system of backwaters similar to 

those created by high discharge in the system today. Pre-dam mean annual maximum flow was 

86,617 cfs and reached 300,000 cfs. Post-dam mean annual maximum flow is 27,898 cfs, 

ranging from 1,000–31,500 cfs. Post-dam flows fluctuate on a daily basis, instead of a seasonal 

basis, with a peak flow and low flow within every 24-hour period. Since closure of the dam, in 

1963 through July 1991, daily discharge release patterns fluctuated widely with no restrictions on 
Humpback Chub Annotated Bibliography 150 September 2009

 

ramping rates. On 1 August 1991, interim operations were implemented, restricting daily flow 

fluctuations to range of 5,000–20,000 cfs. 

Tributaries also contribute to the discharge of the Colorado River in Grand Canyon and 

provide spawning areas for native fishes. Most notable is the LCR, which joins the mainstem 

Colorado River at RM 61.5. Since closure of the dam, the LCR and Paria River (RM 0.9) are the 

major sources of sediment input into the system. Floods in these tributaries can cause high 

discharges of sediment-laden water into the Colorado River and result in the formation of 

numerous sand deposits and associated backwaters. However, these backwaters are generally 

temporary and are usually formed in the mainstem just downstream of the source tributary. 

 Backwaters are pockets of quiet water connected to the main channel with little or no 

flow, and are usually formed in eddies where scouring occurs during high flows. Backwaters 

and other slow water habitats add to the diversity of the riverine environment. Due to changes in 

mainstem habitat caused by dams, particularly decreased water temperature, backwaters have 

become increasingly important as rearing areas for larval and juvenile native fishes in the 

Colorado River system because they provide sheltered habitats with warmer water that contains 

greater densities of food than the mainchannel. However, fluctuations in dam releases can 

inundate or dewater backwaters, reducing their ability to support juvenile fish. These fluctuating 

flow regimes force small fish into the mainchannel where they are stressed by cold temperatures 

and high velocities and are more susceptible to predation. 

The studies addressed herein use a number of sampling protocols and gear types. Six 

general objectives were addressed in an attempt to understand the effects of Glen Canyon Dam 

on the ecology of the fish communities and their habitats in the Colorado River, Grand Canyon: 

 Continue the AGFD monitoring and research program for native fishes of the Colorado 

River and its tributaries in the Grand Canyon. 

 Identify the temporal and spatial distribution patterns and movements of early life stages 

of fishes in the LCR and other tributaries. 

 Determination of the changes in environmental conditions in mainstream and tributary 

confluence zone native fish rearing habitats under different flow regimes. 

 Determine invertebrate standing crops and their relative contributions to diets of young 

native fishes in tributary, backwater and mainchannel habitats under different flow 

regimes. 

 Determine the behavioral responses of larval to juvenile native fishes to changing 

environmental conditions in rearing habitats. 

 Determine the extent to which limnological factors, with emphasis on water chemistry 

and aquatic productivity, potentially limit the distribution and abundance of native fishes 

in the Little Colorado River and other tributaries which might serve as streams for 

augmentation of humpback chub in Grand Canyon. 
Humpback Chub Annotated Bibliography 151 September 2009

 

This report summarizes data collected by the AGFD during 25 research trips conducted 

on the Colorado River from 1991-94. It provides information concerning how changes in habitat 

may affect the distribution and relative abundance of native fishes and their food in the Colorado 

River, Grand Canyon, Arizona. The information in this report, along with data collected by 

AGFD during GCES Phase I studies, will provide baseline data for evaluating the long-term 

effects of Interim or Modified Low Fluctuating Flows, proposed habitat building and habitat 

maintenance flows, and the effects of thermal modification should those studies materialize in 

the future. 

Arizona Game and Fish Department. 1996. Effects of an experimental flood on the 

aquatic biota and their habitats in the Colorado River, Grand Canyon, Arizona. Final 

report. Arizona Game and Fish Department, Phoenix. Abstract excerpted from study 

conclusions. 

The immediate impacts of the experimental flood on the morphology, number, sediments, 

and the benthic macroinvertebrate community of backwaters, and the zooplankton and fish 

communities in the Colorado River, Grand Canyon, have been shown. The number and surface 

area of backwaters immediately after the flood increased from that of the year prior. However, 

the effect of flooding on long-term backwater number and size remains uncertain. It is apparent 

that changes in flow patterns from flood discharge to operating flows and the subsequent 

fluctuating flows of normal dam operations were detrimental to the longevity of backwaters 

created by the flood. Floods of lower magnitude and/or a much slower downramp may alleviate 

some of these problems, making the new backwaters more permanent. The loss of backwaters 

observed after the resumption of operating flows may detrimentally affect survival and growth of 

larval and juvenile native fishes. 

The availability of nursery/rearing habitats to larval and juvenile native fishes in the 

reach below the LCR is important because all native species spawn in the LCR, particularly 

humpback chub. Larval fish migrating out of the LCR are faced with colder water temperatures 

(>8° C mean temperature change), which decreases swimming ability and probably causes larvae 

to have difficulty reaching backwaters. Although large numbers of larvae are transported out of 

the LCR into the mainstem Colorado River each year, few are believed to survive. An increase 

in the number of backwaters immediately below the LCR will likely help increase the survival of 

larval native fishes spawned in the LCR. 

 How closely the environmental conditions within a backwater conform to those preferred 

by larval and juvenile native fishes (i.e., water temperature, depth, area, amount of cover, 

invertebrate density, etc.) is also of importance. It has been reported that YOY humpback chub 

preferred backwaters with no current, a firm silt bottom, 0.6 m maximum depth, and of 

temperature between 21.0–24.4°C. Backwater temperature and conductivity immediately 

following the Experimental Flood were mostly sub-optimal for larval and juvenile native fishes. 

The new backwaters created by the flood had larger surface area and greater zooplankton 

densities, but had no vegetation, sediments made up primarily clean sand, and decreased benthic 

invertebrate densities. Many benthic invertebrate species are important prey items for juvenile 

native fishes and their loss may detrimentally affect growth of these fishes. However, over time 
Humpback Chub Annotated Bibliography 152 September 2009

 

fine sediments and detritus will accumulate in backwaters, and benthic invertebrate will 

recolonize. 

 Native fishes appear to have been unaffected by the flood. The timing of the flood 

largely prevented newly hatched fish from being affected. YOY humpback chub were able to 

maintain themselves in their sheltered, preferred habitats during the flood and showed no 

evidence of being displaced downstream. Diet of adult humpback chub varied, but they 

demonstrated their omnivory and adaptability to this type of perturbation. 

Finney, S. 2006. Adult and juvenile humpback chub monitoring for the Yampa River 

population, 2003-2004. Final report of U.S. Fish and Wildlife Service to Upper Colorado 

River Endangered Fish Recovery Program, Lakewood, Colorado.

The humpback chub (Gila cypha) is an endangered species native to the Colorado River 

Basin listed under the Endangered Species Act in 1967 (32 FR 4001). The “Yampa” population 

of humpback chub includes individuals that may be found in Yampa, Lodore, Whirlpool, and 

Split Mountain canyons and is one of the smallest existing populations of humpback chub. The 

objectives of this study are to define the distribution, length frequency and abundance of the 

adult Yampa humpback chub population and numbers of juveniles in the Yampa humpback chub 

population. 

A two-year study began in 2003 that sampled adult humpback chub using trammel nets, 

boat electrofishing and angling. Juvenile fish were collected using backpack electrofishing and 

seining. All adult humpback chub were measured for TL, weighed, scanned for the presence of 

PIT tags, tagged with PIT tags if none were found and immediately released. All juvenile 

samples were preserved for laboratory identification. 

During the two-year study, 13 adult humpback chub were captured (10 in Yampa Canyon 

and 3 in Whirlpool Canyon) and three hundred and forty nine juvenile Gila spp. were collected 

of which 30 were questionably identified as G. cypha. Abundance estimates were not possible 

due to the low number of captures. Distribution was similar to historical ranges. Catch per effort 

of adult humpback chub dramatically decreased from other recently collected data. 

Gloss, S.P., Lovich, J.E. and Melis, T.S., eds. 2005. The state of the Colorado River 

ecosystem in Grand Canyon: U.S. Geological Survey Circular 1282, Reston, Virginia. 

Research and monitoring conducted by U.S. Geological Survey scientists and their 

cooperators have conclusively demonstrated a net loss of sediment from the system and have 

documented the decline of the federally endangered humpback chub during the last decade. At 

this first milestone, both findings are critical pieces of information to assess conditions and 

adjust management actions in the spirit of adaptive management. 

It is important to note that water-delivery requirements continued to be met throughout 

the decade after the EIS, despite increased costs associated with environmental and experimental 

regulation of flows. 
Humpback Chub Annotated Bibliography 153 September 2009

 

Although incomplete, a substantial body of knowledge now exists for the Colorado River 

ecosystem in Grand Canyon. The overarching question is, “What will society do with the 

knowledge now available to move into the next active phase of the Glen Canyon Dam Adaptive 

Management Program?” The complexity of the natural system presents enormous challenges for 

determining how resources and population numbers vary in time and space and underscores the 

importance of long-term studies to describe patterns and processes. The next critical phase of 

adaptive management requires strategic action on the part of both managers and scientists. 

Along with future action come the continuing challenge and need for greater integration 

of monitoring and research studies. As the complexity of issues in the Glen Canyon Dam 

Adaptive Management Program becomes more obvious, so does the need for interdisciplinary, 

not just multidisciplinary, science. Good examples of recent interdisciplinary science include 

(1) the interface between fine-sediment studies and cultural resources as the result of research 

efforts to understand the deposition of wind-carried sediment, (2) water-quality studies related to 

temperature and fish biology, and (3) the developing link between aquatic ecology studies and 

fish diets. Continued efforts will be required to integrate knowledge across disciplines and scales 

and to develop a more robust conceptual model for the Grand Canyon ecosystem. 

A continued adaptive management approach below Glen Canyon Dam, one focused on 

systematic experimentation, is recommended as a more efficient strategy for learning than the 

approach initially undertaken of monitoring the MLFF operation without comparing it to other 

flow and non-flow (e.g., mechanical removal of nonnative fish) alternatives. Future experimental 

treatments (flow or otherwise) must be evaluated within a strategic framework of periodic 

milestones and with rigorous scientific review so as to effectively identify viable management 

options for achieving the desired mix of resource responses. Success in this approach relies first 

and foremost on managers and stakeholders identifying what is desired, as well as determining 

whether identified objectives are measurable by science and attainable through dam operations. 

In the context of an adaptive ecosystem management process, the information identified 

at this milestone should lead to a dialog between managers and scientists about what other flow 

or non-flow alternatives might be considered to achieve the desired environmental outcomes. 

Because of the uncertainty about the cause and effect of MLFF operations on Grand 

Canyon resources and the even greater uncertainty about other conservation options, such as 

mechanical removal or thermal modification, the next steps in the process seem best approached 

as ongoing management policy experiments in the spirit of adaptive management, punctuated 

with frequent milestones at which the state of knowledge gained is assessed by all interested 

parties. 

Gorman, O.T. and L. Coggins. 2000. Status and trends of native and non-native fishes of 

the Colorado River in Grand Canyon 1990-2000. Final report. U.S. Fish and Wildlife 

Service, Flagstaff, Arizona. 

Status, trends, and seasonal patterns of relative abundance of humpback chub, rainbow 

trout, brown trout, and flannelmouth sucker in Grand Canyon were analyzed for the period 1990-

2000 at the following mainstem reaches: LCR inflow, Bright Angel, Shinumo, Middle Granite 
Humpback Chub Annotated Bibliography 154 September 2009

 

Gorge, Kanab, and Havasu. These 7 reaches were selected because they were the only ones for 

which sufficient data exist for long-term analysis of relative abundance. Humpback chub (HBC) 

were divided into small (<200 mm TL) and adult (>200 mm TL) size groups for analysis. In 

addition, we characterized the long-term and seasonal patterns in condition factor for HBC >200 

mm total length. For the native species, HBC and flannelmouth sucker, no long-term trends in 

abundance were evident nor was a long-term trend condition factor for HBC >200 mm total 

length evident. Abundance of large and small HBC was greatest in the LCR Inflow (RM 60.0–

68.2). Flannelmouth sucker showed increasing abundance downstream of the LCR inflow. 

Rainbow trout was the most abundant of the four species considered in the analysis. Although 

abundance was highest in the Fence Fault reach, rainbow trout was abundant throughout the 

Grand Canyon. Brown trout were most abundant in the Bright Angel reach and were rare 

upstream of this area. Throughout the Canyon, rainbow trout abundance declined after 1990 but 

increased back to 1990 levels after 1996. Brown trout abundance downstream of the LCR 

Inflow increased after 1997. Changes in trout abundance, particularly rainbow trout, appeared to 

be correlated with changes in dam operations and resulting flow regimes over the period of the 

study. Widely fluctuating daily flows prevailed before 1990, greatly reduced fluctuating flows 

were instituted during 1990-1995, and moderately fluctuating flows were practiced after 1997. 

Of the two sampling methods considered, electrofishing was judged effective in sampling all 

species except adult HBC. Trammel netting was effective in capturing adult HBC, but this 

sampling method was focused on known concentrations of fish and showed great variability in 

estimates of abundance. Because extensive amounts of shoreline habitat were sampled by 

electrofishing, this method provided a more representative sample of the mainstem Colorado 

River fish community. Trammel netting may be more successful in capturing rare and highly 

clustered adult HBC but implementation of this method for long-term assessment of abundance 

is fraught with sampling difficulties. 

Hendrickson, D. A. 1997. A preliminary study of utility of data obtainable from otoliths to 

management of humpback chub in the Grand Canyon. Final report to Arizona Game and 

Fish Department KR92-00310-LNR G20019-A. Abstract excerpted from report. 

 This study was initiated with the objective of studying various aspects of the physical and 

chemical structure of otoliths of humpback chub from the Grand Canyon of Arizona, and 

primarily from the LCR. These studies were to shed light on the utility of otolith studies for 

improving knowledge of the life history of this endangered species, and to evaluate the potential 

applications of these techniques to questions posed by resource managers. Specifically, the 

study was to obtain age estimates (years of age) from otoliths of 50 selected skeletonized adult 

specimens of Gila cypha collected from the Grand Canyon by AGFD in 1989 and 1990. It was 

also to obtain age estimates (days of age) for 100 selected YOY G. cypha collected during the 

same subsequent years. Age estimates for YOY were predicated on the assumption that 

increments counted in the otoliths were deposited daily, and that increment counts could thus be 

translated to days of life since the date of first increment formation (generally within the first few 

days following spawning). Since that hypothesis had not been specifically tested in this species, 

the study also was to test the hypothesis that increments form on a daily basis, both in the field 

and in hatchery experiments. Since at least some humpback chub appear to move across a 

typically strong thermal gradient at the interface of mainstem Colorado River (MCR) waters and 

the discharge of the LCR, which is generally much warmer than MCR, it was hypothesized that 
Humpback Chub Annotated Bibliography 155 September 2009

 

this transition might lead to the formation of marks, both physical and chemical, in otoliths and 

that these marks might be used to reconstruct individual life histories with respect to timing of 

this inter-river movement. It had been hypothesized that if swept out of the LCR into the 

mainstem Colorado, the transition might be lethal or have other deleterious impacts on YOY 

survival and growth. A mark in otoliths that unambiguously conveyed information about extent 

and timing of movements across this inter-river interface, could thus be valuable in further 

understanding of population dynamics and movements. It was thus proposed to search for such 

marks in otoliths and to conduct experiments to study the effects of temperature changes on 

otolith structure. The original study design also called for an analysis of the feasibility of 

determining annual growth period duration from otoliths of post YOY individuals of G. cypha

for all growth periods throughout the life of specimens. 

 

Leibfried, W.C., H. Johnstone, S. Rhodes and M. Lauretta. 2005. Feasibility study to 

determine the efficacy of using a weir in Bright Angel Creek to capture brown trout. Final 

report to Grand Canyon Monitoring and Research Center from SWCA Environmental 

Consultants, Flagstaff, Arizona. 

The highest concentration of brown trout in the Colorado River occurs near the 

confluence of Bright Angel Creek. It is likely that Bright Angel Creek is the main spawning 

tributary for brown trout in the Grand Canyon. Over 400 brown trout were caught moving into 

Bright Angel Creek between November 18, 2002 and January 16, 2003, the majority of which 

were in peak spawning condition. The movement of spawning brown trout into the creek may 

have begun prior to the sampling period, as indicated by the steady number of ripe brown trout 

captured at the start of the period. One brown trout caught in Bright Angel Creek had traveled 

over 32 miles upstream from the place in the Colorado River where it was tagged in late 

February 2002. These data support the hypothesis that Bright Angel Creek is the major spawning 

area for brown trout in the Colorado River in Grand Canyon. 

More trout were captured overnight than during the day for each of the days sampled. 

These data imply that trout preferentially move into Bright Angel Creek throughout the night. 

This may be due to greater activity of trout in the Colorado River at night and better protection 

from predators such as bald eagles and osprey, which were observed during the study period 

along Bright Angel Creek. Similar nocturnal movements were observed in Nankoweap Creek for 

rainbow trout. 

Our stomach content analysis revealed little evidence of fish remains in brown trout 

stomachs. However, most stomachs were empty, a typical condition of spawning fish. Mainstem 

studies by the Grand Canyon Monitoring and Research Center and BIO/WEST have shown 

evidence of fish remains in brown trout stomachs. Stomach analyses from 2000 documented 

piscivory in 8% of brown trout sampled from the Colorado River in Grand Canyon and in 21% 

of brown trout from the Little Colorado River reach of the mainstem. There is little doubt that 

brown trout are predatory on native fishes and are a contributing factor in the decline of native 

fishes of the Colorado River. 

The weir proved to be an effective method for capturing adult brown trout that were 

migrating into Bright Angel Creek to spawn. Because the weir was not installed until November 
Humpback Chub Annotated Bibliography 156 September 2009

 

18, it is likely that some brown trout had already moved upstream to spawn. Earlier installation is

recommended to capture and remove a greater number of brown trout from Bright Angel Creek

and thereby increase the effectiveness of the weir. Additional data collection will be necessary to 

determine if removal of brown trout in Bright Angel Creek will benefit native fishes. A baseline 

inventory of both native and non-native fish should be undertaken as soon as possible to 

determine current populations within Bright Angel Creek and enable an evaluation of the effects 

of brown trout removal on the native fish community. Studies conducted by Otis (1994) are more 

than 10 years old and are outdated. The effect of Bright Angel Creek trout removal may also be 

detected by the mainstem monitoring and removal programs coordinated by GCMRC.

Although it is unlikely that every brown trout would be removed from the system, a 

reduction in numbers is possible, as shown by the intensive salmonid removal effort concentrated 

at the confluence of the Colorado River and the Little Colorado River. Based on this first year’s 

weir-removal experiment, it appears that the Bright Angel Creek weir could be a very efficient 

and cost effective way of removing non-native salmonids that are migrating into Bright Angel 

Creek to spawn. The removal of migrating fish, coupled with removal of resident brown trout in 

Bright Angel Creek, could provide an opportunity for the recovery the native fish community in 

the creek and aid mainstem recovery efforts for by reducing predation pressure. 

Recommendations- Based on the results of this study, SWCA recommends the following 

actions for future activities in Bright Angel Creek: 

1) Earlier installation of the weir to coincide with spawning period of brown trout will allow 

for a higher number of captures. 

2) Fish community monitoring in Bright Angel Creek will provide a baseline to determine 

the effectiveness of future trout reductions efforts. 

3) Population estimates of salmonids and native fish in Bright Angel Creek will provide 

baseline population levels to determine the effect of trout removal. 

4) Coordination with main channel fish monitoring programs (GCMRC and AGFD) will 

provide for data exchange and cooperation in a collaborative effort for trout reduction. 

5) Captured trout can be used for additional data collection, such as the use of otolith 

chemical analyses for determining fish movements and age and growth studies 

(GCMRC). 

Lupher, M.L. and R.W. Clarkson. 1994. Temperature tolerance of humpback chub (Gila 

cypha) and Colorado squawfish (Ptychocheilus lucius). Proceedings of the Desert Fishes 

Council 25:38. 

The closure of Glen Canyon Dam on the Colorado River above Grand Canyon, Arizona, 

in 1963 resulted in a depression of spring-summer downstream water temperatures. Post-dam 

temperatures likely have precluded successful mainstem reproduction of most native species due 

to mortality during incubation. In addition, movements of early life stage fishes from the Little 
Humpback Chub Annotated Bibliography 157 September 2009

 

Colorado River, a major undammed tributary used for spawning and rearing, to the Colorado 

River mainstem across a large thermal gradient have been surmised to negatively affect survival 

and growth. We exposed early life stages of endangered humpback chub (Gila cypha) and 

Colorado squawfish (Ptychocheilus lucius) to several temperatures to examine effects on 

survival and growth in the laboratory. All eggs were incubated at 18.6°C and moved to 20°C at 

swimup for a minimum of 24 h. When transferred from 20°C to 10°C for 4 h, 5–7 d old 

humpback chub larvae lost equilibrium and mobility for 90 min, but recovered. Same age 

humpback chub larvae became lethargic but did not lose equilibrium when transferred from 20°C 

to 12°C, and no behavioral effects were observed when moved to 14°C. Similar cold shock 

experiments with 11–13 d chub larvae affected only the 10°C group, which lost equilibrium for 

15 min before recovering. No mortality was observed under any treatment during the 4 h 

observation period. Growth patterns of 6–8 d humpback chub larvae reared at 10°C, 14°C, and 

20°C averaged 10%, 37%, and 83% length gain, respectively, and 28%, 195%, and 951% weight 

gain, over 30 d. Overall patterns of growth of 13–15 d humpback chub and Colorado squawfish 

larvae and 39–41 d chub post-larvae reared at these temperatures were similar. Results suggest 

that detrimental effects of reduced growth on individuals and populations of native fishes in 

Grand Canyon can be ameliorated by reducing levels of daily discharge fluctuations from Glen 

Canyon Dam, which will provide greater stability and potential for warming of mainstem rearing 

habitats. We also recommend consideration of thermal modification of discharges from Glen 

Canyon Dam.

Masslich, W.J., B.R. Cowdell and R.A. Valdez. 1993. Radiotelemetry studies of humpback 

chub Gila cypha in the Colorado River, Grand Canyon, Arizona. Proceedings of the Desert 

Fishes Council 24:68-69. 

Four native fishes of the Colorado River system are listed as endangered under the 

Endangered Species Act: the Colorado squawfish Ptychocheilus lucius, the humpback chub Gila 

cypha, the bonytail chub Gila elegans, and the razorback sucker Xyrauchen texanus. The 

Recovery Implementation Program for Endangered Fish Species in the Upper Colorado River 

Basin (Recovery Program) is a partnership among Federal and State agencies, environmental 

organizations, and private water development interests whose mission is to recover the 

endangered fishes in the upper Colorado River basin while allowing for water development to 

continue. In its first 6 years of existence, major Recovery Program accomplishments include: 

(1) the operation of several Federal reservoirs has been modified to help meet the instream flow 

requirements of the fish, (2) water and water rights have been acquired provide instream flows in 

several critical river reaches; (3) genetic refugia have been established for several of the most 

endangered fish stocks; (4) interim guidelines have been developed for stocking of non-native 

fishes in the upper basin, and (5) a broad based information and education effort has been 

implemented. Over 150 favorable biological opinions have been issued on water depletion 

projects since the inception of the Program in 1988. Recovery Program activities are currently 

focused on acquisition and legal protection of instream flows, expanding refugia for the 

endangered fish, restoration of flooded bottomland habitats, providing fish passage at several 

historic diversion structures, control of non-native fish population in selected river reaches, and 

implementation of an experimental stocking program for the razorback sucker. 
Humpback Chub Annotated Bibliography 158 September 2009

 

Minckley, C.O. 1980. Recovery of the humpback chub Gila cypha and observations on 

that species 1977-1978. Proceedings of the Desert Fishes Council 12:130. 

During 1978, twenty adult humpback chubs were placed at Willow Beach National Fish 

Hatchery, for propagation purposed. The fish were collected from the Little Colorado River, in 

the vicinity of its mouth, flown to the south rim of the Grand Canyon, and transported to Willow 

Beach. All fish arrived in good condition and were in the hatchery raceways within five hours of 

lift-off from the Little Colorado River. 

 During 1978, 555 humpback chubs were collected. Of these fish, 21.5% (196) were 

juveniles, and 78.5% (359) were adults. Distribution of this species within the mainstream 

Colorado River was extended to river mile 194, based on a report from a commercial river 

runner. General distribution within the system reflects the size of fish, with larger adults 

preferring water over two meters in depth. Juvenile fish occurred in water less than two meters 

in depth. Both size groups were usually found in moderate to slow current over silt-sand bottom 

in the Little Colorado River. 

 Schooling was observed both in adult and juvenile humpback chubs, as was feeding 

behavior. Schooling fish were observed feeding both on the bottom substrate and the surface 

film. Adult chubs were observed to take Cladophora as well as food from commercial river 

parties. The stomachs of three YOY humpback chubs were found by direct examination to 

contain dipteran families of Chironomidae, Ceratopogonidae, and Dolichopodidae. 

 Reproduction appeared to have occurred in early June based on the small size of the fish 

collected by seining (mean TL=19 mm). It is suspected that spawning commences in early 

spring (March) and continues through early summer, as observed. 

 Estimated numbers of humpback chubs, based on seining collections, ranged from 

122 fish/ha in May up to 1527 fish/hectare in June. Tagging operations were also implemented 

in July of 1978 using 3/8 in. × 1/8 in. fingerling tags. To date, 120 humpback chubs have been 

tagged and none have been recaptures. 

 Major problems faced by this population of humpback chubs are human impact, water 

fluctuations, and a newly discovered infestation of the anchorworm parasite Learnea. During 

October, 54% of the chubs were infested. 

Minckley, W.L., P.C. Marsh, J.E. Deacon, T.E. Dowling, P.W. Hedrick, W.J. Mathews and 

G. Mueller. 2003. A conservation plan for native fishes of the Lower Colorado River. 

Bioscience 53(3):219-234. Abstract excerpted from report. 

 Among the native fishes of the Colorado River are four “big-river” species: humpback 

chub (Gila cypha), bonytail (Gila elegans), Colorado squawfish (Ptychocheilus lucius), and 

razorback sucker (Xyrauchen texanus). Once generally widespread and abundant, these species 

are now critically imperiled. Water development—damming rivers, creating impoundments and 

cold tailwaters, degrading habitats, and desiccating long reaches—and the introduction and 

establishment of a suite of nonnative species have adversely affected the native fishes. Severely 
Humpback Chub Annotated Bibliography 159 September 2009

 

reduced in abundance and range and under continuing threats, the four big-river species are now 

federally listed as endangered. 

Thirteen fishes, including 10 freshwater species, constituted the original fish fauna of the 

lower Colorado River mainstem. Over the past century, the original fish fauna of the lower 

Colorado River has largely been replaced by nonnative species, especially downstream from 

Hoover (formerly Boulder) Dam. 

This article presents our recommendations for a science-based recovery strategy that 

could aid the recovery of the big-river fishes in the lower Colorado River. The recommendations 

are not new. They are based on our collective knowledge, published papers, and unpublished 

plans. We believe they offer important new perspectives that should be incorporated into criteria 

used by the RIP to determine when a listed big-river species has “recovered.” 

Our proposal deals with the concepts of, rationale for, and uncertainties about the 

numbers of individuals necessary to satisfy the goal of species maintenance. The need to 

maintain large effective population sizes makes it necessary to use space in the main stem, offchannel floodplain, and distributaries (effective size is a term that relates a population in nature 

to an idealized population with certain genetic characteristics). The proposed solution involves 

translocation of native species between predator-free, off-channel habitats and the main channel, 

backwaters, and reservoirs (hereafter, channel plus connectives). Reproduction and recruitment 

take place off-channel, and large, wide-ranging, and panmictic populations of adults maintain 

both population size and genetic variation there and in the channel plus connectives. The plan 

briefly addresses habitats that are needed to accomplish such goals and anticipated problems in 

developing such habitats; it also suggests ways that the native fishes can be managed 

successfully over the long term. 

Rationale for Population Goals. No quantitative data, historic or otherwise, exist on 

original numbers of any native fish in any habitat of the Colorado Basin. It is thus impossible to 

specify numbers required for downlisting or delisting that are based on restoration of historical 

population sizes. Estimates might be made using methods such as population viability analysis, 

but demographic data are too sparse for accuracy or reliability. We therefore used three 

approaches to estimate the numbers of reproducing adults that are sufficient to sustain the four 

species: (1) qualitative observations, (2) genetic information, and (3) empirical data on 

survivorship, standing crops, growth, and other population statistics. 

Off-channel Habitats for Conservation. Part of our proposal’s rationale is to avoid 

competition with sport fishermen. Traditional off-channel angling areas such as backwaters and 

ponds behind levees cannot realistically be expropriated, so new habitats—exclusively for native 

species— must be provided. Costs are also a concern, so these habitats should be secure, simple, 

and low maintenance, and they should exclude nonnative predators while providing adequate 

physicochemical and other conditions for life history requirements of natives. We envision a 

series of excavated habitats resembling the pristine lower Colorado River floodplain—isolated 

oxbow lakes and backwaters—as primary components of dedicated off-channel complexes. A 

successful prototype has been developed on the USFWS Havasu National Wildlife Refuge at 

Beal Lake, Arizona. 
Humpback Chub Annotated Bibliography 160 September 2009

 

Population Goals. We are convinced that large populations and high genetic diversity are 

the only sound biological options for all four species, and these are feasible and sustainable 

through dedicated management. Even a modest effort using off-channel habitats will yield 

populations far exceeding the meager 700 to 5,800 individuals proposed by USFWS. We 

advocate and describe means of producing and rearing recruits in isolated habitats for 

introduction en masse into the channel plus connectives to establish and maintain a large, 

genetically diverse, panmictic population that closes the circle by supplying brood fish for 

ongoing production in isolation. 

National Park Service. 2009, August 12. Humpback chub translocation experiment in 

Shinumo Creek [Press release]. Available at http://www.nps.gov/grca/naturescience/ 

cynsk-v12.htm. 

In June 2009, the National Park Service translocated 300 juvenile humpback chub from 

the Little Colorado River to Shinumo Creek in Grand Canyon National Park. The goal of this 

experiment is to obtain information about how this endangered species will respond to 

translocation in another tributary. 

An intensive three-year monitoring program will follow the translocation of humpback 

chub into Shinumo Creek. Biologists will evaluate the success of the humpback chub 

translocation using established fish surveying techniques such as snorkeling, hoop-netting, 

seining, and electrofishing. Data will be collected on the size, condition and health of humpback 

chub and their distribution in the translocation reach. The habitat characteristics of Shinumo 

Creek, including water flow, water quality and temperature, and other variables, will also be 

monitored. A PIT tag antenna placed near the falls will record any fish that are washed out of the 

stream by monsoonal floods. Specific questions to be evaluated include whether the young 

humpback chub survive the translocation and if they will remain in Shinumo Creek. 

This project will enable biologists to assess the feasibility of using translocation to 

establish an offsite refuge and potentially an additional aggregation of humpback chub in Grand 

Canyon. Regardless of the experiment’s success, it will increase the understanding of 

conservation efforts that must be undertaken in order to ensure that this native fish continues to 

survive in Grand Canyon. 

Patten, D.T., D.A. Harpman, M.I. Voita and T.J. Randle. 2001. A managed flood on the 

Colorado River: background, objectives, design, and implementation. Ecological 

Applications 11(3):635–643. 

The Colorado River ecosystem in lower Glen Canyon and throughout Marble and Grand 

Canyons was greatly altered following closure of Glen Canyon Dam in 1963, as flood control 

and daily fluctuating releases from the dam caused large ecological changes. Ecosystem research 

was conducted from 1983 through 1990, and intensively from 1990 through 1995 when dam 

releases were modified both for scientific purposes and protection of the river ecosystem. High 

flows (e.g., beach/habitat building flows) were included in the Glen Canyon Dam Environmental 

Impact Statement (EIS), which identified a preferred strategy for dam operations and protection 
Humpback Chub Annotated Bibliography 161 September 2009

 

of the downstream ecosystem. Use of high flows partially fulfills recommendations of many 

river and riparian scientists for return of more natural flows, as part of initial efforts in river 

restoration. In 1996, a seven-day experimental controlled flood was conducted at Glen Canyon 

Dam to closely study the effects of a high flow event equivalent to those proposed for future dam 

management. It is an example of modification of operations of a large dam to balance economic 

gains with ecological protection. Limited to 1274 m3/s, the test flood was lower than pre-dam 

spring floods. The experiment was conducted to (1) test the hypothesis that controlled floods can 

improve sediment deposition patterns and alter important ecological attributes of the river 

ecosystem without negatively affecting other canyon resources and (2) learn more about river 

processes, both biotic and abiotic, during a flood event. Along with an explanation of the 

planning and background of this flood experiment, this paper summarizes expected and realized 

changes in canyon resources studied during the flood. Responses of specific resources to the 

flood are synthesized in the following compendium papers. 

Paukert, C.P. 2004. Comparison of electrofishing and trammel netting variability for 

sampling native fishes. Journal of Fish Biology 65(6):1643–1652. 

The variability in size structure and relative abundance (CPUE; number of fish > 200 mm 

total length, LT, collected per hour of electrofishing or trammel netting) of three native Colorado 

River fishes, the endangered humpback chub Gila cypha, flannelmouth sucker Catostomus 

latipinnis and bluehead sucker Catostomus discobolus, collected from electrofishing and 

trammel nets was assessed to determine which gear was most appropriate to detect trends in 

relative abundance of adult fishes. Coefficient of variation (CV) of CPUE ranged from 210 to 

566 for electrofishing and 128 to 575 for trammel netting, depending on season, diel period and 

species. Mean CV was lowest for trammel nets for humpback chub (P=0.004) and tended to 

be lower for flannelmouth sucker (P=0.12), regardless of season or diel period. Only one 

bluehead sucker >200mm was collected with electrofishing. Electrofishing and trammel netting 

CPUE were not related for humpback chub (r = -0.32, P=0.43) or flannelmouth sucker (r=-0.27, 

P=0.46) in samples from the same date, location and hour set. Electrofishing collected a higher 

proportion of smaller (<200 mm LT) humpback chub (P<0.001), flannelmouth suckers 

(P<0.001) and bluehead suckers (P<0.001) than trammel netting, suggesting that conclusions 

derived from one gear may not be the same as from the other gear. This is probably because 

these gears fished different habitats, which are occupied by different fish life stages. To detect a 

25% change in CPUE at a power of 0.9, at least 473 trammel net sets or 1918 electrofishing 

samples would be needed in this 8km reach. This unattainable amount of samples for both 

trammel netting and electrofishing indicates that detecting annual changes in CPUE may not be 

practical and analysis of long-term data or stock assessment models using mark-recapture 

methods may be needed to assess trends in abundance of Colorado River native fishes, and 

probably other rare fishes as well. 
Humpback Chub Annotated Bibliography 162 September 2009

 

Rogers, R.S., D.L. Speas and A.S. Makinster. 2003. Grand Canyon Long-term Nonnative 

Fish Monitoring, 2003 Annual report to Grand Canyon Monitoring and Research Center 

Cooperative Agreement 02WRAG0030, October 2003. Abstract excerpted from study 

introduction and discussion. 

Robust long-term monitoring of aquatic populations is important to adaptive management 

programs because it characterizes a baseline or antecedent context in which response of biota to 

changing management policies or experiments can be interpreted. In the Colorado River below 

Glen Canyon Dam (GCD), Arizona, long-term monitoring of fishery resources is an essential 

component of the Glen Canyon Dam Adaptive Management Program in ensuring that GCD is 

operated in a manner consistent with the pertinent sections of Grand Canyon Protection Act of 

1992. In particular, the non-native salmonids rainbow (Oncorhynchus mykiss, RBT) and brown 

trout (Salmo trutta, BNT) have displayed increased abundance, likely because changes in 

operation of GCD since the early 1990s in the Colorado River in Glen and Grand Canyons 

(GCMRC 2001a; McKinney et al. 1999, 2001). 

Working under cooperative agreement with Grand Canyon Monitoring and Research 

Center (GCMRC), Arizona Game and Fish Department (AGFD) conducted studies of salmonid 

catchability using electrofishing and population size as well as relative abundance, distribution, 

and sampling requirements for long-term monitoring of RBT, BNT, and common carp (Cyprinus 

carpio, CRP) in the Grand Canyon during 2000–2001. In this paper, we report results from nonnative fish monitoring activities in the mainstem Colorado River in Grand Canyon during 2002. 

Specific objectives during 2002 were to: 

(1) Estimate salmonid and carp relative density and distribution, and estimate salmonid 

abundance and evaluate trends in abundance during 2000–2002. 

(2) Reevaluate required annual sample sizes and sample allocation for long-term monitoring 

of salmonids and carp in the Grand Canyon. 

(3) Assist with collections of salmonid genetic materials in the main channel Colorado River 

and select tributaries. 

Bootstrapping indicated that changes in salmonid relative abundance (CPUE) of 20–30% 

and 30–40% for RBT and BNT, respectively, are detectable between consecutive years with the 

current stratified random sample design, provided we complete between 800 and 900 samples 

per year. Long-term (5-year) analysis of the same data yields a much more sensitive monitoring 

tool for 5-year linear changes in CPUE. Confidence intervals of the regression line used to 

model population size are much wider than those obtained for CPUE, which likely precludes 

detection of similar changes in absolute abundance. However, no changes in CPUE or absolute 

abundance of RBT, BNT, and CRP are detectible with the most recent three years of data (2000–

2002). 
Humpback Chub Annotated Bibliography 163 September 2009

 

 We did not expect or observe much movement of BNT over the past three years. 

Most movement of BNT occurs in fish less than 15 months old and with adults during the 

spawning season (Solomon and Templeton 1976). Almost all fish that we mark are older than 15 

months, and our long term monitoring does not occur during the spawning season (Nov – Jan). 

The experimental weir placed in Bright Angel Creek in 2002 by the Park Service has captured at 

least two BNT that have traveled over 50 RM. It is our recommendation that tagging of BNT 

continue only as long as the use of a weir at Bright Angel Creek is maintained. 

The analyses of lengths by trip for BNT and RBT suggest that the low summer steady 

flows of 2000 resulted in relatively strong recruitment of both RBT and BNT. The modes 

observed in the RBT data match length-at-age calculated for age-0 and age-1 RBT from Lees 

Ferry. We have attempted to compute length-at-age for BNT by utilizing mark-recapture data 

from this monitoring program. Attempts to date have been unsuccessful because BNT tagging 

began in 2000 and few fish have grown between mark and recapture events. Future monitoring 

may provide data necessary for estimated growth rates. Future analysis of BNT otoliths may also 

provide length-at-age estimates. 

There is an apparent difference in the CPUE between electrofishing boats. Variation in 

catch between boats may be caused by the individual boat driver or the physical electronic 

equipment on the boat. Regardless of the source of this variation, there are apparent differences 

between boats that account for a large portion (15%) of the variability within the dataset. Small 

differences in catchability can have large effects on population estimates derived using CPUE. 

When CPUE data are used to evaluate population trends, the assumption is made that 

catchability remains constant over time. This assumption may not be met because of variations 

in discharge, turbidity, boat driver, or netters between and among trips. All of these factors have 

the potential to affect catchability. Attempts to minimize changes in these factors are made by 

sampling during the same months each year and attempting to keep crews consistent. All of our 

sampling has used the same two boat drivers, but future changes in boat driver may increase 

variance in the dataset, potentially confounding CPUE trends. We strongly recommend that any 

new boat drivers receive training prior to monitoring trips. We also recommend that information 

on the specific electronic units (CPS units) used on each boat along with the name of the boat 

driver must be recorded so that differences in catch can be evaluated further. 

Schmidt, J.C., R.H. Webb, R.A. Valdez, G.R. Marzolf and L.E. Stevens. 1998. Science and 

values in river restoration in the Grand Canyon. BioScience 48: 735–747. Abstract 

excerpted from article. 

 Restoration of riverine ecosystems is often stated as a management objective for 

regulated rivers, and floods are one of the most effective tools for accomplishing restoration. In 

the case of some large rivers, restoration may be impossible; a more feasible goal may be 

rehabilitation of some ecosystem components and processes in parts of the river. We examine 

the appropriate role of science in determining whether or not to restore or rehabilitate the 

Colorado River in the Grand Canyon by summarizing studies carried out by numerous agencies, 

universities, and consulting firms since 1983. The segment of the Colorado River flowing 

through the Grand Canyon is federally designated as critical habitat for two endemic endangered 

fish: the razorback sucker (Xyrauchen texanus) and the humpback chub (Gila cypha). In 
Humpback Chub Annotated Bibliography 164 September 2009

 

addition, the river provides essential water for humans as well. Because the discharge of 

Colorado River is relatively small for the basin’s size, large reservoirs have been constructed to 

assure water availability where the potential for flood control and sediment reduction is nearly 

complete. As such, restoration or rehabilitation of the river can only be achieved by changing 

the dams or their operations. 

 The Colorado River ecosystem in the Grand Canyon is sustained by the flow of water and 

nutrients released by Glen Canyon Dam, but other controlling factors are unrelated to the dam, 

such as regional geology and geomorphology, climate, tributary inflows of water and sediment, 

and human activities. Changes in these factors have caused adjustments in channel 

geomorphology, alterations in riparian vegetation and fish assemblages, decreases in habitat 

availability for endangered fish, and changes in water temperature and quality. 

 The construction and operation of Glen Canyon Dam reduced the frequency, magnitude, 

and duration of floods through the Grand Canyon as well as the amount of sediment transport. 

Debris fans have also increased in volume, and thus narrowed adjacent rapids. Unvegetated 

sandbars have been replaced by a near-river riparian zone consisting of marsh vegetation. 

 Fish assemblages native to the Colorado River evolved in an environment of highly 

variable discharge, large annual temperature fluctuation, high turbidity, large input of organic 

material, and the opportunity for basin-wide fish migration. These conditions have all changed. 

River temperatures no longer vary seasonally. What’s more, releases of cold, clear water and 

reduced transport of organic material have dramatically changed the conditions for the aquatic 

macroinvertebrates downstream from the dam. Thus, the food supply available for native fish in 

the Grand Canyon has changed greatly. 

 The fish assemblages of the Colorado River through the Grand Canyon have altered 

dramatically during the past century due to dam-related impacts as well as the introduction of 

nonnative fish species. Cold water releases impede reproduction of native fish. These effects 

are compounded by the increased competition and predation by nonnative fish. 

 From a continuum of possibilities, we identify five management approaches: traditional 

river management; managing the river as a naturalized ecosystem; rehabilitating it as a simulated 

natural ecosystem; rehabilitating it as a substantially restored ecosystem; and reestablishing a 

fully restored ecosystem. 

Sharber, N.G. and S.W. Carothers. 1987. Submerged, electrically shielded live tank for 

electrofishing boats. North American Journal of Fisheries Management 7:450–453. 

 Fish caught by electrofishing are usually held in live tanks before appropriate data are 

recorded; however, if the tank water is not circulated, changes in water temperature and oxygen 

concentration may harm the fish. Also, if the water is circulated by pumps or other mechanical 

means, the power required may reduce the effectiveness of the electrofishing gear. We designed 

and successfully used a live tank which is submerged through the hull of a catamaran-type whitewater raft. The live tank is placed in the water being electrofished so that power-free but 

continuous water circulation is maintained. Fish in the tank are protected from the electrofishing 
Humpback Chub Annotated Bibliography 165 September 2009

 

field by the design of the tank, which uses to advantage a phenomenon known as Faraday 

shielding. The tank is easy and inexpensive to construct and safe to use. 

Stone, D.M. 2005. Effect of baiting on hoop net catch rates of endangered humpback 

chub. North American Journal of Fisheries Management 25(2):640-645. 

The effects of unbaited, scented (odor emitted by inaccessible hatchery feed), and baited 

(accessible feed) single-throated hoop nets on the catch rates of the federally endangered 

humpback chub Gila cypha ( greater than or equal to 100 mm total length) were assessed in the 

Little Colorado River, Arizona, to determine how baiting affected the catch of these fish. Of a 

total of 1,297 unique humpback chub captured, 262 (20%) were caught in 179 unbaited nets, 330 

(25%) in 179 scented nets, and 705 (54%) in 178 baited nets. Humpback chub retention in 

unbaited nets did not differ from a 50:50 chance event (P=0.075) but probably peaked in baited 

nets where these fish were preoccupied with feeding (i.e., gorging themselves), which would 

explain the higher catch rates in baited than in scented or unbaited nets (P less than or equal to 

0.001). Moreover, humpback chub catch rates were not significantly higher in scented than in 

unbaited nets (P=0.779), which suggests that elevating both "fish attraction" and "fish retention" 

are essential to substantially increase their captures in these nets. However, scenting may still be 

a viable option when used in conjunction with passive gears possessing higher fish retention 

capabilities or to target species less prone to escape. The findings of this study should provide 

valuable insight to anyone wishing to optimize catch rates by baiting or scenting passive 

entrapment gear. 

Thompson, J.M., E.P. Bergersen, C.A. Carlson and L.R. Kaeding. 1991. Role of size, 

condition, and lipid content in the overwinter survival of age-0 Colorado squawfish. 

Transactions of the American Fisheries Society 120:346–353. 

In a survey study conducted to obtain base-line data, eleven extensive float trips were 

made down the Colorado River in the period from September 1970 through mid-June 1976. 

Samples of fish, mammals, plants and herpetofauna were collected; species collected are listed. 

In addition, terrestrial surveys were made at various land sites in the region. Major results of this 

survey were the lack of success in obtaining a specimen of the humpback sucker, Xyrauchen 

texanus, and the discovery of the relative scarcity of chubs of the genus Gila. Both of these 

outcomes have been tied to the low water temperatures caused by releases from the Grand 

Canyon Dam, as well as to the barrier that the dam presents to upstream movement to suitable 

spawning areas. 

Trammel, M. and R. Valdez. 2003. Native fish monitoring activities in the Colorado River 

within Grand Canyon during 2001. SWCA, Inc., Flagstaff, Arizona, to Grand Canyon 

Monitoring and Research Center, Flagstaff, Arizona. 

The feasibility of and effort required to conduct a population estimate for humpback chub 

(Gila cypha) in the Colorado River in the Grand Canyon near the Little Colorado River (LCR) 

inflow were assessed in 2001. The largest aggregation of HBC in the Colorado River mainstem 

occurs in the LCR area from RM 56.3, above the LCR, to RM 68.3 below the LCR. The LCR 

enters the Colorado River near RM 61.5. Population size was estimated using a two-pass mark-
Humpback Chub Annotated Bibliography 166 September 2009

 

recapture design. Two sampling trips were conducted; one in July/August and the other in 

August/September using trammel nets and hoop nets to capture HBC. Sampling effort included a 

total of 264 person days, 605 hoop net sets comprising 13,524.5 sampling hours, and 1,102 

trammel net sets comprising 2,151.9 sampling hours and resulted in 425 HBC captured. HBC 

greater than 100 mm TL were marked with PIT tags on the first trip and examined for marks on 

the second trip. We captured 104 HBC >100 mm TL on the first trip and 160 on the second trip. 

During the second trip no fish less than 200 mm TL were recaptured from the first trip. Thus, the 

population estimate was stratified to include only fish greater than 200 mm TL, resulting in 83 

marked on the first trip and 111 examined on the second trip, with 8 recaptured fish, for a 

population estimate of 1,044 fish > 200 mm TL (95% confidence interval 559 to 2,137), with a 

coefficient of variation (CV) of 29%. Despite the large effort, the number of captures and 

recaptures was lower than expected, and the precision of the estimate was less than desired. 

Increased effort is recommended for future population estimates. However, the 2001 estimate 

was significantly different from similar estimates made in 1991-1993 (Valdez and Ryel 1995) 

and suggests a significant decline in the abundance of HBC in the mainstem Colorado River near 

the LCR. 

Tyus, H.M. 1992. An instream flow philosophy for recovering endangered Colorado River 

fishes. Rivers 3:27–36. 

Remnant stocks of some endangered Colorado River fishes persist, including Colorado 

squawfish (Ptychocheilus lucius), humpback chub (Gila cypha), razorback sucker (Xyrauchen 

texanus), and bonytail (Gila elegans). Recovery of these species to a non-endangered status is 

problematic. Provision of flows to maintain habitats in which the fish are declining may do little 

to slow their decline or prevent their loss. It is argued that determination of instream flows for 

endangered fishes should be based on the premise that the fish are not occupying optimal, or 

perhaps even acceptable habitats, a philosophically different approach than that addressed by 

prevailing flow methodologies. A recovery rather than survival philosophy is recommended that 

includes developing instream flow needs through a combination of empirical studies, 

simulations, and assessments. 

Tyus, H.M. and J.F. Saunders, III. 2000. Non-native fish control and endangered fish 

recovery: lessons from the Colorado River. Fisheries 25(9):848-855. 

Native freshwater fish populations are declining in North America and more than 100 

fishes are federally listed as threatened or endangered. The Colorado River system in the 

southwestern United States has been especially affected. Most of its native fish populations are 

in decline, including four “big river” fishes, Colorado pikeminnow (Ptychocheilus lucius), 

humpback chub (Gila cypha), bonytail (G. elegans), and razorback sucker (Xyrauchen texanus), 

whose populations have declined so precipitously that they are endangered. Physical habitat 

alteration caused native fish declines, but nonnative fishes pose a more serious threat to native 

fishes than previously thought. Nonnative fish control measures needed in the upper Colorado 

River system, identified in part by a workshop of experts, include: (1) preventing movements of 

game fishes out of impoundments and curtailing future stockings, (2) reducing numbers of small, 

nonnative cyprinids in shoreline habitat used as rearing areas by young native fishes, and (3) 

increasing the harvest of channel catfish (Ictalurus punctatus) and common carp (Cyprinus 
Humpback Chub Annotated Bibliography 167 September 2009

 

carpio) in the mainstream. Large-scale implementation of these nonnative fish control measures 

has proven difficult. Recovery efforts have identified the need for developing nonnative fish 

control strategies and testing methodologies, but no solutions have emerged. A holistic approach, 

including ecosystem recovery plans, should be used in systems where more than one species 

share common problems, such as interactions with nonnative fishes. Nonnative fish interactions 

should be suspected as a potential cause of declining native fish populations.

Tyus, H.M., J.L. Cooper and R.H. Hamre. 1991. Management of Colorado River fishes. 

USDA Forest Service, Washington, D.C. 

Native warmwater fishes of the upper Colorado River basin have declined, and four bigriver fishes are in danger of extinction. Of these, Colorado squawfish Ptychocheilus lucius, 

humpback chub Gila cypha, and bonytail G. elegans are listed as federally-endangered, and 

razorback sucker Xyrauchen texanus, is proposed for listing Rare status, continuing habitat 

change, and lack of knowledge about their habitat needs have made management programs 

difficult to develop and implement. Recent efforts to recover the listed fishes have provided 

some information about all of the native fishes and prompted some management activities. The 

future of native Colorado River fishes is uncertain, but efforts of an interagency recovery 

implementation program offers some hope for them. 

U.S. Bureau of Reclamation. 1999. Glen Canyon Dam modification to control downstream 

temperatures. Plan and draft environmental assessment. U.S. Bureau of Reclamation, 

Upper Colorado Region, Salt Lake City, Utah. 

The U.S. Bureau of Reclamation is considering whether on not to modify Glen Canyon 

Dam to allow downstream temperatures to be managed. It is believed by the U.S. Fish and 

Wildlife Service and Reclamation that the cold summer temperatures created by the dam are a 

constraint to native and endangered warmwater fish, but there are other ecological interactions 

complicating the issue that cannot be conclusively resolved without physical testing. 

Reclamation has developed a relatively inexpensive way to modify the dam to allow 

temperatures to be controlled and tested. The plan includes a monitoring program to further our 

understanding of the ecosystem’s response to temperature and an adaptive management program 

to apply this knowledge. 

Before Glen Canyon Dam was constructed, the temperature of the Colorado River in the 

Grand Canyon would increase from near freezing in the winter to about 30°C (86°F) in the late 

summer. Though several native fish were present in the river system, Leibfried and Zimmerman 

(1994) reported that the fish community was dominated by warmwater non-native species. 

Channel catfish comprised 90% of the fish community in Glen Canyon. The dominant forms of 

non-native fish were channel catfish and carp, with red shiners, largemouth bass, green sunfish, 

and bullheads present but less abundant. Once the dam was constructed, release temperatures 

became relatively cold during the summer season. Water is now drawn year round from the deep 

intakes used for power production. Release temperatures vary little and are typically 8°C-10°C 

(46°F-50°F). 
Humpback Chub Annotated Bibliography 168 September 2009

 

Cold mainstem temperatures and high water velocity are thought to have expatriated (or 

at least greatly limited) most non-native competitors in the mainstem. Of the non-native species, 

rainbow trout do well in the clear water near the dam. Carp and catfish are abundant further 

downstream, in and near warm tributaries like the Little Colorado River. Native, warmwater fish 

have also been greatly limited by cold-water releases. Some are no longer present below Glen 

Canyon Dam. The endangered humpback chub are essentially limited to the area in and near the 

Little Colorado River. 

Cold-water releases from Glen Canyon Dam are below optimal for the existing trout 

fishery and far below those temperatures needed to allow native and endangered warmwater fish 

(such as the humpback chub) to thrive in the mainstem of the Colorado River. Thermal shock 

from cold mainstem temperatures has been recognized as a likely cause of mortality for young 

endangered fish leaving seasonally warmed tributaries. In their integration report on studies in 

Glen and Grand Canyons, Valdez and Carothers (1998) concluded that, “We believe that most 

larval flannelmouth suckers, bluehead suckers, and humpback chub descending from warm natal 

tributaries into the cold mainstem die of thermal shock or from predation elicited by erratic 

swimming behavior. For those fish old enough to survive the transition, swimming ability may 

be reduced by as much as 98 percent by cold mainstem temperatures.” 

In commenting on the proposed plan, Gorman (Arizona Game and Fish) suggested that 

temperature controls could be an effective tool to reduce this thermal shock problem during the 

relatively short period of time that the humpback chub are descending into the mainstem (mid to 

late summer) without greatly favoring their competitors. Furthermore, once recruited, these longlived native fish would potentially out-live their competitors by well over a decade. 

According to the Fish and Wildlife Service’s (FWS) biological opinion on the operation 

of Glen Canyon Dam, main channel spawning of endangered fish (critical habitat) is severely 

limited by cold-water releases from Glen Canyon Dam. In their biological opinion on the 

operation of the dam, the FWS’s reasonable and prudent alternative recommended that 

Reclamation evaluate methods to control release temperatures and, if viable, implement controls. 

Reclamation agreed with this recommendation and included it in the U.S. Department of the 

Interior’s (USDI) Final Environmental Impact Statement (USDI 1995) and Record of Decision 

on the Operation of Glen Canyon Dam. 

This report integrates two purposes, planning and an environmental assessment of the 

alternatives. In Chapter II, the report summarizes Reclamation’s study of various methods 

available to control temperature. Several designs were found to meet the temperature control 

needs of the project and are technically viable; however, costs varied significantly. The 

proposed alternative takes maximum advantage of the existing intake structures to reduce costs, 

yet meets the performance goals for temperature controls. This innovative approach would cost 

an estimated $15 million (to modify all eight intakes) and would be within Reclamation’s 

spending authority. More traditional designs like those used at Flaming Gorge Dam and Shasta 

Dam would cost up to $149 million at Glen Canyon Dam, would have far exceeded 

Reclamation’s spending authority, and would have required returning to Congress for legislation. 

The least costly method (the 4-intake modification at $10 million) was rejected by Reclamation 

because it lacked the flexibility needed to meet the downstream temperature objectives. 
Humpback Chub Annotated Bibliography 169 September 2009

 

In Chapter III, the report compares the effects of the proposed warmer-water releases to 

those of the no action alternative (continued coldwater releases). It should be noted that although 

the proposed alternative is discussed as warmwater releases, in effect temperature controls would 

actually release water that is only about 5°C (10°F) warmer than the existing condition. To most 

rafters and recreationists, the water would still seem quite cold (59°F vs. 46°F). The goal of the 

proposed alternative would be to modify Glen Canyon Dam to allow release temperatures to be 

controlled to improve conditions for endangered fish while at the same time protecting other 

important resources like the Lees Ferry trout fishery. The proposed plan would create a tiered 

(cold/warmwater) fishery. Release temperatures would be increased from the existing levels 

(8°C–10°C) to about 15°C during the summer months. This would improve temperatures for 

rainbow trout in the reach immediately below the dam (first 16 miles to Lees Ferry). Then, as the 

water flows downstream and warms, it would quickly reach temperatures preferred by native and 

endangered (warmwater) fish. Warmwater releases may not be made in every year to help 

control competitors to the humpback chub. Release periods might be as short as a month to 

prevent thermal shock as the chub descend into the main channel, or as long as the May through 

September season to promote better growth rates. 

Input received at scoping meetings identified several areas of particular interest to the 

public and scientific community. More detailed discussions are included in Chapter III of this 

assessment. In summary, this report finds: 

Lake Powell Fishery - Temperatures in Lake Powell are already low enough to cause 

occasional winter-kill of threadfin shad, an important forage fish for the lake (game) fishery. It 

was recommended that Reclamation carefully evaluate the potential impact on this resource of 

releasing warm water from the reservoir. Computer modeling of the reservoir shows that 

temperatures in the surface layer of Lake Powell would be cooled by up to 1°C if warmwater 

releases were maintained through the entire “summer” season (140 days). Shorter duration 

releases would have even smaller effects on lake temperatures. Little or no impact is expected to 

threadfin shad or the lake fishery. However, the existing lake monitoring program would be 

continued to confirm or refute these predictions. 

Primary Productivity - Field and laboratory experiments conducted for Reclamation by 

Northern Arizona University indicate that the existing macroinvertebrates in the downstream 

environment can tolerate warmwater releases of 20°C for at least 30 days (the duration of the 

study). Release temperatures for the proposed action would normally be limited to a maximum 

of 15°C. Computer modeling of Lake Powell shows that surface withdrawals from the reservoir 

would increase nutrient and detritus release levels below the dam by up to 300 percent; thus, 

potentially improving the productivity of the river ecosystem. Studies of warmwater releases at 

Flaming Gorge Dam suggest that some minor changes (increases) may occur in diversity and 

abundance. The effects would be carefully monitored through the adaptive management process 

and the Grand Canyon Monitoring and Research Center. 

Endangered Fish - Under present conditions (the no-action alternative), endangered fish 

do not reproduce in the river, young fish thermal shock while entering the main channel from 

warm tributaries, and those that survive are easy prey due to their reduced swimming efficiency. 
Humpback Chub Annotated Bibliography 170 September 2009

 

The proposed temperature control alternative would allow releases to be made to improve the 

reproductive success of humpback chub by reducing thermal shock with late-summer, 

warmwater releases. Additionally, summer-long warmwater releases may be used in an attempt 

to further improve conditions for endangered species; however, nonnative fish may also benefit 

from sustained releases. Of primary concern is competition between carp/catfish and humpback 

chub. Summer-long, warmwater releases would likely cause carp and catfish populations to 

increase in the mainstem (along with other non-native species). 

However, this does not necessarily mean that humpback chub will be unable to find 

opportunities once the cold-water restraints are eliminated. For example, it is a well know fact 

that the humpback chub thrive in the warm water of the Little Colorado River and that they 

compete very successfully against carp, catfish, and other competitors in that warmwater system. 

Clear, summer-long, warmed releases (about 13.5°C) from Flaming Gorge Dam have also 

improved conditions for native fish populations even though non-native fish are present in great 

numbers. 

Predator Controls - Modeling studies underway by the Grand Canyon Monitoring and 

Research Center suggest that carp and channel catfish populations may need to be controlled by 

methods beyond the timing and duration of temperature controls. Physical controls (harvesting) 

may be needed to reduce predation on native fish in specific areas. Careful monitoring of these 

competitors would be an important part of the proposed alternative. If physical controls are 

needed, the Adaptive Management Work Group may recommend to the Secretary of the Interior 

actions that would be appropriate given the details of the monitoring results and the problems 

that are identified. 

Rainbow Trout - Numerous experiences at other dams strongly suggest that the proposed 

warmwater release of up to 15°C would benefit the rainbow trout fishery below Glen Canyon 

Dam by removing temperature stresses. The current 8°C (46°F) releases are well below the 15°C 

(59°F) optimum for rainbow trout. Reservoir modeling studies also suggest that nutrient and 

detritus releases from the dam would increase, potentially improving the food base for trout in 

the Lees Ferry reach of the river. 

Adaptive management is an essential component of the proposed alternative. Because of 

the complexity of the ecological interactions in the Grand Canyon, no one (fixed) plan of 

operation could be expected to optimize the goals of the proposed temperature control 

alternative. Modeling and predictions are of limited usefulness when dealing with complex 

environmental systems. It is clear that temperature release patterns (operations) will need to be 

adjusted and evolve as our knowledge increases from each successive year of testing. Carefully 

monitored experiments are necessary to assure that these adaptations help (not harm) the 

resources. The testing and monitoring program would be developed by the Glen Canyon 

Technical Work Group and Grand Canyon Monitoring and Research Center within the existing 

adaptive management process. The Glen Canyon Adaptive Management Work Group would 

then review this work and make recommendations to the Secretary of the Interior for 

implementation. 
Humpback Chub Annotated Bibliography 171 September 2009

 

The temperature control alternative included in this assessment proposes to avoid or 

mitigate the potential adverse impacts that have been identified in this assessment. It also 

includes the Adaptive Management Program and Grand Canyon Monitoring and Research 

Center to monitor and evaluate management options to avoid unforeseen impacts that may occur 

in the future. And finally, if monitoring shows that warmwater releases do not to benefit 

endangered species, cold-water releases would be available anytime. With time, the proposed 

action would be reversible (except for the expense of the modifications). 

If, after a public review, Reclamation finds that endangered fish are likely to benefit from 

warmwater releases and all significant adverse impacts can be avoided or mitigated or reversed, 

Reclamation would then consider proceeding with a Finding of No Significant Impact and would 

begin modifying the intakes in fiscal year 2000. On this schedule, temperature controls would 

potentially be available as early as the summer of 2002. 

U.S. Bureau of Reclamation. 2002. Proposed experimental releases from Glen Canyon 

Dam and removal of non-native fish. U.S. Department of the Interior, Bureau of 

Reclamation, Upper Colorado Region, Salt Lake City, Utah. 

The Grand Canyon is one of the Nation’s treasures. The Department of the Interior is 

proposing a series of experimental actions, some of which involve modifying the operations of 

Glen Canyon Dam, which is located upstream of the Grand Canyon, to improve the condition of 

the habitat within the Grand Canyon and the species that have their home in the canyon. This 

proposed action was deemed necessary by the GCDAMP because endangered species and 

sandbars in the Grand Canyon have not responded as well as predicted to past management 

actions regarding the operation of Glen Canyon Dam. The proposed actions, detailed in the 

accompanying report, are the product of years of scientific study and would implement the 

recommendation of an independent advisory committee that has been studying the natural and 

cultural resources of the Grand Canyon since 1997. The proposed actions presented in this report 

are multifaceted and complex, and have been designed to protect both the endangered species 

and the important beach habitat found in the Grand Canyon. 

The 1996 Record of Decision (ROD) on the Operation of Glen Canyon Dam Final 

Environmental Impact Statement (FEIS) modified the operation of the dam in an effort to protect 

downstream resources. An adaptive management program was established by the ROD to 

monitor the effects of this change, perform research necessary to measure whether these resource 

protection objectives were met, and make recommendations to the Secretary of the Interior. 

Since 1996, the non-native trout population in the Grand Canyon has tripled, the 

endangered humpback chub population has declined precipitously, and tributary sediment inputs 

are not being conserved as expected in the FEIS. These trends are contrary to the expectations of 

the FEIS and the goals of the adaptive management program. If no actions are taken and current 

operations continue, these trends are expected to continue. 

An experiment consisting of a combination of Glen Canyon Dam releases and 

mechanical removal of non-native fish is proposed to determine if these proposed actions can 

reverse current trends. The proposed dam releases are intended to conserve sediment inputs from 
Humpback Chub Annotated Bibliography 172 September 2009

 

the Paria River and reduce spawning and recruitment success of non-native trout. Mechanical 

removal of non-native fish is proposed in order to remove trout who feed on young chubs near 

the confluence of the LCR, which is the only known stream in Grand Canyon where the 

endangered humpback chub reproduces and survives to adulthood. 

To conserve Paria sediment inputs, proposed dam releases will either be reduced to store 

sediment in the main channel or raised to powerplant capacity to store the sediment in eddies 

following Paria River inputs. In addition, dam releases up to 45,000 cfs, similar to the 1996 test 

flow are proposed in an attempt to rebuild beaches. 

Non-native trout are known to negatively impact native fish. Daily high fluctuating 

releases are proposed during January-March to interrupt spawning of adult trout and to displace 

small trout from their preferred habitats. Proposed mechanical removal of trout by electrofishing 

will test whether the juvenile and adult trout population can be reduced in a 10-mile reach of 

Colorado River that contains the largest known number of mainstream humpback chub. About 

20,000 rainbow and brown trout are expected to be removed from this river reach in each of two 

years under the experiment. 

The environmental consequences of the Proposed Action are expected to be positive for 

resources intended to be benefited by the action, though due to the experimental nature of the 

proposal, there is some uncertainty as to the outcome. The estimated financial cost of the 

proposed experiment to power customers is about $1.7 million as compared with estimated 2003 

power revenues of $130 million under ROD operations. Objectives of this proposed action are in 

agreement with the 12 management goals of the Glen Canyon Dam Adaptive Management 

Program and applicable provisions of federal law. 

The effects of the various components of the Proposed Action on endangered species 

have been fully described in Section 3.8, “Endangered Species”. With respect to the Proposed 

Action in total, a condition of “may affect, not likely to adversely affect” is projected for the 

California condor, razorback sucker, and Southwestern willow flycatcher. A condition of “may 

affect, likely to adversely affect” is projected for the humpback chub, Kanab amber snail, and 

bald eagle. It is important to note that the Proposed Action is expected to produce an overall 

positive benefit to the ecosystem downstream of Glen Canyon Dam, including the endangered 

species, despite short-term minor impacts to some resources. 

The proposed combination of experimental dam releases and non-native fish removal has 

been developed using knowledge gained in nearly 20 years of research and monitoring of 

resources in this reach of the Colorado River, first under the Glen Canyon Environmental Studies 

and now as part of the Adaptive Management Program. Accordingly, this EA provides analysis 

that builds upon the scientific information developed over this entire period. 
Humpback Chub Annotated Bibliography 173 September 2009

 

U.S. Bureau of Reclamation. 2007. Biological assessment of the Colorado River interim 

guidelines for lower basin shortages and coordinated operations for Lake Powell and Lake 

Mead, final environmental impact statement. U.S. Bureau of Reclamation, Boulder Canyon 

Operations Office, Boulder City, Nevada. Abstract excerpted from report. 

The proposed action for this biological opinion consists of the Bureau of Reclamation’s 

(Reclamation) implementation of the Colorado River interim guidelines for Lower Basin 

shortages and coordinated operations for Lake Powell and Lake Mead (Guidelines). The 

Guidelines have four operational elements that collectively are designed to address shortages and 

coordinated operations for Lake Powell and Lake Mead and will be used by the Secretary to: 

(1) determine those circumstances under which the Secretary would reduce the annual amount of 

water available for consumptive use from Lake Mead to the Colorado River Lower Division 

states (Arizona, California, and Nevada) below 7.5 million acre-feet (maf) (a “Shortage”) 

pursuant to Article II(B)(3) of the United States Supreme Court in the case of Arizona v. 

California, 547 U.S. (2006) (Consolidated Decree); (2) define the coordinated operation of Lake 

Powell and Lake Mead to provide improved operation of these two reservoirs, particularly under 

low reservoir conditions; (3) allow for the storage and delivery, pursuant to applicable Federal 

law, of conserved Colorado River system and non-system water in Lake Mead to increase the 

flexibility of meeting water-use needs from Lake Mead Intentionally Created Surplus (ICS), 

particularly under drought and low reservoir conditions; and (4) determine those conditions 

under which the Secretary may declare the availability of surplus water for use within the lower 

division states. The proposed Federal action would modify the substance of the existing Interim 

Surplus Guidelines (ISG), published in the Federal Register on January 25, 2001 (66 FR 7772), 

and the term of the ISG from 2016 to 2026. 

Reclamation has included the following conservation measures for the listed species, 

including the humpback chub, in the action area as part of its proposed action. 

Nonnative Fish Control. In coordination with other Department of the Interior (DOI) 

Adaptive Management Program (AMP) participants and through the AMP, Reclamation will 

continue efforts to control both cold- and warm-water nonnative fish species in the mainstem of 

Marble and Grand Canyons, including determining and implementing levels of nonnative fish 

control, as necessary. Control of these species using mechanical removal and other methods will 

help to reduce this threat. 

Humpback Chub Refuge. Reclamation will assist USFWS in development and funding of 

a broodstock management plan and creation and maintenance of a humpback chub refuge 

population at a Federal hatchery or other appropriate facility by providing expedited 

advancement of $200,000 in funding to the USFWS during CY 2008; this amount shall be 

funded from, and within, the amount identified in the Multispecies Conservation Plan Biological 

Opinion (MSCP BO) (USFWS 2005a; page 26). Creation of a humpback chub refuge will 

reduce or eliminate the potential for a catastrophic loss of the Grand Canyon population of 

humpback chub by providing a permanent source of genetically representative stock for 

repatriating the species. 
Humpback Chub Annotated Bibliography 174 September 2009

 

Genetic Biocontrol Symposium. Reclamation will transfer up to $20,000 in fiscal year 

2008 to USFWS to help fund an international symposium on the use and development of genetic 

biocontrol of nonnative invasive aquatic species, which is tentatively scheduled for October 

2009. Although only in its infancy, genetic biocontrol of nonnative species is attracting 

worldwide attention as a potential method of controlling aquatic invasive species. Helping fund 

an effort to bring researchers together will further awareness of this potential method of control 

and help mobilize efforts for its research and development. 

Sediment Research. In coordination with other DOI AMP participants and through the 

AMP, Reclamation will monitor the effect of sediment transport on humpback chub habitat and 

will work with the GCMRC to develop and implement a scientific monitoring plan acceptable to 

USFWS. Although the effects of dam operation-related changes in sediment transport on 

humpback chub habitat are not well understood, humpback chub are known to utilize backwaters 

and other habitat features that require fine sediment for their formation and maintenance. 

Additional research will help clarify this relationship. 

Parasite Monitoring. In coordination with other DOI AMP participants and through the 

AMP, Reclamation will continue to support research on the effects of Asian tapeworm 

(Bothriocephalus acheilognathi) on humpback chub and potential methods to control this 

parasite. Continuing research will help better understand the degree of this threat and the 

potential for management actions to minimize it. 

Our analysis of the effects of the proposed action relies in part on Reclamation’s analysis 

from its EIS and biological assessment (Reclamation 2007a, 2007b, 2007c). Potential effects of 

the proposed action on listed species, including the humpback chub, could result from changes in 

Lake Powell reservoir storage and release operations from current conditions. The potential 

hydrologic effects could result in changes in the range and duration of the water elevations 

maintained in Lake Powell and river flow, river temperature, and sediment transport in the 

Colorado River that support habitat conditions for the listed species. Reclamation compared 

Lake Powell elevations; river flows; average monthly river temperatures at Lees Ferry, the LCR 

confluence, and below Diamond Creek; and river sediment transport under current conditions to 

corresponding values expected under the proposed action, to evaluate if differences in hydrologic 

conditions under the proposed action would affect listed species and designated critical habitats. 

Future Colorado River system characteristics under current and proposed action conditions were 

simulated using the Colorado River Simulation System (CRSS). 

Reclamation’s CE-QUAL-W2 model was used to simulate Lake Powell’s seasonal 

transformation to analyze dam release temperatures for various reservoir starting elevations and 

inflows. The Generalized Environmental Modeling System for Surface Waters (GEMSS) model 

was used to route Glen Canyon Dam release temperatures through the Grand Canyon 

downstream to Lake Mead. To estimate the effects of modifying the annual release volumes 

from Glen Canyon Dam under the proposed action on sediment transport, the USGS prepared an 

analysis relating normalized sediment transport from the Grand Canyon to annual release 

volumes. The hydrologic model, CRSS, used as the primary basis of Reclamation’s effects 

analysis does not project future inflows, but rather relies on the historic record to analyze a range 

of possible future inflows. 
Humpback Chub Annotated Bibliography 175 September 2009

 

 

The proposed action could alter critical habitat including the Primary Constituent 

Elements (PCEs) related to sediment transport, water temperature, and flow volumes in the 

Colorado River below Glen Canyon Dam relative to current conditions. These changes could 

result in adverse effects to humpback chub in three primary ways: (1) increased competition and 

predation from nonnative fish species; (2) increased parasitism from Asian tapeworm and 

anchorworm (Lernaea cyprinacea); and (3) reduced suitability of mainstem nearshore habitats 

due to changes in river flow and sediment transport. 

In order to be exempt from the prohibitions of Section 9 of the Endangered Species Act, 

Reclamation must comply with the following terms and conditions, which implement the 

following reasonable and prudent measures as well as terms and conditions that are 

nondiscretionary: (1) monitor the effects of the proposed action on humpback chub and its 

habitat to document levels of incidental take and report the findings to the USFWS. Reclamation 

shall work in collaboration with the AMP participants, including GCMRC and other cooperators, 

to complete this monitoring; and (2) Reclamation, in collaboration with the AMP participants, 

including the GCMRC and other cooperators, shall submit a written report to the USFWS 

annually documenting activities of the proposed action for the year that resulted in documented 

take. The report will include a discussion of the progress of the implementation of Reclamation’s 

conservation measures included in the proposed action. 

U.S. Bureau of Reclamation. 2007. Biological assessment on the operation of Glen Canyon 

Dam and proposed experimental flows for the Colorado River below Glen Canyon Dam 

during the years 2008-2012. U.S. Bureau of Reclamation, Upper Colorado River Region, 

Salt Lake City, Utah. Abstract excerpted from report and accompanying letter. 

Pursuant to Section 7(a)(2) of the Endangered Species Act, 16 USC 1531 et seq. and the 

implementing regulations at 50 CFR 402.16, the U.S. Bureau of Reclamation (Reclamation ) 

requested reinitiation of formal consultation with the U.S. Fish and Wildlife Service (Service) 

regarding operations of Glen Dam, Colorado River Storage Project, Coconino County, Arizona. 

The basis of this request is new information that may reveal effects of dam operations that may 

affect listed species including the humpback chub (Gila cypha) or designated critical habitat in a 

manner or to an extent not previously considered. This new information pertaining to the 

humpback chub includes: 

 Recruitment failure through the mid-1990s resulted in a decline of the Little Colorado 

River (LCR) population of humpback chub to 2,400 to 4,400 adult fish. 

 Increase in recruitment of humpback chub under MLFF began 4 to 9 years prior to 

implementation of non-native fish control, warmer dam release temperatures, the 2000 

steady-flow experiment, and the 2004 high-flow test. 

 Significantly greater numbers of young humpback chub have been found in the mainstem 

during 2002 to 2006, including upstream of the LCR. 
Humpback Chub Annotated Bibliography 176 September 2009

 

 Current adult population estimates for humpback chub have increased to an estimated 

5,300 to 6,800 adult fish in 2006. 

 Humpback chub translocated above Chute Falls have experienced high survival and 

growth rates, and are a source of recruitment to the lower LCR and the mainstem. 

 Douglas and Douglas (2007) recommended further study of the 30-mile aggregation of 

humpback chub to evaluate their potential distinctiveness. 

 Mainstem parasite infestation rates in humpback chub are much lower than fish in the 

LCR and may be temperature-limited. 

 Hoffnagle (2000) reported greater condition and abdominal fat of humpback chub in the 

mainstem than the LCR, possibly due to increased prevalence of parasites in the LCR 

fish. 

The biological assessment incorporates results of onsite inspections, updates information 

on listed species and designated habitats based on views of recognized experts, reviews the 

literature, and reaches new findings about the status of listed species and critical habitat in the 

action area below the dam. The findings are that the proposed action: (1) is likely to adversely 

affect the humpback chub due to potential take of individuals from proposed high-flow test of 

41,500 cubic feet per second in March 2008; and (2) is not likely to result in destruction or 

adverse modification of designated critical habitat for the endangered humpback chub. 

U.S. Fish and Wildlife Service. 1994. Determination of critical habitat for four endangered 

Colorado River fishes. Federal Register 59(54):13374–13400. 

This document amends and supplements the Humpback Chub Recovery Plan of 1990. 

The purpose of this document is to describe site-specific management actions/tasks; provide 

objective, measurable recovery criteria; and provide an estimate of the time to achieve recovery 

of the endangered humpback chub (Gila cypha), according to Section 4(f)(1) of the Endangered 

Species Act of 1973, as amended. Recovery or conservation programs that include the humpback 

chub will direct research, management, and monitoring activities and determine costs associated 

with recovery. 

The humpback chub is listed as endangered under the Endangered Species Act of 1973, 

as amended. The species is endemic to the Colorado River Basin of the southwestern United 

States. Adults attain a maximum size of about 480 mm total length (TL) and 1.2 kg in weight. 

Six extant wild populations are known: (1) Black Rocks, Colorado River, Colorado; 

(2) Westwater Canyon, Colorado River, Utah; (3) Yampa Canyon, Yampa River, Colorado; 

(4) Desolation/Gray Canyons, Green River, Utah; (5) Cataract Canyon, Colorado River, Utah; 

and (6) the mainstem Colorado River in Marble and Grand Canyons and the Little Colorado 

River, Arizona. The first five populations are in the Upper Colorado River Basin (i.e., upstream 

of Glen Canyon Dam, Arizona), and the sixth population is in the Lower Colorado River Basin. 
Humpback Chub Annotated Bibliography 177 September 2009

 

Populations of humpback chub are restricted to deep, swift, canyon-bound regions of the 

mainstem and large tributaries of the Colorado River Basin. Adults require eddies and sheltered 

shoreline habitats maintained by high spring flows. These high spring flows maintain channel 

and habitat diversity, flush sediments from spawning areas, rejuvenate food production, and form 

gravel and cobble deposits used for spawning. 

Spawning occurs on the descending limb of the spring hydrograph at water temperatures 

typically between 16 and 22°C. Young require low-velocity shoreline habitats, including eddies 

and backwaters, that are more prevalent under base-flow conditions. Threats to the species 

include streamflow regulation, habitat modification, predation by nonnative fish species, 

parasitism, hybridization with other native Gila, and pesticides and pollutants. 

Objective, measurable criteria for recovery of humpback chub in the Colorado River 

Basin are presented for each of two recovery units (i.e., the upper basin, including the Green 

River and upper Colorado River subbasins; and the lower basin, including the mainstem and its 

tributaries from Glen Canyon Dam downstream to Lake Mead National Recreation Area) 

because of different recovery or conservation programs and to address unique threats and sitespecific management actions/tasks necessary to minimize or remove those threats. Recovery of 

the species is considered necessary in both the upper and lower basins because of the present 

status of populations and existing information on humpback chub biology. The humpback chub 

was listed prior to the 1996 distinct population segment (DPS) policy, and the U.S. Fish and 

Wildlife Service (Service) may conduct an evaluation to designate DPSs in a future rule-making 

process. If DPSs are designated, criteria for recovery of humpback chub will need to be 

reevaluated. These recovery goals are based on the best available scientific information, and are 

structured to attain a balance between reasonably achievable criteria (which include an 

acceptable level of uncertainty) and ensuring the viability of the species beyond delisting. 

Additional data and improved understanding of humpback chub biology may prompt future 

revision of these recovery goals. 

Downlisting can occur if, over a 5-year period: (1) the trend in adult (age 4+; 200 mm 

TL) point estimates for each of the six extant populations does not decline significantly; and (2) 

mean estimated recruitment of age-3 (150–199 mm TL) naturally produced fish equals or 

exceeds mean annual adult mortality for each of the six extant populations; and (3) two 

genetically and demographically viable, self-sustaining core populations are maintained, such 

that each point estimate for each core population exceeds 2,100 adults (2,100 is the estimated 

minimum viable population [MVP] needed to ensure long-term genetic and demographic 

viability); and (4) when certain site-specific management tasks to minimize or remove threats 

have been identified, developed, and implemented. Delisting can occur if, over a 3-year period 

beyond downlisting: (1) the trend in adult point estimates for each of the six extant populations 

does not decline significantly; and (2) mean estimated recruitment of age-3 naturally produced 

fish equals or exceeds mean annual adult mortality for each of the six extant populations; and (3) 

three genetically and demographically viable, self-sustaining core populations are maintained, 

such that each point estimate for each core population exceeds 2,100 adults; and (4) when certain 

site-specific management tasks to minimize or remove threats have been finalized and 

implemented, and necessary levels of protection are attained. 
Humpback Chub Annotated Bibliography 178 September 2009

 

Management actions needed include: 1) Provide and legally protect habitat (including 

flow regimes necessary to restore and maintain required environmental conditions) necessary to 

provide adequate habitat and sufficient range for all life stages to support recovered populations; 

2) Investigate the role of the mainstem Colorado River in maintaining the Grand Canyon 

population; 3) Investigate the anticipated effects of and options for providing warmer water 

temperatures in the mainstem Colorado River through Grand Canyon; 4) Ensure adequate 

protection from overutilization; 5) Ensure adequate protection from diseases and parasites; 6 

Regulate nonnative fish releases and escapement into the main river, floodplain, and tributaries; 

7) Control problematic nonnative fishes as needed; 8) Minimize the risk of increased 

hybridization among Gila spp.; 9) Minimize the risk of hazardous-materials spills in critical 

habitat; and 10) Provide for the long-term management and protection of populations and their 

habitats beyond delisting (i.e., conservation plans). 

U.S. Fish and Wildlife Service. 1994. Final rule, determination of critical habitat for the 

Colorado River endangered fishes: razorback sucker, Colorado squawfish, humpback 

chub and bonytail chub. Federal Register 59:13374–13400. Abstract excerpted from 

summary and affected habitat. 

.

The U.S. Fish and Wildlife Service designates critical habitat for four species of endemic 

Colorado River Basin fishes: Razorback sucker (Xyrauchen texanus), Colorado squawfish 

(Ptychocheilus lucius), humpback chub (Gila cypha), and bonytail chub (Gila elegans). These 

species are listed as endangered under the Endangered Species Act 1973, as amended. The 

critical habitat designated is located primarily on Federal land and, to a lesser extent, on tribal, 

state, and private lands. The designation provides additional protection required under Section 7 

of the Endangered Species Act with regard to activities that require Federal agency action. The 

Service designates 3,168 km (1,980 mi) of critical habitat for the four Colorado River 

endangered fishes in portions of Colorado, Utah, New Mexico, Arizona, Nevada, and California. 

The historical abundance and distribution of the species are not well known. In the 

Lower Basin, the humpback chub occurs in the Little Colorado and Colorado Rivers in the Grand 

Canyon. This population is the largest remaining in the Basin. In the Upper Basin, humpback 

chub are found in the Black Rocks/Westwater Canyon and Cataract Canyon of the Colorado 

River, Desolation and Gray Canyons of the Green River, and Yampa and Whirlpool Canyons in 

the Green and Yampa Rivers of the Dinosaur National Monument. 

Spawning occurs soon after the highest spring flows when water temperatures approach 

20°C (68°F). Flow reductions and low water temperatures in the Grand Canyon have been 

implicated as factors curtailing successful spawning of the humpback chub and increasing 

competition from other species. 

Populations of humpback chub are found in river canyons, where they use a variety of 

habitats, including pools, riffles, and eddies. This diversity in habitat use suggests that the adult 

fish are adapted to a variety of habitats, and studies of tagged fish indicated that they move 

between habitats, presumably in response to seasonal habitat changes and life history needs. 

Reduced spring peak flows, availability of shoreline eddy and deep canyon habitats, and 

competition and predation from nonnative fish were reported as potential limiting factors for 
Humpback Chub Annotated Bibliography 179 September 2009

 

humpback chub in the Yampa River. The impact of hybridization with other species is currently 

being evaluated. 

U.S. Fish and Wildlife Service. 2002. Recovery goals: amendment and supplement to the 

humpback chub recovery plan. Mountain-Prairie Region, Denver, Colorado. 

This document amends and supplements the Humpback Chub Recovery Plan of 1990. 

The purpose of this document is to describe site-specific management actions/tasks; provide 

objective, measurable recovery criteria; and provide an estimate of the time to achieve recovery 

of the endangered humpback chub (Gila cypha), according to Section 4(f)(1) of the Endangered 

Species Act of 1973, as amended. Recovery or conservation programs that include the humpback 

chub will direct research, management, and monitoring activities and determine costs associated 

with recovery. 

Current Species Status: The humpback chub is listed as endangered under the 

Endangered Species Act of 1973, as amended. The species is endemic to the Colorado River 

Basin of the southwestern United States. Adults attain a maximum size of about 480 mm total 

length (TL) and 1.2 kg in weight. Six extant wild populations are known: (1) Black Rocks, 

Colorado River, Colorado; (2) Westwater Canyon, Colorado River, Utah; (3) Yampa Canyon, 

Yampa River, Colorado; (4) Desolation/Gray Canyons, Green River, Utah; (5) Cataract Canyon, 

Colorado River, Utah; and (6) the mainstem Colorado River in Marble and Grand Canyons and 

the Little Colorado River, Arizona. The first five populations are in the Upper Colorado River 

Basin (i.e., upstream of Glen Canyon Dam, Arizona), and the sixth population is in the Lower 

Colorado River Basin. 

Habitat Requirements and Limiting Factors: Populations of humpback chub are restricted 

to deep, swift, canyon-bound regions of the mainstem and large tributaries of the Colorado River 

Basin. Adults require eddies and sheltered shoreline habitats maintained by high spring flows. 

These high spring flows maintain channel and habitat diversity, flush sediments from spawning 

areas, rejuvenate food production, and form gravel and cobble deposits used for spawning. 

Spawning occurs on the descending limb of the spring hydrograph at water temperatures 

typically between 16 and 22°C. Young require low-velocity shoreline habitats, including eddies 

and backwaters, that are more prevalent under base-flow conditions. Threats to the species 

include streamflow regulation, habitat modification, predation by nonnative fish species, 

parasitism, hybridization with other native Gila, and pesticides and pollutants. 

Recovery Objective: Downlisting and Delisting. 

Recovery Criteria: Objective, measurable criteria for recovery of humpback chub in the 

Colorado River Basin are presented for each of two recovery units (i.e., the upper basin, 

including the Green River and upper Colorado River subbasins; and the lower basin, including 

the mainstem and its tributaries from Glen Canyon Dam downstream to Lake Mead National 

Recreation Area) because of different recovery or conservation programs and to address unique 

threats and site-specific management actions/tasks necessary to minimize or remove those 

threats. Recovery of the species is considered necessary in both the upper and lower basins 

because of the present status of populations and existing information on humpback chub biology. 
Humpback Chub Annotated Bibliography 180 September 2009

 

The humpback chub was listed prior to the 1996 distinct population segment (DPS) policy, and 

the U.S. Fish and Wildlife Service (Service) may conduct an evaluation to designate DPSs in a 

future rule-making process. If DPSs are designated, criteria for recovery of humpback chub will 

need to be reevaluated. These recovery goals are based on the best available scientific 

information, and are structured to attain a balance between reasonably achievable criteria (which 

include an acceptable level of uncertainty) and ensuring the viability of the species beyond 

delisting. Additional data and improved understanding of humpback chub biology may prompt 

future revision of these recovery goals. Downlisting can occur if, over a 5-year period: (1) the 

trend in adult (age 4+; 200 mm TL) point estimates for each of the six extant populations does 

not decline significantly; and (2) mean estimated recruitment of age-3 (150–199 mm TL) 

naturally produced fish equals or exceeds mean annual adult mortality for each of the six extant 

populations; and (3) two genetically and demographically viable, self-sustaining core 

populations are maintained, such that each point estimate for each core population exceeds 2,100 

adults (2,100 is the estimated minimum viable population [MVP] needed to ensure long-term 

genetic and demographic viability); and (4) when certain site-specific management tasks to 

minimize or remove threats have been identified, developed, and implemented. 

Delisting can occur if, over a 3-year period beyond downlisting: (1) the trend in adult 

point estimates for each of the six extant populations does not decline significantly; and (2) mean 

estimated recruitment of age-3 naturally produced fish equals or exceeds mean annual adult 

mortality for each of the six extant populations; and (3) three genetically and demographically 

viable, self-sustaining core populations are maintained, such that each point estimate for each 

core population exceeds 2,100 adults; and (4) when certain site-specific management tasks to 

minimize or remove threats have been finalized and implemented, and necessary levels of 

protection are attained. 

Conservation plans will go into effect at delisting to provide for long-term management 

and protection of the species, and to provide reasonable assurances that recovered humpback 

chub populations will be maintained without the need for relisting. Elements of those plans could 

include (but are not limited to) provision of flows for maintenance of habitat conditions required 

for all life stages, regulation and/or control of nonnative fishes, minimization of the risk of 

hazardous-materials spills, and monitoring of populations and habitats. Signed agreements 

among State agencies, Federal agencies, American Indian tribes, and other interested parties 

must be in place to implement the conservation plans before delisting can occur. 

Management Actions Needed:1) Provide and legally protect habitat (including flow 

regimes necessary to restore and maintain required environmental conditions) necessary to 

provide adequate habitat and sufficient range for all life stages to support recovered populations; 

2) Investigate the role of the mainstem Colorado River in maintaining the Grand Canyon 

population; 3) Investigate the anticipated effects of and options for providing warmer water 

temperatures in the mainstem Colorado River through Grand Canyon; 4) Ensure adequate 

protection from over-utilization; 5) Ensure adequate protection from diseases and parasites; 6) 

Regulate nonnative fish releases and escapement into the main river, floodplain, and tributaries; 

7) Control problematic nonnative fishes as needed; 8) Minimize the risk of increased 

hybridization among Gila spp.; 9) Minimize the risk of hazardous-materials spills in critical 
Humpback Chub Annotated Bibliography 181 September 2009

 

habitat; and 10) Provide for the long-term management and protection of populations and their 

habitats beyond delisting (i.e., conservation plans). 

Estimated Time to Achieve Recovery: Reliable population estimates, based on a multiple 

mark-recapture model, are needed for all six extant populations over a 5-year monitoring period 

for downlisting and over a 3-year monitoring period beyond downlisting in order to achieve 

delisting. The accuracy and precision of each point estimate will be assessed by the Service in 

cooperation with the respective recovery or conservation programs, and in consultation with 

investigators conducting the point estimates and with qualified statisticians and population 

ecologists. First reliable point estimates are expected for all populations by 2002. If those 

estimates are acceptable to the Service and all recovery criteria are met, downlisting could be 

proposed in 2007 and delisting could be proposed in 2010. This estimated time frame is based on 

current understanding of the status and trends of populations and on the monitoring time required 

to meet the downlisting and delisting criteria. 

U.S. Fish and Wildlife Service. 2007. Final biological opinion for the proposed adoption of 

Colorado River interim guidelines for lower basin shortages and coordinated operations 

for Lake Powell and Lake Mead. Consultation number 22410-2006-F-0224. U.S. Fish and 

Wildlife Service, Phoenix, Arizona. Abstract excerpted from report. 

At issue are impacts that may result from the proposed adoption of the Colorado River 

interim guidelines for Lower Basin shortages and coordinated operations for Lake Powell and 

Lake Mead in Coconino and Mohave Counties, Arizona, and Clark County, Nevada. The 

proposed action may affect humpback chub (Gila cypha) and its critical habitat, Kanab 

ambersnail (Oxyloma haydeni kanabensis), and southwestern willow flycatcher (Empidonax

traillii extimus) and its critical habitat. 

The proposed action will take place on the Colorado River from Lake Powell to the 

international border with Mexico, and in general concerns how water will be delivered through 

this reach of the river (specifically via the Guidelines) for the period from December 2008 

through September 2026. The Guidelines include a coordinated operation of Lake Powell and 

Lake Mead, designed to minimize shortages in the Lower Basin and avoid risk of curtailments of 

use in the Upper Basin. They also provide a mechanism, called Intentionally Created Surplus 

(ICS), for promoting water conservation in the Lower Basin. 

Our analysis of the effects of the proposed action relies in part on Reclamation’s analysis 

from its EIS and biological assessment. This section describes the methods and assumptions used 

by Reclamation to conduct the analysis of potential effects of the proposed action on species in 

the Lake Powell to Lake Mead portion of the action area. Potential effects of the proposed action 

on listed species could result from changes in Lake Powell reservoir storage and release 

operations from current conditions. The potential hydrologic effects could result in changes in 

the range and duration of the water elevations maintained in Lake Powell and river flow, river 

temperature, and sediment transport in the Colorado River that support habitat conditions for the 

listed species. 
Humpback Chub Annotated Bibliography 182 September 2009

 

Changes in allowable annual release volume under the proposed action will essentially 

create a more variable and potentially drier Colorado River in Grand Canyon annually. Whereas 

release volume in low runoff years has been restricted to 8.23 million acre-feet per year (mafy) 

under current conditions, the Guidelines will allow more flexibility, generally allowing from 7.0 

to 9.0 mafy. Thus, the proposed action could alter critical habitat including the Primary 

Constituent Elements (PCEs) related to sediment transport, water temperature, and flow volumes 

in the Colorado River below Glen Canyon Dam relative to current conditions. These changes 

could result in adverse effects to humpback chub in three primary ways: (1) increased 

competition and predation from nonnative fish species; (2) increased parasitism from Asian 

tapeworm and anchorworm (Lernaea cyprinacea); and (3) a reduction in the suitability of 

mainstem nearshore habitats due to changes in river flow and sediment transport. 

After reviewing the current status of the humpback chub and its critical habitat, the 

current status of the southwestern willow flycatcher and its critical habitat, the current status of 

the Kanab ambersnail, the environmental baseline for the action area, the effects of 

implementation of the proposed Guidelines, and the cumulative effects, it is our biological 

opinion that implementation of the Guidelines, as proposed, is not likely to jeopardize the 

continued existence of the humpback chub, the southwestern willow flycatcher, or the Kanab 

ambersnail, and is not likely to destroy or adversely modify designated critical habitat for the 

humpback chub or the southwestern willow flycatcher. 

U.S. Fish and Wildlife Service. 2008. Final biological opinion on the operation of Glen 

Canyon Dam. U.S. Fish and Wildlife Service, Phoenix, Arizona. Abstract excerpted from 

report. 

At issue are impacts that may result from the proposed adoption of the experimental dam 

operations of Glen Canyon Dam in Coconino County, Arizona. The proposed action may affect 

humpback chub (Gila cypha) and its critical habitat. We note that one of the purposes of the 

proposed action is to benefit the Grand Canyon population of humpback chub. Thus the 

proposed action takes a conservative approach to changes in dam releases in an attempt to 

capitalize on this trend in status without unduly risking these gains with more drastic changes in 

dam operations. However, there exists the possibility that the population could decline, despite 

the current trend and the potential for beneficial effects from Reclamation’s proposed action. 

 The proposed action is to continue MLFF releases as described in the 1995 EIS (U.S. 

Bureau of Reclamation 1995, 1996). As part of this experimental action, Reclamation also 

proposes to incorporate experimental flows that have been designed to benefit endangered 

humpback chub and conservation of sediment resources in the Grand Canyon. The experimental 

proposed action is: (1) an experimental high-flow test of approximately 41,500 cfs for a 

maximum duration of 60 hours in March 2008 (only one high-flow test is proposed for the 5-year 

period), and (2) fall (September and October) steady flows over the next 5 years (2008–2012). 

After reviewing the current status of the humpback chub and its critical habitat, the 

environmental baseline for the action area, the effects of implementation of the proposed action, 

and the cumulative effects, it is our biological opinion that implementation of the March 2008 

high-flow test and the 5-year implementation of MLFF with steady releases in September and 
Humpback Chub Annotated Bibliography 183 September 2009

 

October, as proposed, are not likely to jeopardize the continued existence of the humpback chub 

and are not likely to destroy or adversely modify designated critical habitat for the humpback 

chub. 

U.S. Fish and Wildlife Service. 2009. A plan for the captive maintenance of humpback 

chub from the Yampa River population. Upper Colorado River Endangered Fish 

Recovery Program, Lakewood, Colorado. 

Population estimates for humpback chub (Gila cypha) in the Yampa River have never 

been successful because too few fish have been collected. It was recommended to remove 

individuals from the Yampa River into captivity to preserve their unique genetics. This plan 

recommends maintaining humpback chub collected from an initial effort in October 2007, as 

well as future collections, at the Ouray National Fish Hatchery and J.W. Mumma Aquatic 

Species Restoration Facility as a captive population and for potential future propagation. This 

plan recommends maintaining 500 adults in captivity, with active genetic monitoring and 

maintenance, which should provide an initial buffer for the accumulation of deleterious 

mutations, as well as maintaining genetic diversity available in the Yampa River population. 

This plan provides three objectives with associated management actions and tasks for 

maintaining captive humpback chub from the Yampa River population. 

U.S. Geological Survey. 2007. Science Plan for Potential 2008 Experimental High Flow at 

Glen Canyon Dam, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona. 

104 p. 

This science plan describes proposed monitoring and research activities to be conducted 

by the U.S. Geological Survey’s Grand Canyon Monitoring and Research Center (GCMRC), 

should the Secretary of the Interior approve an experimental high flow at Glen Canyon Dam in 

spring 2008. A high-flow release from the dam has been proposed in 2008, not only to rebuild 

sandbars and aid the endangered humpback chub, but also to benefit various downstream 

resources, including rainbow trout (Oncorhynchus mykiss), the aquatic food base, riparian 

vegetation, and archaeological sites. Additionally, the system is currently enriched with sediment 

as a result of repeated tributary floods from the Paria River in late 2006 and fall 2007; the current 

level of sand enrichment is greater than it has been since at least 1998. 

The international prominence of Grand Canyon National Park and public concern about 

the impacts of Glen Canyon Dam resulted in Federal efforts to protect downstream resources. In 

1992, the Grand Canyon Protection Act (GCPA) was enacted “to protect, mitigate adverse 

impacts to and improve the values for which Grand Canyon National Park and Glen Canyon 

National Recreation Area were established.” The 1996 Record of Decision on the Operation of 

Glen Canyon Dam Environmental Impact Statement established an adaptive management 

program, of which the GCMRC is a part, to ensure that the primary mandate of the GCPA is met. 

Before the dam, the Colorado River swelled with spring snowmelt from the Rocky 

Mountains in most years, producing flood events and transporting large quantities of sediment 

that created and maintained sandbars in Grand Canyon. In Grand Canyon, sandbars provide 

camping beaches for river runners and hikers, serve as a source of sediment needed to protect 
Humpback Chub Annotated Bibliography 184 September 2009

 

archaeological resources from weathering and erosion, and create habitats used by native fish 

and other wildlife. Today, the river usually runs clear below Glen Canyon Dam, because Lake 

Powell traps all of the sediment upstream from the dam. As a result, Grand Canyon receives 6%–

16% of its pre-dam sand supply, which comes primarily from the Paria and Little Colorado 

Rivers when they enter the mainstem below the dam. 

The native fish community found in Grand Canyon evolved in the large, turbid, and 

seasonally variable pre-dam Colorado River. Today, three of the eight native fish species have 

been eliminated from the Colorado River in the study area and two are federally listed as 

endangered, razorback sucker (Xyrauchen texanus) and humpback chub (Gila cypha), under the 

Endangered Species Act of 1973. The razorback sucker is widely thought to no longer be present 

in Grand Canyon. Only six populations of humpback chub are known to exist, five in the 

Colorado River Basin above Lees Ferry, Arizona, and the one in Grand Canyon, Arizona, which 

is the largest population remaining in the basin. 

Importantly, the design of the proposed 2008 high flow and the accompanying 

experimental studies outlined in this plan build on learning that occurred as the result of highflow experiments conducted in 1996 and 2004. For example, from the 1996 high-flow, scientists 

learned that tributary-supplied sand does not accumulate on the riverbed over multiyear periods 

under typical dam operations. In fact, erosion of low-elevation sandbars caused by the 1996 high 

flow actually resulted in a net reduction in overall sandbar size. Approval of a supplemental 

environmental assessment allowed scientists to evaluate the efficacy of conducting a high flow 

following tributary floods in 2004 for the first time and generated the following conclusions: 

 The 2004 experiment resulted in an increase of total sandbar area and volume in the 

upper half of Marble Canyon, but further downstream, where sand was less abundant, a 

net transfer of sand out of eddies occurred that was similar to that observed during the 

1996 experiment. 

 More sand will be required than was available during the 2004 high flow (800,000 to 

1,000,000 metric tons) to achieve increases in total sandbar area and volume throughout 

all of Marble and Grand Canyons in the future. 

 Sandbars created by the 2004 high flow increased the windborne transport of sand toward 

some archaeological sites in Grand Canyon. This led to the hypothesis that increased 

sand carried by the wind from restored sandbars may reduce erosion and increase 

preservation potential at some archaeological sites. 

The sediment-related data that researchers propose to collect for a possible 2008 high 

flow would facilitate comparison with data collected during the two previous experiments. 

Proposed experimental studies will also generate new data that can be compared to previous tests 

on the physical processes regulating sandbar erosion and deposition during high-flow 

experiments, sediment deposition at archaeological sites and camping areas, ecosystem flux 

measurements related to organic tributary inputs, effects of flood disturbance on vegetation, and 

formation of backwater habitats used by native and nonnative fishes. These comparisons are 

required to determine whether greater and more geographically extensive sandbar rebuilding is 
Humpback Chub Annotated Bibliography 185 September 2009

 

possible with a future high flow than occurred in 1996 and 2004. The data are also needed to 

determine if consecutive high flows in the future might cause sand to accumulate through time to 

reverse erosion documented after the closure of Glen Canyon Dam in 1963. 

Sandbar rebuilding is thought to be important in creating backwater habitat that may lead 

to increased production of young fish by native species. Overall, recruitment of humpback chub 

has been increasing from 1994 to 2002, a period that includes the 1996 high flow, though the 

uncertainty in these estimates is large. These data suggest that high flows have not been 

detrimental to humpback chub. It is also possible that high flows offer advantages to humpback 

chub, including the temporary displacement of nonnative fishes and the maintenance and 

construction of backwater habitats, which may offer growth advantages to humpback chub and 

other native fishes. 

The best timing to conduct a high flow to maximize resource benefits or to avoid 

undesirable impacts has yet to be determined. For 2007–08, the earliest practical time for a high 

flow would be early March 2008, given the logistical, administrative, and compliance 

requirements associated with conducting the research outlined in this plan. 

The GCMRC proposes replication of the 2004 hydrograph in a potential 2008 high flow 

(41,500 cubic feet per second (cfs) for 60 hours). These conditions would allow scientists to 

determine whether the locally robust and consistent sandbar-building responses that occurred in 

upper Marble Canyon in 2004 can be repeated and possibly enhanced. However, a possible 2008 

experiment would be different from the two high-flow experiments conducted previously in 

several important ways. In November 2007, for example, sand supplies in the main channel of 

the Colorado River were two to three times larger and distributed differently than in 2004. The 

system is currently enriched with sediment as a result of repeated tributary floods from the Paria 

River in October 2006 and August–September 2007 that delivered 2,500,000 metric tons 

(±500,000 metric tons) of sand into the Colorado River ecosystem below Glen Canyon Dam. 

Based on the entire period of record on the Paria River (1923–present), this annual magnitude of 

sand supply from the river occurs, on average, once in every 10 years. A second important 

difference is that a 2008 high flow would be followed by normal Record of Decision operations 

associated with annual release volumes, unlike previous experiments, which were followed by 

higher fluctuating flows than would have otherwise occurred. 

Additionally, this science plan focuses on a wider range of research questions than 

previous high-flow experiments. For example, experimental study 1 (parts A–D) addresses 

questions related to sediment and seeks to determine not only if high-flow releases are an 

effective tool that will rebuild and maintain sandbars over time, but also if they have the ability 

to create additional backwater habitats for native fish and how new sand deposits affect 

archaeological sites. Experimental study 1 expands on work begun with the 2004 high flow to 

document the connection between high-flow releases and the transfer of sand to cultural sites by 

the wind and the formation and persistence of backwaters as the result of high flows. 

Additionally, data gathered as a result of a possible 2008 high-flow experiment would provide 

information to inform the continued development of a sediment model, which will help 

determine the optimum frequency, timing, duration, and magnitude of future high flows under 

varying sediment enrichment conditions. Experimental studies 2–5 address the impacts of high-
Humpback Chub Annotated Bibliography 186 September 2009

 

flow experiments on riparian vegetation, the food base, rainbow trout, and Lake Powell water 

quality, respectively. Study 7 will provide a comprehensive synthesis of the results of all of the 

experimental studies conducted in association with a possible 2008 high-flow experiment. A 

well-calibrated, robust predictive sediment model will help minimize the impacts of high-flow 

tests on Glen Canyon Dam hydropower production. 

The experimental studies outlined in this plan are designed to address strategic science 

questions identified in the Grand Canyon Monitoring and Research Center’s monitoring and 

research plan; strategic science questions are designed to guide science activities over the next 

5 years. Questions specific to the impacts of a high-flow flow are also identified for each study 

and would be addressed during the 2008 high-flow experiment, if it occurs. 

Based on the two previous high-flow experiments conducted to date, scientists cannot say 

at this time whether such experiments are an effective strategy for stopping the ongoing erosion 

of sand and sandbars in the Colorado River ecosystem. A long-term research strategy involving 

further high-flow experimentation and model development will be necessary to assess whether 

high flows can effectively conserve sediment and help achieve other related resource benefits 

(increased humpback chub recruitment, enhanced camping beaches, protection of cultural 

resource, minimized hydropower impacts, etc). At this time, it is not anticipated that a single 

high-flow release can answer all such relevant questions: accordingly, it is very likely that 

additional high-flow experiments will be needed to address the major uncertainties associated 

with the use such dam operations as an effective long-term management tool. 

Upper Colorado River Endangered Fish Recovery Program. 2008. A plan for the captive 

maintenance of humpback chub from the Yampa River. Draft report, Upper Colorado 

River Endangered Fish Recovery Program, Lakewood, Colorado. 

Population estimates for humpback chub (Gila cypha) in the Yampa River have never 

been successful because too few fish have been collected. It was recommended to remove 

individuals from the Yampa River into captivity to preserve their unique genetics. This plan 

recommends maintaining humpback chub collected from an initial effort in October 2007, as 

well as future collections, at the Ouray National Fish Hatchery and J.W. Mumma Aquatic 

Species Restoration Facility as a captive population and for potential future propagation. This 

plan recommends maintaining 500 adults in captivity, with active genetic monitoring and 

maintenance, which should provide an initial buffer for the accumulation of deleterious 

mutations, as well as maintaining genetic diversity available in the Yampa River population. 

This plan provides three objectives with associated management actions and tasks for 

maintaining captive humpback chub from the Yampa River population. 

Valdez, R.A. and R.T. Muth. 2005. Ecology and conservation of native fish in the Upper 

Colorado River Basin. American Fisheries Society Symposium 45:157–204. 

The upper Colorado River basin supports a native ichthyofauna of 14 species or 

subspecies that have been impacted by poor land-use practices, altered flows, physical habitat 

fragmentation, competition and predation from nonnative fish species, and degraded water 

quality. Five taxa are federally endangered, including the large-river species, Colorado 
Humpback Chub Annotated Bibliography 187 September 2009

 

pikeminnow Ptychocheilus lucius, humpback chub Gila cypha, bonytail G. elegans, razorback 

sucker Xyrauchen texanus, and a warm-stream subspecies, Kendall Warm Springs dace 

Rhinichthys osculus thermalis. Two recovery programs, formed through cooperative agreements 

among federal, state, tribal, and private agencies and stakeholders, coordinate activities in the 

upper basin that have helped to resolve water resource issues, implement management actions to 

minimize or remove threats, and conserve endangered species. A cooperative biological 

management program among state and federal agencies works to protect the Kendall Warm 

Springs dace. Conservation agreements have also been established for the other native fish 

species. Continued public and institutional support for these programs is vital to species recovery 

and to the balance between long-term species conservation and human demands on the Colorado 

River system. 

Valdez, R.A., S.W. Carothers, M.E. Douglas, M. Douglas, R.J. Ryel, K.R. Bestgen and D.L. 

Wegner. 2000. Research and implementation plan for establishing a second population of 

humpback chub in Grand Canyon, Final report to U.S. Department of the Interior, U.S. 

Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona. 

Introduction-The humpback chub (Gila cypha) is an endangered cyprinid fish species 

endemic to the Colorado River Basin in Colorado, Utah, and Arizona. Six populations remain, 

including five in the upper basin and one in the lower basin in Grand Canyon. The Grand 

Canyon population consists of nine mainstem Colorado River aggregations and one spawning 

aggregation in the Little Colorado River (LCR), a major tributary located about 123 km 

downstream of Glen Canyon Dam. Humpback chub that spawn in the LCR, which includes fish 

from the mainstem aggregation around the LCR inflow, are considered a single successfully 

reproducing population. Fish in the remaining eight mainstem aggregations are unable to spawn 

successfully, presumably because of cold water temperatures from Glen Canyon Dam releases. 

Establishing a second self-sustaining population in Grand Canyon will reduce the risks 

associated with a catastrophic loss of the LCR population, thereby aiding in conservation of the 

species, and helping to address the “jeopardy” determination of the Biological Opinion on the 

Operation of Glen Canyon Dam. 

This plan for establishing a second population of humpback chub in Grand Canyon was 

developed jointly by a team of biologists, population ecologists, and geneticists. Only biological 

factors were taken into consideration; potential cultural and political constraints were 

disregarded. The plan identifies specific time-line action items with contingencies in case a 

particular action fails or is ineffective. A description of hatchery needs and availability is 

provided, along with estimated costs for each element of the plan. 

Criteria for the Second Plan- The primary criteria for establishing a second population of 

humpback chub in Grand Canyon are (1) establishing successfully reproducing adults of 

sufficient number to maintain the maximum genetic viability of the species and (2) achieving 

long-term demographic stability in suitable habitat reasonably protected from threats and 

catastrophes. A genetic effective population size (Ne) was determined to be 1,667 adults and is 

presented in this document to serve as a guideline to help evaluate alternative approaches to 

establishing a second population. Demographic structure is presented as the estimated numbers 

of adults (age 4+) and juveniles (ages 3, 2, 1, and 0) that are thought to constitute long-term 
Humpback Chub Annotated Bibliography 188 September 2009

 

demographic stability. Suitable habitat is ascertained from evaluation of various parameters, 

including water quantity, water quality, barriers to movement, presence of non-native fishes, and 

proximity to other populations of humpback chub. 

Alternatives- The plan evaluates four alternatives: (1) Existing Mainstem Aggregation, 

(2) Metapopulation Approach, (3) Tributaries, and (4) Tributary and Mainstem. Preliminary 

habitat analyses show that genetic criteria (i.e., target population size and structure) are unlikely 

to be met in a tributary, but may be met in two contiguous aggregations (Stephen Aisle/Middle 

Granite Gorge) or in the mainstem taken as a whole (the metapopulation concept, which assumes 

sub-populations periodically exchange individuals and, hence, are linked genetically). The 

metapopulation concept is thought to present the greatest likelihood for success in establishing a 

new, genetically viable population of humpback chub in Grand Canyon. 

Existing Mainstem Aggregation- The principal factor now limiting successful 

reproduction and recruitment of humpback chub in the Colorado River in Grand Canyon is 

thought to be cold water temperatures released from Glen Canyon Dam. Thus, implementation of 

the U.S. Bureau of Reclamation’s proposal to modify the dam penstocks to warm downstream 

water temperatures is the key feature of this element. Providing warmer water temperatures of 

16-22°C at aggregation sites from May through September is expected to promote successful 

reproduction and enhance survival and growth of young. Although the proposal to warm dam 

releases is likely to affect all eight non-spawning mainstem aggregations, we believe the greatest 

chance of success is with the two largest existing mainstem aggregations: Stephen Aisle and 

Middle Granite Gorge (210-235 km downstream from Glen Canyon Dam). Assuming that 

habitat for adults is determined by availability of eddy complexes, we estimate that the 25-km 

reach occupied by these two aggregations could support enough fish to meet the criteria of 

genetic viability and long-term demographic stability. The Middle Granite Gorge aggregation by 

itself appears to have a sufficient number of adults to minimize the effect of inbreeding and this 

aggregation receives downstream migrants from the LCR. Transfer or stocking of fish is not a 

feature of this alternative. The aggregations would be monitored for 5-10 years to evaluate 

success, based on the criteria for success. 

Metapopulation Approach- This alternative acknowledges possible responses to warming 

by fish from most of the mainstem aggregations. The criteria of a second population would be 

met as the sum of proximate aggregations which exhibit some exchange of individuals and, 

hence, genetic linkage. This alternative was selected as the most feasible for meeting the goals 

of a second population. 

Tributaries- Establishing a resident population of humpback chub in one or more 

tributaries other than the LCR is the third alternative of the plan. Two seasonally warmed 

tributaries, Havasu Creek and Shinumo Creek, were selected as most likely to meet the life 

history needs of the species. Introductions would be made in both streams in reaches above falls 

that prevent passage of non-native fishes upstream from the Colorado River. Of the two 

tributaries, Havasu Creek is preferred because it is more similar in hydrology and habitat to the 

currently occupied reach of the LCR. Shinumo Creek is recommended as an additional site 

because it appears to have appropriate water quality, low densities of non-native fish predators, 

and little human disturbance. These recommendations are preliminary; detailed assessments of 
Humpback Chub Annotated Bibliography 189 September 2009

 

habitat suitability and current fish communities in these two streams would have to be conducted 

before a final determination is made. 

Since these tributaries do not currently support humpback chub, fish would be transferred 

from the LCR to initiate and possibly augment a population. We do not advocate use of a 

hatchery as a primary tool for establishing a new population of humpback chub in Grand Canyon 

because hatchery programs may result in reduced genetic viability in the target species. Instead, 

fish would be transferred from the LCR in totals of 500 YOY (50-100 mm total length) and 100 

juveniles (100-250 mm) to each tributary annually for 3 consecutive years. If the numbers of 

young fish from the LCR are inadequate and if genetic variability can be assured, hatcheryreared fish would be used. These initial transfers would be experimental to determine the best 

release methods for survival and residence of fish. Positive results of these field experiments 

could lead to additional transfers of fish to these tributaries over a 3-year period. As a 

contingency, if transfer of LCR fish fails, hatchery-reared humpback chub would be released in 

large numbers over a 2-year period. Releasing young hatchery-reared fish into small earthen 

ponds in the lower Paria River or lower Bright Angel Creek may also be considered a 

contingency. 

Tributary and Mainstem- This alternative considers establishing a population of fish in a 

tributary with free access to the mainstem. The new population would be expected to move to 

and from the mainstem in the same manner as the existing LCR population. No tributary in 

Grand Canyon meets the criteria for this alterative since those with suitable habitat have natural 

fish barriers near their outflows (Havasu Creek, Shinumo Creek); cold water temperatures 

(Tapeats Creek); support large populations of non-native fish predators, such as brown trout or 

rainbow trout (Bright Angel Creek); or lack sufficient flow volume and suitable habitat (Paria 

River, Kanab Creek). 

Hatcheries and Genetic Considerations- We recommend initiating a hatchery program at 

the outset of this plan (1) as a refuge for unique genetic stocks if they are found to exist, (2) to 

develop a brood stock of humpback chub, and (3) to produce fish for supplementation, if 

necessary. Fish and/or gametes from at least the 30-Mile aggregation should be taken into a 

hatchery refuge in the first year of the plan for genetic assessment and to protect unique genetic 

material if it is found. These fish are behaviorally distinct from the LCR population and may be 

relicts of mainstem stocks. Genetic profiles should be developed to determine if significant 

genetic differences exist among any of the nine aggregations in Grand Canyon, and if transfer of 

fish among aggregations or use of hatchery products is feasible. If various genetic markers show 

no significant differences, a brood stock will be developed from progeny of LCR fish. 

Approximately 200 YOY fish would be captured and transferred from the LCR for rearing at a 

hatchery facility. Assuming losses from handling and mortality over time, 100–150 would be 

expected to reach adulthood at 4+ years of age (assume 50:50 gender ratio). Fish for 

supplementation (F1 progeny of wild fish) would be produced from paired matings of this brood 

stock to maximize genetic diversity. The numbers of males and females needed would be 

determined by assessing the genetic diversity of the population. Once established, this brood 

stock would be capable of producing approximately 200,000 young annually for stocking. 
Humpback Chub Annotated Bibliography 190 September 2009

 

Contingencies and Costs- This plan contains several alternative actions and contingencies 

to provide the maximum likelihood of success. If efforts to establish a mainstem population fail, 

the concept of a second population and the efficacy of the temperature control device on Glen 

Canyon Dam will have to be re-evaluated. If all efforts to establish a new population fail, the 

feasibility of establishing a second population of humpback chub in Grand Canyon will have to 

be re-evaluated. Total estimated cost of establishing a second population of humpback chub in 

Grand Canyon is $4.7–$6.2 million. This cost assumes that existing hatchery facilities will be 

used and that a new hatchery will not need to be constructed. Estimated costs are divided into 

four elements: mainstem monitoring, tributary stocking and monitoring, hatchery program, and 

genetic profiles. At the full development scenario for the program, the most expensive elements 

would be the mainstem monitoring ($2.0–$2.5 million) and the hatchery program ($2.0–

$2.4 million). Monitoring for a second population of humpback chub would be merged with 

monitoring programs for the temperature control device and experimental steady flows, both of 

which require mainstem monitoring of fish assemblages. To the extent possible, requirements of 

all three efforts should be satisfied with one monitoring program. 

Van Haverbeke, D.R. and L.G. Coggins, Jr. 2002. Stock assessment and fisheries 

monitoring activities in the Little Colorado River within Grand Canyon during 2001. 

Document number USFWS-AZFRO-FL-02-002. U.S. Fish and Wildlife Service, Flagstaff, 

Arizona. 82 pages. 

The GCMRC determined that a rigorous stock assessment program for the LCR was a 

priority for 2001 (USFWS 2001). As a result, the USFWS was contracted by the GCMRC to 

conduct stock assessment and monitoring activities in the LCR. A total of four monitoring trips 

were conducted during 2001: (1) 30 April to 11 May, (2) 4 to 15 June, (3) 1 to 12 October, and 

(4) 5 to 16 November. The primary goal of these trips was to obtain information for stock 

assessment of the humpback chub (Gila cypha; hereafter HBC). In addition, a secondary goal of 

these trips was to provide information for characterizing attributes of the natural history of the 

LCR fish community (e.g., species composition, sexual condition, parasites, etc.). 

The four trips were used to conduct two mark-recapture experiments to estimate the 

abundance of HBC in the lower 14.2 kilometers of the LCR. The results of the spring markrecapture effort indicate that there were 3,510 (SE=282) HBC ≥100 mm TL residing in the lower 

LCR during the spring of 2001. Of these fish, it is estimated that there were 1,470 (SE=240) 

HBC ≥200 mm (4+ year old adults). The results of the fall effort indicate that there were 2,424 

(SE=129) HBC ≥100 mm total length residing in the lower LCR during the fall of 2001. The fall 

2001 estimate was not significantly different from the fall 2000 effort (Coggins and Van 

Haverbeke 2001). 
Humpback Chub Annotated Bibliography 191 September 2009

 

Van Haverbeke, D.R. and R.L. Simmonds, Jr. 2004. Feasibility of developing a program 

to augment the population of humpback chub (Gila Cypha) in Grand Canyon. USFWSAZFRO-FL-03-007. U.S. Fish and Wildlife, Arizona Fishery Resources Office, Flagstaff. 

This report summarizes findings by the U.S. Fish and Wildlife Service on the feasibility 

of performing three management actions to promote the conservation of the humpback chub 

(Gila cypha) in Grand Canyon. 

First, we address the feasibility of establishing a captive broodstock program for 

humpback chub. Broodstock development is considered within the context of captive 

propagation policy as defined by the U.S. Fish and Wildlife Service and the National Oceanic 

and Atmospheric Association, and within the context of the scientific literature. Part of this 

policy requires that captive broodstock activities are based on the specific recommendations of 

recovery strategies identified in recovery plans whenever practical; a feature for which the 

current Recovery Goals for the species make no provision. 

Establishment of a captive broodstock may serve as a genetic refugium, and the activity 

by itself poses no risk to the wild population. However release of captive propagated individuals 

into the wild poses serious biological risks, and as such should not be considered as a 

management strategy unless all other conservation measures fail. Potential biological risks 

involved with release of captive propagated fish into the wild include introgression, inbreeding 

depression, domestication, and potential to decrease the genetic effective population size of the 

wild population. 

A captive broodstock program will require being preceded by completion of genetics 

studies being performed on humpback chub, development of a formal captive broodstock 

management plan, identification of a an adequate site equipped with a quarantine facility and 

capable of holding several thousand fish, development of a formal reintroduction plan, and 

commitment of significant long term funding. This document discusses basic questions in 

relation to broodstock development, and lists hatchery attributes required to raise broodstock 

fish. The humpback chub currently held at Willow Beach National Fish Hatchery may serve as a 

starting point for such an activity. 

Second, we address the feasibility of establishing a program for captive grow-out of wild 

caught age-0 humpback chub for release into the wild. Modeling suggests that if ~960 to 1,400 

age-0 humpback chub were captured per year from the Little Colorado River (LCR), and grown 

out to ~170 mm before release, this should arrest further population decline and maintain the 

abundance of age-4+ humpback chub at levels estimated in 2000. Alternatively, the model 

predicts that if ~4,300 to 6,350 age-0 fish were captured per year from the LCR, and grown out 

to ~170 mm before release, this may achieve a positive increase in the abundance of age-4+ fish 

to the level estimated in 1990. These predicted numbers may need to be inflated, depending upon 

the rate of post-release mortality (i.e., they may need to be doubled). These predicted effects 

should be fully realized by the year 2020. The primary biological risks associated with this 

activity appear to be related to ethological issues, such as lack of anti-predator responses or lack 

of ability to feed efficiently. In addition, depending on where the fish are released, a potential 

exists to effect density-dependant dynamics in the wild population. It is recommended that if this 

action is performed, and is to succeed, a naturalistic rearing facility and methodologies are used. 

Although the action, if properly performed, appears to pose no serious biological risks to the 

wild population, the action would not promote a self sustaining population, a feature required in 
Humpback Chub Annotated Bibliography 192 September 2009

 

the recovery criteria for the species. In addition, this management action would likely require 

significant long term effort and funding (years to decades) to achieve a sustained positive 

population response. 

Third, we address the feasibility of augmenting the Grand Canyon population of 

humpback chub via translocation. Considered are 1) translocation of fish within the LCR, and 2) 

translocation of fish into other tributaries (Bright Angel, Shinumo, and Havasu creeks) in Grand 

Canyon. 

Translocation of humpback chub within the LCR appears to offer potential for minor gain 

in the wild census population, and may significantly expand the current spawning range of the 

species, but may pose some potential for genetic risk to the main population in Grand Canyon. 

These risks are related to inbreeding and depression of genetic effective population size. 

Corrective measures to avoid these problems (should they occur) appear to be available, 

provided monitoring and funding is emplaced to detect them. 

Translocation of humpback chub to other tributaries in Grand Canyon may offer potential 

for augmenting mainstem aggregations, and some potential exists for creation or significant 

expansion of downstream aggregations. Translocation efforts to these tributaries may need to be 

accompanied by sizeable predator removal efforts to effect a change. Genetic risks to the main 

population of humpback chub in Grand Canyon appear to be minor. 

It is recommended that if any of these actions are pursued, they be carried out with the 

priorities in mind of: 1) posing least potential for genetic harm to the wild population, and 2) 

having the best potential for promoting a self-sustaining wild population. This suggests that 

translocations might be a first priority, followed by supplemental stocking of wild caught age-0 

fish, and as a last resort the release of captive propagated fish. Maintaining fish in captivity for 

refugium purposes poses no genetic risks to the wild population, however, the release into the 

wild of captive reared individuals does pose numerous genetic risks that need to be seriously 

evaluated. 

Van Haverbeke, D.R., R.S. Rogers, M.V. Lauretta and K. Christensen. 2007. 2005 Grand 

Canyon Long-Term Fish Monitoring Colorado River, Diamond Creek to Lake Mead. 2005 

Annual report to Grand Canyon Monitoring and Research Center from U.S. Fish and 

Wildlife Service, Hualapai Tribe and SWCA Environmental Consultants, Flagstaff, 

Arizona. Abstract excerpted from study introduction and discussion. 

The purpose of the 2005 Annual Report for Grand Canyon long-term fish monitoring 

from Diamond Creek to Pearce Ferry is to provide analysis and discussion of 2005 (Trip ID: 

GC20050531) and previous monitoring efforts downstream of Diamond Creek. In addition, the 

2005 annual report addresses the objectives and sub-objectives of the Diamond Creek to Pearce 

Ferry fish monitoring program. The global objectives of the program are to detect changes in fish 

abundance, distribution, and length structure in the Colorado River between Diamond Creek and 

Pearce Ferry, and, more specifically, to provide information on the distribution, movement, and 

sources of warm water non-native species that inhabit this portion of the Colorado River 
Humpback Chub Annotated Bibliography 193 September 2009

 

ecosystem. This information will be used in combination with other long-term monitoring data to 

elucidate best management of native and non-native fishes in the Colorado River, Grand Canyon. 

In addition to the global objective, the sub-objectives of 2005 sampling efforts below 

Diamond Creek are to: 

 Evaluate the utility of different fish sampling gears for detection of long-term trends in 

fish abundance, distribution, and movement. 

 Evaluate tributaries downstream of Diamond Creek as potential future refugia for native 

fishes. 

 Document presence of native and non-native fishes in selected tributaries downstream of 

Diamond Creek. 

Monitoring efforts upriver of Diamond Creek rely on CPUE as an index to detect 

changes in the relative abundance of fish. The ability to estimate changes in the relative 

abundance of species and therefore to make inferences regarding population trends is related to 

the variation of the catch rates. Sampling strategies have been designed to detect a 20% change 

in CPUE over a 5-year period for native and nonnative species. A CV of 0.1 is necessary for this 

level of detection; however, sampling efforts in 2005 were unable to achieve this target for any 

species or gear type. 

The methods employed during the trip were evaluated by comparing the catch rates and 

variances for each species and gear type. The CV for each species was compared across gear 

types, and the gear type with the lowest CV was assumed to have the greatest ability to estimate 

species’ relative abundance and to monitor trends in the population. Electrofishing was the most 

effective method of sampling for the majority of species captured, including carp, fathead 

minnow, flannelmouth sucker, red shiner, smallmouth bass, speckled dace, and striped bass. 

Angling proved to be the most effective gear type for monitoring channel catfish. Hoop netting 

and seining were the only sampling methods that detected the presence of humpback chub; 

trammel netting was the only method that captured threadfin shad; and backpack electrofishing 

was the only method that detected the presence of mosquitofish. Long lines captured channel 

catfish and striped bass; however, comparison of variances indicates that angling is a much more 

effective method of monitoring channel catfish, and long lines are the least effective method of 

monitoring striped bass. 

Power analyses were completed for several of the most common species captured by 

electrofishing, trammel netting, and hoop netting to assess the change in variance associated with 

increased sample sizes. These analyses indicate that current monitoring efforts with 

electrofishing are the most effective in monitoring carp, red shiner, and striped bass; however, 

current monitoring efforts are not likely to be able to estimate yearly changes in relative 

abundance with enough precision to assess the impact of management actions on the fish 

community in this reach of the Grand Canyon. Similarly, analyses of hoop and trammel netting 

data suggest that current monitoring efforts will not achieve target variance levels for any 

species. No power analysis was completed for seining because the sample size is limited by the 
Humpback Chub Annotated Bibliography 194 September 2009

 

number of backwaters present. No power analysis was conducted for angling since the angling 

effort is limited by sampling opportunistically while traveling downstream, and increased effort 

would impact the ability to sample with other gear types at designated sites. Furthermore, the 

current angling effort produced a relatively low variance for channel catfish (CV = 0.18), which 

indicates that this method may be suitable for monitoring this species at current effort levels. A 

power analysis was not completed for backpack electrofishing because sampling with this gear 

type occurs opportunistically during travel between study sites. An analysis of long lines was not 

completed since other methods are shown to be more effective in monitoring species captured 

with this gear type. 

Sampling during 2005 established an initial baseline of the species composition, age 

structure, and distribution of native and non-native species. A comparison of the fish community 

present in 2005 with historical capture information gives some interesting insight into the 

changes of the fish community over the last decade. During sampling trips from 1992 to 1995, 

Valdez et al. (1995) noted a dramatic change in the ichthyofauna downstream of Bridge Canyon 

(RM 235). Numbers of species increased from 9 to 20 below Bridge Canyon, and densities of 

non-native species increased dramatically. Included in the species captured below Bridge 

Canyon were: black crappie, black bullhead, bluegill, green sunfish, largemouth bass, walleye, 

plains killifish, and golden shiner, with bluegill and largemouth bass captures being particularly 

high in fall 1992. None of these species were identified during 2004 or 2005. Furthermore, 

smallmouth bass, a species not observed during the 1990s, was captured during 2005 sampling. 

Additionally, captures of fathead minnow, red shiner, and threadfin shad were noticeably higher 

during most of the 1990s sampling, particularly in fall 1992. Finally, the presence of age-0 

flannelmouth sucker inhabiting mainstem habitat appears to have increased compared with 

studies during the 1990s. 

Habitat characteristics in the Diamond Creek to Pearce Ferry reach were assessed. 

Because the elevation of Lake Mead has dropped over the past decade, aquatic habitat conditions 

have undergone extensive changes. In previous years, low-gradient braided channels 

characterized the stretch of river from Quartermaster to Dry Canyons, with numerous offchannel habitats (e.g., overflow channels, backwaters, etc.). On both of the 2004 and 2005 

sampling trips, it was observed that the mainstem has undergone extensive downcutting and 

channelization. This was evident from Separation Canyon downstream, but the effects were 

particularly dramatic below Quartermaster. Many stands of cottonwood and willow that had 

previously been close to water level are now stranded several meters above the riverbed, which 

has been dramatically downcut into alluvial deposits. Some vegetative stands have recolonized at 

lower levels, while other higher stands have perished, leaving large, dead stands of trees. The 

river is now characterized in many places by high, collapsing, alluvial cut-banks. 

As a result of these hydrological changes, the system has undergone a change from being 

somewhat lentic to riverine. Rather than river currents’ abating near Separation Canyon 

(RM 240), as they have in former years, strong currents now flow well below Pearce Ferry 

(RM 280) and continue (albeit in a somewhat abated form) into Iceberg Canyon. A river channel 

and small rapid are now present near Pearce Ferry, where formerly a wide bay provided access to 

a boat ramp (now land-locked). The Lake Mead inflow area has shifted from the Pearce Ferry 

area to below Iceberg Canyon. Currents are channelized and moderately fast to Pearce Ferry and 
Humpback Chub Annotated Bibliography 195 September 2009

 

continue until the lake interface at the bottom of Iceberg Canyon. Substrates are largely sandy, 

and limited off-channel habitat exists (only a few small backwaters are present). 

Species captured in tributaries included channel catfish, carp, flannelmouth sucker, 

mosquitofish, red shiner, and speckled dace, with the majority of the catch being composed of 

speckled dace and red shiner. The presence of YOY native species in the tributaries indicated 

that these streams might be suitable for native fish rearing. Large-bodied non-native species were 

observed within Spencer Creek; however, no adult native species were captured or observed 

within the tributaries. 

Wieringa, M.J. and A.G. Morton. 1996. Hydropower, adaptive management and 

biodiversity: Environmental Management 20(6):831–840. 

Adaptive management is a policy framework within which an iterative process of 

decision making is followed based on the observed responses to and effectiveness of previous 

decisions. The use of adaptive management allows science-based research and monitoring of 

natural resource and ecological community responses, in conjunction with societal values and 

goals, to guide decisions concerning man’s activities. The adaptive management process has 

been proposed for application to hydropower operations at Glen Canyon Dam on the Colorado 

River, a situation that requires complex balancing of natural resources requirements and 

competing human uses. This example is representative of the general increase in public interest 

in the operation of hydropower facilities and possible effects on downstream natural resources 

and of the growing conflicts between uses and users of river-based resources. This paper 

describes the adaptive management process, using the Glen Canyon Dam example, and discusses 

ways to make the process work effectively in managing downstream natural resources and 

biodiversity. 

Wyodoski, R.S., and E.J. Wick. 1998. Ecological value of floodplain habitats to razorback 

suckers in the upper Colorado River basin. Final report of U.S. Fish and Wildlife Service 

and U.S. National Park Service to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

This report is intended as a reference document for persons working on habitat 

enhancement projects related to the Recovery Implementation Program for Endangered Fishes in 

the Upper Colorado River Basin (Recovery Program). It summarizes the published literature on 

the ecological value of floodplains to riverine fish communities and relates this literature to 

reports that have been developed through the Recovery Program and management endeavors in 

the Lower Colorado River Basin. The report emphasizes the need for concurrent integration of 

all Recovery Program elements, specially habitat development and maintenance, management of 

nonnative fishes and sport fishing, and captive propagation. 
Humpback Chub Annotated Bibliography 196 September 2009

 

6.2 MONITORING TECHNIQUES 

Bestgen, K. R., D. W. Beyers, J. A. Rice, and G. B. Haines. 2006. Factors affecting 

recruitment of young Colorado pikeminnow: Synthesis of predation experiments, field 

studies, and individual-based modelling. 2006. Transactions of the American Fisheries 

Society 135:1722-1742. 

Predation experiments, field studies, and individual-based-model (IBM) simulations 

revealed factors that affected the survival and recruitment of early life stages of endangered 

Colorado pikeminnow Ptychocheilus lucius in the Green River basin, Utah and Colorado. Smallbodied, nonnative red shiners Cyprinella lutrensis attacked Colorado pikeminnow larvae an 

average of once per minute, and predation success approached 30% in laboratory aquaria. Attack 

rate was also high in mesocosm experiments; turbidity and alternative prey reduced predation 

success. Distributions of hatching dates derived from otolith daily increment analysis showed 

that large cohorts of Colorado pikeminnow larvae that hatched in the Green River in early 

summer had low survival to autumn and that the few survivors were fast growing. Larvae 

hatched in midsummer or later had higher survival. Autumn juveniles grew 12–73% faster than 

summer juveniles, which suggested differential mortality of slow-growing fish. The IBM 

simulations integrated size-dependent predator–prey relationships, Colorado pikeminnow life 

history information, temperature-dependent pikeminnow growth, Green River predator sizestructure dynamics, seasonally variable Green River water temperatures, and turbidity and 

alternative prey availability effects; the simulations showed that red shiner predation interacting 

with environmental variables may significantly reduce age-0 pikeminnow recruitment in autumn. 

Recruitment and growth patterns from simulations and field observations were consistent and 

suggested that the IBM is useful in evaluating management scenarios. Experiments, field studies, 

and predictive modeling provided consistent evidence that interacting effects of predation and 

environmental variables, including flow fluctuations, may structure intra-annual growth and 

recruitment patterns of age-0 Colorado pikeminnow. Flow management to benefit growth and 

survival of young pikeminnow, particularly early hatching ones, and reduced nonnative predator 

abundance in Green River backwaters may enhance the Colorado pikeminnow populations. 

Elsdon, T. S., B. K. Wells, S. E. Campana, B. M. Gillanders, C. M. Jones, K. E. Limburg, 

D. H. Secor, S. R. Thorrold, and B. D. Walther. 2008. Otolith chemistry to describe 

movements and life-history parameters of fishes: hypotheses, assumptions, limitations, and 

inferences. Oceanography and Marine Biology: an Annual Review 46: 297-330. 

In ever-increasing numbers, researchers wish to extract information based on chemical 

analyses from otoliths to determine movements and life-history patterns of fish. Such analyses 

make assumptions about chemical incorporation and interpretation that are beyond those that are 

important for stock discrimination studies, another common application. The authors aim to 

clarify the methods of determining fish movement based on natural and artificial otolith chemical 

tags and review current trends in determining movement using otolith chemistry, otolith 

sampling methods, and what influences otolith chemistry. Both spatial and temporal variability 

in water and otolith chemistries, which underpin the assumptions of several methods, are 

discussed. Five methods for determining movement and migration of fish are outlined: (1) 

estimates of movement and life-history traits of a single fish group, (2) assessing connectivity 
Humpback Chub Annotated Bibliography 197 September 2009

 

among groups using natural chemical tags in otoliths, (3) transgenerational marks to determine 

parentage and natal origins, (4) profile analysis to define life-history variation within a 

population and (5) profile analysis to describe movements through different environments. 

Within each of these methods, background information, specific hypotheses being tested and 

assumptions and limitations of each technique are provided. Finally, research directions required 

to fill current knowledge gaps and enhance the usefulness of otolith chemistry to determine fish 

movement are identified. 

Minckley, W.L. 1995. Translocation as a tool for conserving imperiled fishes: Experiences 

in western United States. Biological Conservation 72(2):297-309. 

Conservation efforts for imperiled fishes in western United States have included 

numerous translocations, either among natural localities or from nature to propagation 

facilities then back into nature. The goal has been to increase population size and dispersion 

while maintaining genetic diversity, thus increasing probability of survival Environmental laws 

governing translocations of fishes for conservation purposes involve complexities often equally 

as difficult to cope with as the biological problems of species' endangerment. Translocations 

perceived not to impinge on resource use or proprietary rights may be readily approved, while 

those which interfere with actual or projected development may meet strong resistance. Major 

biological considerations include the suitability and security of transplant sites (assurances that 

each meets a taxon's life-history and other requirements) and appropriateness of transplanted 

individuals (genetic' and population structure, sufficient numbers of individuals, freedom from 

disease, etc.) for establishing new populations. Success of translocation is difficult to define and 

major inadequacies exist in information exchange -- the latter can be remedied by publication in 

the peer-reviewed literature. It is anticipated that fish translocations and the technology required 

to support them will expand along with future needs and desires to re-establish native biotic 

elements in depleted communities and ecosystems. 

Paukert, C.P., D.L. Ward, P.J. Sponholtz and K.D. Hilwig. 2005. Effects of repeated 

hoopnetting and handling of bonytail chub. Journal of Freshwater Ecology 20:649–653. 

We evaluated the effects of repeated hoop net sampling and subsequent handling on the 

endangered bony tail chub (Gila elegans) to determine if these sampling techniques cause 

increased mortality or reduce fish growth. A total of 327 bonytail chub was tagged with PIT tags 

and placed in a 0.04 ha pond on July 2003. These fish were sampled with hoop nets during four, 

three-day sampling events, two in fall (September-October 2003) and two in spring (June 2004). 

Fish were measured and weighed with the time required to complete all steps for processing an 

individual fish being recorded. Individual fish were handled from one to eight times during the 

study, with >95% recaptured five or fewer times. Fish that were recaptured multiple times grew 

less in length (P<0.001) and weight (P<0.001) than fish that were not recaptured. Fish recaptured 

up to five times grew only 12.8% of their initial weight compared to fish not recaptured which 

grew 29.7% of their initial weight. 
Humpback Chub Annotated Bibliography 198 September 2009

 

Pine, W. E., III, K. H. Pollock, J. E. Hightower, T. J. Kwak, J. A. Rice. 2003. A review of 

tagging methods for estimating fish population size and components of mortality. 

Fisheries 28:10-23. 

Techniques to improve estimation of animal population size and mortality from tagging 

studies have received substantial attention from terrestrial biologists and statisticians during the 

last 20 years. However, these techniques have received little notice from fisheries biologists, 

despite the widespread applicability to fisheries research, the wide variety of tag types used in 

fisheries research (from traditional fin clips to telemetry tags), and the development of new 

computer software to assist with analyses. We present a brief review of population models based 

on recaptures, returns, or telemetry relocations of tagged fish that can be used to estimate 

population size, total mortality, and components of mortality (i.e., fishing and natural) that are 

frequently of interest to fisheries biologists. Recommended strategies include (1) use closed 

population models (e.g., Lincoln-Peterson) to estimate population size for short term studies 

where closure assumption can be met, (2) use the robust design to estimate population size for 

studies of longer duration, (3) use high-reward tags in conjunction with other methods of 

estimating reporting rate in tag-return studies, (4) combine a subset of telemetry tagged fish with 

either a high-reward tagging program or a traditional capture-recapture study to improve 

mortality estimates and understanding of mortality components, and (5) use pilot studies and 

simulation analyses to assess precision of estimated parameters to evaluate study feasibility. 

Incorporation of these improved techniques could lead to greater accuracy and precision of 

parameter estimates from tagging studies and thus to improved understanding and management 

of fish populations. 

Pollock, K. H., H. Jiang, H. and J. E. Hightower. 2004. Combining radio-telemetry and 

fisheries tagging models to estimate fishing and natural mortality rates. Transactions of the 

American Fisheries Society, 133:639-648. 

The traditional multiple-year tag return method is a fundamental approach to estimating 

fishing and natural mortality rates in fisheries. It can provide reliable and precise estimation of 

the parameters when the tag reporting rate, l, is known. However, it is often difficult to estimate 

λ accurately. An additional disadvantage is that this method has to estimate natural mortality 

indirectly because natural deaths are not observable. Recently, fisheries biologists have begun to 

implement telemetry methods to estimate fishing and natural mortality. The advantage of a 

telemetry method is that it contains direct information about natural mortality and survival. A 

shortcoming is that there is no direct information on fishing deaths. In this paper, we combine the 

two methods, using direct information about both fishing and natural mortality to obtain more 

precise and effectively unbiased parameter estimates, including reporting rate estimates for the 

regular tags. Using simulation when the telemetry tag relocation probability equals 1, we found 

that the relative standard error (RSE) of natural mortality estimates in the combination method is 

much improved relative to those of the tag return and telemetry methods. Annual fishing 

mortality estimates can also be estimated precisely. As expected, as the relocation probability of 

telemetry tags decreases the RSE of natural mortality and the other parameter estimates 

increases, but only slightly. Studies clearly should have relocation probabilities that are as high 

as possible. The tag reporting rate estimates are typically precisely estimated in the combined 
Humpback Chub Annotated Bibliography 199 September 2009

 

model. This is very important, as the tag reporting rate is not easy to estimate with other 

methods. 

Ruppert, J.B. and R.T. Muth. 1997. Effects of electrofishing fields on captive juveniles of 

two endangered cyprinids. North American Journal of Fisheries Management 17:314–320. 

We conducted laboratory experiments to address concerns about potential harmful effects 

of electrofishing on juvenile humpback chubs Gila cypha. Four types of square-wave pulsed DC 

in homogeneous fields were tested: 30 Hz (12% duty cycle), 60 Hz (24% duty cycle), 80 Hz 

(40% duty cycle), and a complex pulse train of three 240-Hz, 2.6-ms pulses delivered at 15 Hz 

(12% duty cycle). We first determined peak-voltage gradients for each current sufficient to 

induce the electroshock responses of taxis, narcosis, or tetany in captive-reared early juvenile 

humpback chubs (49-96 mm total length) and bonytails G. elegans (46-79 mm). Bonytails were 

intended as surrogates for humpback chubs in most subsequent tests. However, mean voltagegradient response thresholds were 8-43% lower for humpback chubs than for bonytails. We then 

exposed 30 humpback chubs for 10 s to the complex pulse current at mean tetanizing field 

intensity and 60 bonytails for 10 s to one of the four currents at mean field intensities required 

for each of the three responses. All humpback chubs and half of the bonytails were euthanized, 

frozen, and later examined for internal injuries; remaining bonytails were reared for 98 d to 

assess effects on growth and survival. No mortalities, external injuries, or vertebral injuries were 

observed in either species. Moderately severe spinal hemorrhages were found in 20% of shocked 

humpback chubs and 13% of shocked bonytails. Shocked humpback chubs had a significantly 

higher (P < 0.05) incidence of injuries than unshocked control fish. The number of injured 

bonytails was significantly higher (P < 0.05) than controls in the 80-Hz taxis treatment and the 

30-, 60-, and 80-Hz tetany treatments. Differences in the number of shocked bonytails with 

injuries among currents at each response threshold and among response thresholds for each 

current were not significant. No significant differences in injury rates were detected between 

humpback chubs and bonytails exposed to the complex pulse current at tetanizing field 

intensities. Growth of bonytails was not affected by shocking. Results suggest that electrofishing 

could cause spinal hemorrhages in some early juvenile humpback chubs but does not affect 

short-term growth or survival. Studies are needed to evaluate the significance of electrofishing 

injuries in humpback chubs at the population level. 

Simpfendorfer, C. A., M. R. Heupel, and A. B Collins. 2008. Variation in the performance 

of acoustic receivers and its implication for positioning algorithms in a riverine setting. 

Canadian Journal of Fisheries and Aquatic Sciences 65:482-492. 

The performance of an array of data-logging single frequency acoustic receivers in the 

Caloosahatchee River (Florida, USA) was examined and the results incorporated into a 

positioning algorithm for animals tracked within the system. The mean code detection efficiency 

across all individual receivers and all download periods was 0.414 detections per 

synchronization code. On average, the code rejection coefficient was approximately 4%, 

indicating that it was only a minor factor in reducing code detection efficiency. There were 

significant performance differences between stations and download periods, but no interaction 

between these two factors for all three metrics. Code detection efficiency, the rejection 

coefficient, and the noise quotient all showed significant variations with distance from the river 
Humpback Chub Annotated Bibliography 200 September 2009

 

mouth and time since deployment. Comparison of position estimates with and without efficiency 

produced small differences for bull sharks (Carcharhinus leucas) and cownose rays (Rhinoptera 

bonasus) monitored via this system. Root mean square errors were higher for cownose rays 

(48 m) than for bull sharks (23 m). Mean differences for individuals were always slightly 

downstream because of the increasing code detection efficiency of upriver receivers. The results 

of this comparison indicated that the inclusion of code detection efficiency did not significantly 

improve the results of the positioning algorithm. 

Stevenson, D.K. and Campana, S.E. (Editors). 1992. Otolith microstructure examination 

and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. 

The field of otolith microstructure research has experienced phenomenal growth since the 

early 1970’s and now forms the basis for hundreds of studies of early life history, age, growth, 

recruitment, migration, mortality, and stock structure. While the field continues to grow and 

evolve, there is no question that otolith microstructure examination is now an important and 

accepted technology in fisheries biology. 

This book represents the first effort to compile and summarize the many techniques and 

procedures associated with studies of otolith microstructure. The complete sequence of events, 

from sample collection to data analysis, is covered comprehensively, so as to be applicable to 

most species and situations. The various chapters include both published and unpublished 

procedures, making the book valuable to beginning and experienced investigators alike. 

Valdez, R.A. 1993. Use of scales to determine emigration of juvenile humpback chub Gila cypha

from the Little Colorado River in Grand Canyon, Arizona. Proceedings of the Desert Fishes 

Council 24:61. 

 

Scales from age groups 0, I, and II humpback chub Gila cypha, examined 

microscopically, revealed marks or checks believed to represent emigration from spawning and 

nursery areas in the Little Colorado River to the mainstem Colorado River in Grand Canyon. The 

checks were identified by closely- spaced and incomplete circular rings believed to be formed 

when individual fish descended from LCR temperatures of about 20 C to mainstem temperatures 

of 10 C. Aging was coordinated with length- frequency histograms. Determining timing and size 

of descent by young- and adult- humpback chub may reveal size- specific survival of emigrating 

chub. 

6.3 COMPUTER MODELING 

Allen, E.J., J.M. Harris and L.J.S. Allen. 1992. Persistence-time models for use in viability 

analyses of vanishing species. Journal of Theoretical Biology 155: 33–53. 

Mathematical models can provide guidance as to the size and number of wildlife refuges 

required for long-term persistence of various species. Simple mathematical models for rough 

estimation of persistence time have been developed, but efficient algorithms for calculating 

persistence times using these models are unavailable. In addition, the mathematical relations 
Humpback Chub Annotated Bibliography 201 September 2009

 

required between critical parameters in the models have not been thoroughly studied. In this 

investigation, an efficient algorithm for implementing the models is developed and several 

different relations among the parameters in the models are tested against mammalian persistence 

data available for montane habitat of the south-western U.S.A. Furthermore, these models are 

compared with a new persistence-time model which is described in the present investigation. 

Baedecker, M.J. and L.C. Friedman, eds. 2000. Modeling and experimental flooding in the 

Grand Canyon. Pages 10-11. In M.J. Baedecker and L.C. Friedman, eds. U.S. Geological 

Survey National Research Program in the Hydrologic Sciences. U.S. Geological Survey 

Circular 1195. 

The USGS has a strong commitment to understand and predict flow and sediment 

transport in rivers, including the impacts of dams, the processes responsible for building and 

eroding sand bars, and the manner in which sediment is supplied to the river systems. The 

knowledge gained from these studies is being applied to a problem on the Colorado River in 

Grand Canyon National Park. In 1963, Glen Canyon Dam was constructed about 24 kilometers 

upstream from the Park boundary at Lees Ferry, which is the launch point for boating trips 

through the Grand Canyon. Prior to the dam, the river’s floodwaters prevented growth of 

vegetation on the channel banks, deposited sand bars, and eroded boulder deposits in the main 

channel left by flash floods in tributaries. After the dam was completed and most large floods 

were controlled, a riparian zone developed along the river, marshes were formed, sand bars 

eroded, and boulders were left in the main channel. By the mid-1970s, river runners expressed 

concern about eroding sand bars that were used as campsites. In 1978, the USFWS concluded 

that Glen Canyon Dam and its operation were jeopardizing an endangered fish, the humpback 

chub (Gila cypha). These findings led the U.S. Bureau of Reclamation to establish the Glen 

Canyon Environmental Studies, which organized and supported research in Grand Canyon 

starting in 1983. 

Beyers, D.W., J.A. Rice. and W.H. Clements. 1999. Evaluating biological significance of 

chemical exposure to fish using a bioenergetics-based stressor-response model. Canadian 

Journal of Fisheries and Aquatic Sciences 56:823–829. 

We demonstrate how contaminant exposure-response relationships can be integrated with 

a bioenergetics model to estimate the biological significance of sublethal exposure under 

fluctuating environmental conditions. The integrated bioenergetics-based stressor-response 

model (SRM) was evaluated by comparing observed and predicted growth of largemouth bass 

(Micropterus salmoides) exposed to several dieldrin concentrations and by conducting sensitivity 

analyses. Predictions of the SRM suggest that energetic effects of exposure of largemouth bass to 

ambient concentrations of dieldrin in lakes at the Rocky Mountain Arsenal National Wildlife 

Refuge are not biologically significant because the amount of energy lost by resident fish is 

small compared with variation in food consumption. Furthermore, influence of dieldrin exposure 

is small compared with the effects of a natural stressor like water temperature. The SRM 

provides a general framework for integrating laboratory-derived exposure-response relationships 

with ecological processes to determine the biological significance of multiple stressors in a 

natural environment. Comparisons of relative effects of anthropogenic and natural stressors can 

be used to assess potential costs and benefits of alternative ecosystem management strategies. 
Humpback Chub Annotated Bibliography 202 September 2009

 

Grand, T., C.S.F. Railsback, J.W. Hayse and K.E. LaGory. 2006. A physical habitat 

model for predicting the effects of flow fluctuations in nursery habitats of the endangered 

Colorado pikeminnow Ptychocheilus lucius. River Research and Applications 22:1125–

1142. 

Larval and juvenile Colorado pikeminnow (Ptychocheilus lucius) use shallow, lowvelocity, channel-margin areas (backwaters) as nursery habitats. It is hypothesized that withinday flow fluctuations caused by hydropower operations can directly affect the suitability of such 

habitats by altering water temperature and habitat geometry. Despite the importance of 

backwaters to juvenile fishes, there is a lack of established approaches for modeling how river 

management affects these habitats. Here, we describe a physical habitat model that predicts the 

effects of mainstem flow variation on backwater temperature, geometry and invertebrate 

availability. We specifically modeled these effects on habitat in a portion of the Green River in 

Utah below Flaming Gorge Dam. 

The overall model combines a cell-based model of backwater geometry, a pond-based 

temperature model and a model of invertebrate production. Results from a series of simulations 

suggest that the most important biological effects of within-day flow fluctuations are likely to be 

those associated with the availability of invertebrate prey including (1) minimum wetted area, 

(2) the proportion of the backwater’s volume exchanged with the mainstem, and, to a lesser 

degree, (3) backwater temperature. Taken together, such effects could have important 

implications for the growth and survival of juvenile fish when flow fluctuations are sufficiently 

large. 

Harvey, M.D., R.A. Mussetter and E.J. Wick. 1993. A physical process-biological response 

model for spawning habitat formation for the endangered Colorado squawfish. Rivers 

4:114–131. 

The Colorado squawfish (Ptychocheilus lucius), a federally listed endangered species, 

spawns at a limited number of sites within the lower Yampa River, Colorado, during the 

recessional limb of the annual snowmelt hydrograph. A three-level, physical process-biological 

response model for spawning habitat formation was developed from field measurements, 

hydraulic modeling (HEC-2), and analysis of a known spawning bar at RM 16.5. Sediment 

deposition and bar formation occur at discharges greater than 10,000 cfs, a discharge at which 

downstream hydraulic controls cause backwater and reduced transport capacity of the flows. 

Spawning habitat is formed by bar dissection and erosion at a range of flows between 400 and 

5,000 cfs when the local hydraulic energy is greatest because of reduced tailwater downstream, 

and sediment delivery to the chute channels is reduced by deposition in an upstream pool. The 

process-response model appears to be validated by fish-capture data at this, and another 

spawning bar at RM 18.5, on the Yampa River during both the 1991 and 1992 runoff seasons. 
Humpback Chub Annotated Bibliography 203 September 2009

 

Korman, J, S.M. Wiele and M. Torizzo. 2004. Modeling effects of discharge on habitat 

quality and dispersal of juvenile humpback chub (Gila cypha) in the Colorado River, 

Grand Canyon. Regulated Rivers 20:379–400. 

A two-dimensional hydrodynamic model was applied to seven study reaches in the 

Colorado River within Grand Canyon to examine how operation of Glen Canyon Dam has 

affected availability of suitable shoreline habitat and dispersal of juvenile humpback chub (Gila 

cypha). Suitable shoreline habitat typically declined with increasing discharges above 226-

425 m3

/s, although the response varied among modeled reaches and was strongly dependent on 

local morphology. The area of suitable shoreline habitat over cover types that are preferred by 

juvenile humpback chub, however, stayed constant, and in some reaches, actually increased with 

discharge. In general, changes in discharge caused by impoundment tended to decrease 

availability of suitable shoreline habitat from September to February, but increased habitat 

availability in spring (May-June). Hourly variation in discharge from Glen Canyon Dam 

substantially reduced the amount of persistent shoreline habitat at all reaches. Changes in 

suitable shoreline habitat with discharge were shown to potentially bias historical catch per unit 

effort indices of native fish abundance up to fourfold. Physical retention of randomly placed 

particles simulating the movement of juvenile humpback chub in the study reaches tended to 

decline with increasing discharge, but the pattern varied considerably due to differences in the 

local morphology among reaches and the type of swimming behavior modeled. Implications of 

these results to current hypotheses about the effects of Glen Canyon Dam on juvenile humpback 

chub survival in the mainstem Colorado River are discussed. 

Mankin, J.B., R.H. Gardner, R.V. O’Neill and J.H. Carney. 1981. A comparison of 

sensitvity analysis and error analysis based on a stream ecosystem model. Ecological 

Modelling 12(3):173–190. 

 Changes in the water level in the Colorado River as a result of manipulations at Glen 

Canyon Dam are discussed. These uneven releases of water through the Dam cause man-made 

tides to surge along the banks of the river, disrupting the naturally alternating erosion and 

redeposition of silt, enabling exotic species of plants to flourish on the banks while killing others 

that have been established there for years, eliminating some populations of birds, and allowing 

fish and eggs to be stranded far from the water when the surge has gone by. Beaches are washed 

away. The shallowness of the water at times prohibits groups of white water enthusiasts from 

completing their trips. Plans are in the works for making changes which will increase the 

destruction already being seen. These plans are being laid in supposed answer to increasing 

electricity needs, but opponents of the plans suggest that existing power plants could be used for 

far less money than will be required to make the changes, and without doing further 

environmental damage. 

Peterseni, J.H., D.L. Deangelas and C.P. Paukert. 2008. An overview of methods for 

developing bioenergetic and life history models for rare and endangered species. 

Transactions of the American Fisheries Society 137(1):244–253. 

Many fish species are at risk to some degree, and conservation efforts are planned or 

underway to preserve sensitive populations. For many imperiled species, models could serve as 
Humpback Chub Annotated Bibliography 204 September 2009

 

useful tools for researchers and managers as they seek to understand individual growth, quantify 

predator-prey dynamics, and identify critical sources of mortality. Development and application 

of models for rare species however, has been constrained by small population sizes, difficulty in 

obtaining sampling permits, limited opportunities for funding, and regulations on how 

endangered species can be used in laboratory studies. Bioenergetic and life history models 

should help with endangered species-recovery planning since these types of models have been 

used successfully in the last 25 years to address management problems for many commercially 

and recreationally important fish species. In this paper we discuss five approaches to developing 

models and parameters for rare species. Borrowing model functions and parameters from related 

species is simple, but uncorroborated results can be misleading. Directly estimating parameters 

with laboratory studies may be possible for rare species that have locally abundant populations. 

Monte Carlo filtering can be used to estimate several parameters by means of performing simple 

laboratory growth experiments to first determine test criteria. Pattern-oriented modeling (POM) 

is a new and developing field of research that uses field-observed patterns to build, test, and 

parameterize models, Models developed using the POM approach are closely linked to field data, 

produce testable hypotheses, and require a close working relationship between modelers and 

empiricists. Artificial evolution in individual-based models can be used to gain insight into 

adaptive behaviors for poorly understood species and thus can fill in knowledge gaps. 

Peterson, J.H. and C.P. Paukert. 2005. Development of a bioenergetics model for 

humpback chub and evaluation of water temperature changes in the Grand Canyon, 

Colorado River. Transactions of the American Fisheries Society 134:960–974. 

The construction of Glen Canyon Dam above the Grand Canyon (Arizona) has reduced 

the water temperature in the Colorado River and altered the growth rate and feeding patterns of 

the federally endangered humpback chub Gila cypha. A bioenergetics model for humpback chub 

was developed and used to examine how warmer water temperatures in the lower Colorado River 

(achieved through a temperature control device [TCD] at Glen Canyon Dam) might influence 

their growth rate and food requirements. Parameter values for humpback chub were developed 

by Monte Carlo filtering and fitting to laboratory growth. Parameter bounds were established 

from the literature for Gila species, random parameter sets were selected within these bounds, 

and the growth of modeled humpback chub was compared with criteria from a laboratory growth 

experiment at 24°C. This method of parameter estimation could be applied to other imperiled 

fishes where physiological studies are impractical. Final parameter values were corroborated by 

comparison with the growth rates of humpback chub from independent field and laboratory 

studies. Simulations indicated that increasing water temperatures from approximately 9°C to 

16°C during summer and fall, the change expected from the TCD, may have a minimal effect on 

humpback chub growth rate unless food availability also increases with temperature. To evaluate 

the effects of increased temperatures on humpback chub in the lower Colorado River, it will be 

essential to monitor their growth rate, the invertebrate community, and the predators of 

humpback chub, which are also influenced by temperature changes. Bioenergetics models for 

humpback chub and their predators should be helpful tools for identifying potential scenarios and 

evaluating the complex interactions resulting from a TCD. 
Humpback Chub Annotated Bibliography 205 September 2009

 

Turner, D.S. and M.D. List. 2007. Habitat mapping and conservation analysis to identify 

critical streams for Arizona’s native fish. Aquatic Conservation: Marine and Freshwater 

Ecosystems 17:737-748. 

1) Arizona’s native fish species are among the most imperiled fauna in North America. 

Knowing the current distribution of native fish and their habitat is critical to their 

management and conservation, but the last detailed mapping effort was more than 30 

years ago and predated computer mapping techniques. 

2) Current distribution of 34 native fish species was modeled by identifying perennial 

stream segments for which species presence had been documented. A composite of these 

single-species maps displays a pattern of species richness that can inform conservation, 

especially when overlaid with maps of management status or invasive species. 

3) The map overlays suggest that conservation priorities should include Eagle Creek, the 

Verde River and its tributaries, Aravaipa Canyon, the Virgin River, and Black Draw, 

which together hold 63% of native fish species. Of the 32 streams which support 5 or 

more native species, 28 have at least one non-native fish species, indicating that a more 

aggressive program of removing non-natives may be critical to maintaining those native 

populations. 

4) The U.S. Forest Service and Native American tribes administer the majority of occupied 

stream habitat (30 and 27%, respectively). While private lands hold the third-highest 

amount of occupied habitat (19%), they control streams occupied by the greatest total 

number of native species (30). Conservationists should work more with private land 

owners, while also coordinating efforts with the U.S. Forest Service and North American 

tribes. 

Valdez, R.A. and D.W. Speas. 2007. A risk assessment model to evaluate risks and benefits 

to aquatic resources from a selective withdrawal structure on Glen Canyon Dam. Bureau 

of Reclamation, Salt Lake City, Utah. 

A risk assessment was conducted to help evaluate possible responses by aquatic resources 

in Grand Canyon to a selective withdrawal structure (SWS) on Glen Canyon Dam. A 

mathematical model was used as a tool to quantify risks and benefits to fish, fish parasites, 

zooplankton, and macroinvertebrates from water temperature changes resulting from 

modification of 2 of the 8 power release units on the dam. All taxa present or with potential to 

access the area were inventoried for each of six regions, including lower Lake Powell, Glen 

Canyon Dam to Paria River, Paria River to Little Colorado River (LCR), LCR to Bridge Canyon, 

and Bridge Canyon to Pearce Ferry. Base scores were developed that described the presence or 

absence of each taxon and their position in the community for each region. Median, minimum, 

and maximum predicted temperatures were obtained from Bureau of Reclamation’s GEMSS 

model for No Action (1990-2005) and a 2-unit SWS. Temperature degree days (TDD) were 

computed for spawning, incubation, and growth for fish and life history requirements for other 

taxa and compared with the predicted water temperatures to determine if the temperature change 

would benefit particular taxa. The TDDs were added to the base scores to derive a score for each 
Humpback Chub Annotated Bibliography 206 September 2009

 

taxon; higher scores indicate greater benefit to a taxon. Scores were calibrated for fish by 

comparing modeled fish composition with composition from four prior surveys reflecting predam temperatures (1958), cold temperatures during high flow fluctuations (1977-78), modified 

low fluctuating flows (1990-94), and low lake levels with warm releases (2003-04). Preliminary 

results show benefits to all native fishes, but also benefits to many nonnative fish species that 

may compete with or prey upon native species. Preliminary results also show more suitable 

conditions for warm-water fish parasites. The effect of cooling in the Lake Powell forebay is 

small on zooplankton populations, but primary producers and macroinvertebrates throughout 

Grand Canyon are likely to be affected by warmer water temperatures. We emphasize that these 

results are preliminary and that the primary intent of this document is to provide a documentation 

of a risk assessment model that could be used as a tool to evaluate effects of a SWS on aquatic 

resources in the Grand Canyon area. 

Walters, C., J. Korman, l.E. Stevens and B. Gold. 2000. Ecosystem modelling for 

evaluation of adaptive management policies in the Grand Canyon. Conservation Ecology 

4(2):24. 

An Adaptive Environmental Assessment and Management workshop process was used to 

assist Grand Canyon scientists and managers in developing conceptual and simulation models for 

the Colorado ecosystem affected by Glen Canyon Dam. This model examines ecosystem 

variables and processes at multiple scales in space and time, ranging from feet and hours for 

benthic algal response to diurnal flow changes, to reaches and decades for sediment storage and 

dynamics of long-lived native fish species. Its aim is to help screen policy options ranging from 

changes in hourly variation in flow allowed from Glen Canyon Dam, to major structural changes 

for restoration of more natural temperature regimes. It appears that we can make fairly accurate 

predictions about some components of ecosystem response to policy change (e.g., autochthonous 

primary production, insect communities, riparian vegetation, rainbow trout population), but we 

are moderately or grossly uncertain about others (e.g., long-term sediment storage, response of 

native and non-native fishes to physical habitat restoration). Further, we do not believe that 

existing monitoring programs are adequate to detect responses of native fishes or vegetation to 

anything short of gross habitat changes. Some experimental manipulations (such as controlled 

floods for beach/habitat-building) should proceed, but most should await development of better 

monitoring programs and sound temporal baseline information from those programs. 

White, M.A., J.C. Schmidt and D.J. Topping, 2005. Application of wavelet analysis for 

monitoring the hydrologic effects of dam operations: Glen Canyon Dam and the Colorado 

River at Lees Ferry, Arizona. River Research and Applications 21(5):551–565. 

Wavelet analysis is a powerful tool with which to analyze the hydrologic effects of dam 

construction and operation on river systems. Using continuous records of instantaneous 

discharge from the Lees Ferry gauging station and records of daily mean discharge from 

upstream tributaries, we conducted wavelet analyses of the hydrologic structure of the Colorado 

River in Grand Canyon. The wavelet power spectrum (WPS) of daily mean discharge provided a 

highly compressed and integrative picture of the post-dam elimination of pronounced annual and 

sub-annual flow features. The WPS of the continuous record showed the influence of diurnal and 

weekly power generation cycles, shifts in discharge management, and the 1996 experimental 
Humpback Chub Annotated Bibliography 207 September 2009

 

flood in the post-dam period. Normalization of the WPS by local wavelet spectra revealed the 

fine structure of modulation in discharge scale and amplitude and provides an extremely efficient 

tool with which to assess the relationships among hydrologic cycles and ecological and 

geomorphic systems. We extended our analysis to sections of the Snake River and showed how 

wavelet analysis can be used as a data mining technique. The wavelet approach is an especially 

promising tool with which to assess dam operation in less well-studied regions and to evaluate 

management attempts to reconstruct desired flow characteristics. 

Wiele, S.M. 1998. Modeling of flood-deposited sand distributions in a reach of the 

Colorado River below the Little Colorado River, Grand Canyon, Arizona. U.S. Geological 

Survey Water-Resources Investigations Report. 

A release from Glen Canyon Dam during March- April 1996 was designed to test the 

effectiveness with which the riparian environment could be renewed with discharges greatly in 

excess of the normal powerplant-restricted maximum. Of primary concern was the rebuilding of 

sand deposits along the channel sides that are important to the flora and fauna along the river 

corridor and that provide the only camp sites for riverside visitors of the Grand Canyon National 

Park. Analysis of the depositional processes with a model of flow, sand transport, and bed 

evolution shows that the sand deposits formed along the channel sides early during the high flow 

were affected only slightly by the decline in suspended-sand concentrations over the course of 

the controlled flood. Modeling results suggest that the removal of a large sand deposit over 

several hours was not a response to declining suspended-sand concentrations. Comparisons of 

the controlled-flood deposits with deposits formed during a flood in January 1993 on the Little 

Colorado River that contributed sufficient sand to raise the suspended-sand concentrations to 

pre-dam levels in the main stem show that the depositional pattern as well as the magnitude is 

strongly influenced by the suspended- sand concentrations. 

Wolock, D.M. and G.J. McCabe. 1999. Estimates of runoff using water-balance and 

atmospheric General Circulation Models. Journal of the American Water Resources 

Association 35: 1341–1350. 

The effects of potential climate change on mean annual runoff in the conterminous 

United States (U.S.) are examined using a simple water-balance model and output from two 

atmospheric general circulation models (GCMs). The two GCMs are from the Canadian Centre 

for Climate Prediction and Analysis (CCC) and the Hadley Centre for Climate Prediction and 

Research (HAD). In general, the CCC GCM climate results in decreases in runoff for the 

conterminous U.S, and the HAD GCM climate produces increases in runoff. These estimated 

changes in runoff primarily are the result of estimated changes in precipitation. The changes in 

mean annual runoff, however, mostly are smaller than the decade-to-decade variability in GCMbased mean annual runoff and errors in GCM-based runoff. The differences in simulated runoff 

between the two GCMs, together with decade-to-decade variability and errors in GCM-based 

runoff, cause the estimates of changes in runoff to be uncertain and unreliable.
Humpback Chub Annotated Bibliography 208 September 2009

 

Wright, S.A., C.R. Anderson and N. Voichick. 2009. A simplified water temperature 

model for the Colorado River below Glen Canyon Dam. River Research and Applications 

25(6):675–686. 

 Glen Canyon Dam, located on the Colorado River in northern Arizona, has affected the 

physical, biological and cultural resources of the river downstream in Grand Canyon. One of the 

impacts to the downstream physical environment that has important implications for the aquatic 

ecosystem is the transformation of the thermal regime from highly variable seasonally to 

relatively constant year-round, owing to hypolimnetic releases from the upstream reservoir, Lake 

Powell. Because of the perceived impacts on the downstream aquatic ecosystem and native fish 

communities, the Glen Canyon Dam Adaptive Management Program has considered 

modifications to flow releases and release temperatures designed to increase downstream 

temperatures. Here, we present a new model of monthly average water temperatures below Glen 

Canyon Dam designed for first-order, relatively simple evaluation of various alternative dam 

operations. The model is based on a simplified heat-exchange equation, and model parameters 

are estimated empirically. The model predicts monthly average temperatures at locations up to 

421 km downstream from the dam with average absolute errors less than 0.5 DGC for the dataset 

considered. The modeling approach used here may also prove useful for other systems, 

particularly below large dams where release temperatures are substantially out of equilibrium 

with meteorological conditions. We also present some examples of how the model can be used to 

evaluate scenarios for the operation of Glen Canyon Dam. 

6.4 SUPPORTING ARTICLES 

Allendorf, F.W., D. Bayles, D.L. Bottom, K.P. Currens, C.A. Frissell, D. Hankin, J.A. 

Lichatowich, W. Nehlsen, P.C. Trotter and T.H. Williams. 1997. Prioritizing Pacific 

salmon stocks for conservation. Conservation Biology 11: 140–152. 

Over 300 native stocks of Pacific salmon, steelhead, and coastal cutthroat trout 

(Oncorhynchus spp.) are at risk of extinction in the Pacific Northwest. With only limited 

resources available for conservation and recovery, prioritization of these stocks may become 

necessary if meaningful measures are to be implemented. We propose criteria by which 

prioritization may be guided. First, we rank stocks for risk of extinction, either by population 

viability analysis or by a set of surrogate measures. Then we rank stocks for biological 

consequences of extinction, using sets of questions designed to establish the genetic and 

evolutionary consequences and the ecological consequences if a stock were to become extinct. 

Together, these rankings al- low stocks to be prioritized for a range of possible actions, with 

those stocks at highest risk and bearing the greatest biological consequences of extinction 

receiving attention first. Application of the prioritization process to 20 Pacific anadromous 

salmonid stocks worked as intended, although data limitations are considerable. The process is 

most likely to work successfully when applied to many stocks on which data exist, when several 

experts carry out the prioritization, and when the results are peer reviewed. 
Humpback Chub Annotated Bibliography 209 September 2009

 

Ehrlich, P.R. and D.D. Murphy. 1987. Conservation lessons from long-term studies of 

checkerspot butterflies. Conservation Biology 1: 122–131. 

 

Long-term studies of checkerspot butterflies (Euphydras spp.) are used to draw 

conservation lessons with implications for the design and management of reserves for 

invertebrates. We discuss: 1) The importance of determining the structure of and patterns of 

mating within demographic units; 2) The lack of congruence between migration and gene flow; 

3) The crucial role of habitat diversity in the protection of species which otherwise require only 

small areas of habitat; 4) The importance of identifying and preserving “reservoir” populations 

within metapopulations; 5) The necessity of identifying subtle habitat requirements; 6)The key 

role of environmental stochasticity in the extinction of small population; and 7) The difficulty of 

protecting metapopulations and of introducing populations into “empty” habitat patches. We 

conclude, among other things, that the size of reserves required to preserve herbivorous insects is 

often underestimated; that a “ minimum viable metapopulation” approach to their conservation 

may be needed; that long-term studies of the biology of populations of sample invertebrates 

groups would greatly aid conservation biologists; and that more effort is needed to inform the 

public and decision makers about the need to conserve population as well as species. 

Hamman, R.L. 1987. Survival of razorback sucker cultured in earthen ponds. Progressive 

Fish-Culturist 49:187–189. 

Razorback sucker (Xyrauchen texanus) swim-up fry and fingerlings were successfully 

reared in earthen ponds at the Dexter, New Mexico, National Fish Hatchery. Swim-up fry 

(71,000/lb) were stocked in 0.34-1.08-acre ponds at the rate of 101,000-109,000 fry/acre; 

subfingerling fish (724/lb) were stocked in 0.86-0.98-acre ponds at the rate of 51,000-58,000 

fingerlings/acre; fingerling fish (158/lb) were stocked in 0.98-acre ponds at the rate of 26,000-

27,000 fingerlings/acre. Ponds were treated initially with organic and inorganic fertilizers, in 

addition to periodic addition of alfalfa pellets. The swim-up fry were supplementally fed a 

formulated trout feed. Survival ranged from 87.8 to 98.6% for swim-up fry and 92.7 to 95.8% for 

subfingerlings and averaged 96.2% for fingerlings. 

Muth, R.T. and S.M. Meismer. 1995. Marking otoliths of razorback sucker embryos and 

larvae with fluorescent chemicals. Southwestern Naturalist 40:241–244. 

Laboratory experiments were conducted to determine optimum treatments of alizarin 

complexone (ALC) or tetracycline hydrochloride (TC) for marking otoliths in late embryos or 

recently hatched larvae of razorback sucker (Xyrauchen texanus) through immersion in solutions 

of these chemicals. Once deposited in bone, ALC fluoresces red and TC fluoresces yellow when 

illuminated by ultraviolet light. Fish survival and mark quality were evaluated in different ALC 

or TC concentrations and immersion durations for (1) single treatment of embryos with either 

chemical, producing single marks and (2) single treatment of larvae with each chemical, 

producing double marks. Otoliths from all larvae in the single-mark or double-mark experiments 

had fluorescent marks. Embryo and larval survival decreased and mark quality increased as 

chemical concentrations and immersion durations increased. For best fish survival and mark 

quality, recommended ALC treatments are 12 to 30 h in 150 to 350 mg/L for embryos and 6 to 

18 h in 12.5 to 50 mg/L for larvae. Recommended TC treatments are 18 to 30 h in 150 to 
Humpback Chub Annotated Bibliography 210 September 2009

 

350 mg/L for embryos and 6 to 18 h in 150 to 350 mg/L for larvae. Rapid mass marking of 

otoliths in razorback sucker embryos or larvae has great potential for use in stock identification, 

assessment of stocking success, and life-history studies. 

Snyder, D.E. and S.M. Meismer. 1997. Effectiveness of light traps for capture and 

retention of larval and early juvenile Xyrauchen texanus and larval Ptychocheilus lucius

and Gila elegans. Final report of Colorado State University Larval Fish Laboratory to U.S. 

National Park Service Cooperative Parks Study Unit, Fort Collins, Colorado. 

Light traps are used to capture the larvae of many fishes. To assess the potential of 

floating, low-intensity, quatrefoil-style light traps for capture of the larvae or early juveniles of 

endangered Colorado River basin fishes, provide guidelines for trap use, and better interpret field 

results, we conducted experiments in 1.2-m diameter tanks under light-excluding tents. For each 

capture trial, 50 laboratory-reared larvae or (for razorback sucker Xyrauchen texanus only) 25 

juveniles were released into a tank and allowed to acclimate through simulated daylight, dusk, 

and full darkness before traps were set for 1, 4, or (for razorback sucker larvae only) 8 h. In 

corresponding retention experiments, fish were placed in trap catch basins and allowed to calm 

before traps were placed in tanks. Mean capture percentages (MCPs) for larvae in 1 and 4-h trials 

were 13 to 36% for razorback sucker (33 to 44% in 8-h trials), 3 to 15% for Colorado squawfish 

Ptychocheilus lucius, and 5 to 30% for bonytail Gila elegans. MCPs usually, but not always, 

increased with set duration for larvae. For early juvenile razorback suckers, maximum MCP, 

51%, occurred within 1 h. Once in the trap, most larvae stayed; mean retention percentages 

(MRPs) were 85 to 99% for razorback sucker larvae in 1, 4, and 8-h trials, and 95 to 99% for 

Colorado squawfish larvae in 1 and 4-h trials (bonytails were not tested for retention). Retention 

of juvenile razorback suckers was notably less with MRPs of 65 to 73%. For fish in close 

proximity to the trap, these results suggest that the light traps tested are at least moderately 

effective in clear water for the capture and retention of razorback sucker and bonytail larvae and 

even better for the capture of early juvenile razorback suckers. 

Additional experiments were conducted with razorback suckers. With trap lights off, few 

or no fish were captured and MRPs were lower, strikingly so for protolarvae with only 16% 

retention in 4-h trials. Light is critical for the effective capture and retention of fish larvae. Under 

simulated dusk, 1-h MCPs were lower than during night trials, but not significantly different. 

Setting traps prior to night fall might increase the ultimate number of fish collected but reduce 

catch per unit time. Under simulated dawn, 1-h MRPs dropped to 69% for protolarvae but 

remained 99% for postflexion mesolarvae. Traps should probably be retrieved before dawn to 

avoid significant losses of at least small larvae. In 1-h turbid-water trials, MCPs were 2.6 to 2.8 

times greater for larvae but 70% less for juveniles in 50 to 75 FTU water than in clear water. For 

fish in close proximity to the trap, effectiveness significantly increased for larvae in turbid water 

but decreased for early juveniles. Although maximum body width of the larger postflexion 

mesolarvae approximated 2 mm, MCPs and MRPs for those larvae did not change significantly 

when 4-mm silt traps were used instead of 2-mm traps. However, early juveniles were unable to 

enter 2-mm traps. Maximum total length for capture of razorback suckers by 2-mm slit traps was 

between 20 and 27 mm. MCPs for postflexion mesolarvae did not change significantly when 

tested in a comparable trap with 300 times greater light intensity at trap perimeter. MCPs for 

early juveniles dropped by over two-thirds to 19% in trials using a larger three-lobed light trap 
Humpback Chub Annotated Bibliography 211 September 2009

 

with comparable low-light intensity and to just 8% with 500 times greater light intensity. 

Dramatically increasing trap light intensity did not affect the capture of postflexion mesolarvae 

but significantly reduced the catch of early juveniles. Differences in trap design can affect the 

number of early juveniles captured. 

Welcomme, R.L. 1995. Relationships between fisheries and the integrity of river systems. 

Regulated Rivers 11:121–136. 

Human use of river systems has intensified considerably in the last century due to 

increasing population and the associated higher demand for water through industrial and 

agricultural technologies. This intensification process has impacted rivers and resident 

organisms. Natural rivers have rich and varied fish faunas adapted to the variable climate and 

morphology of such systems. Much of the diversity and resilience can be traced to the 

connectivity between two very different components, the channel and the floodplain. Fisheries in 

rivers are as diverse as the fish communities and are adjusted for capturing most species and life 

stages throughout the year. Fisheries reasonably conducted have proved sustainable with a high 

rate of catch correlated with the intensity of flooding in the same or preceding years. Fish 

communities react in a predictable manner to externally imposed stresses, whether 

eutrophication, induced by humans or natural environmental modification, or fishing, through 

successive loss of large species and their replacement by smaller, faster growing species. 

Generally, the overall weight of catch remains little affected by this process until excessive 

levels of exploitation are reached and the stock collapses. Damage to fish communities through 

overfishing and environmental modification is widespread. Improvement of the situation 

demands stricter management of riverine systems through the protection of the few that remain 

in a relatively pristine state, and those modified should be restored if social, political and 

economic conditions allow. Should this not be possible, approaches to the mitigation of 

externally imposed stresses should be sought and applied.

7 CITATIONS INCLUDED IN BIBLIOGRAPHY 

Ackerman, M.W., D. Ward, T. Hunt, R.S. Rogers, D.R. Van Haverbeke, A. Morgan and C. 

Cannon. 2006. 2006 Grand Canyon long-term fish monitoring in the Colorado River, Diamond 

Creek to Lake Mead. Annual report to the U.S. Geological Survey, Grand Canyon Monitoring 

and Research Center, Flagstaff, Arizona. 

Allen, E.J., J.M. Harris and L.J.S. Allen. 1992. Persistence-time models for use in viability 

analyses of vanishing species. Journal of Theoretical Biology 155: 33–53. 

Allendorf, F.W., D. Bayles, D.L. Bottom, K.P. Currens, C.A. Frissell, D. Hankin, J.A. 

Lichatowich, W. Nehlsen, P.C. Trotter and T.H. Williams. 1997. Prioritizing Pacific salmon 

stocks for conservation. Conservation Biology 11: 140–152. 

Arizona Game and Fish Department. 1996. Ecology of Grand Canyon backwaters. Final report 

to U.S. Bureau of Reclamation, Upper Colorado Region. Arizona Game and Fish Department, 

Phoenix. 
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Arizona Game and Fish Department. 1996. Effects of an experimental flood on the aquatic 

biota and their habitats in the Colorado River, Grand Canyon, Arizona. Final report. Arizona 

Game and Fish Department, Phoenix. 94 pages. 

Badame, P.V. 2008. Population estimates for humpback chub (Gila cypha) in Cataract Canyon, 

Colorado River, Utah, 2003–2005. Final report of Utah Division of Wildlife Resources to Upper 

Colorado River Endangered Fish Recovery Program, Lakewood, Colorado. 

Baedecker, M.J. and L.C. Friedman, eds. 2000. Modeling and experimental flooding in the 

Grand Canyon. Pages 10-11. In M.J. Baedecker and L.C. Friedman, eds. U.S. Geological Survey 

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linkages: Lake Powell and the Colordao River, Arizona. Journal of the North American 

Benthological Society 19(4):742–755. 

Benenati, E.P., J.P. Shannon, J.S. Hagan and D.W. Blinn. 2001. Drifting fine particulate 

organic matter below Glen Canyon Dam in the Colorado River, Arizona. Journal of Freshwater 

Ecology 16(2):235–248. 

Berry, C.R. 1988. Effects of cold shock on Colorado River squawfish larvae. Southwestern 

Naturalist 33(2):193–197. 

Berry, C.R. and R. Pimentel. 1985. Swimming performances of three rare Colorado River 

fishes. Transactions of the American Fisheries Society 114:397–402. 

Berry, D.R. 1984. Hematology of four rare Colorado River fishes. Copeia 3:790–793. 

Bestgen, K. and L.W. Crist. 2000. Response of the Green River fish community to construction 

and re-regulation of Flaming Gorge Dam, 1962–1996. Final report of Colorado State University 

Larval Fish Laboratory to Upper Colorado River Endangered Fish Recovery Program, 

Lakewood, Colorado. 

Bestgen, K.R. 1996. Growth, survival and starvation resistance of Colorado squawfish larvae. 

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Bestgen, K.R. 1997. Interacting effects of physical and biological processes on recruitment of 

Colorado squawfish. Doctoral Dissertation, Chapter 4. Colorado State University, Fort Collins. 

Bestgen, K. R., D. W. Beyers, J. A. Rice, and G. B. Haines. 2006. Factors affecting 

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and individual-based modelling. 2006. Transactions of the American Fisheries Society 

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and otolith growth in young Colorado squawfish. Transactions of the American Fisheries Society 

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early development and survival of Colorado squawfish. Transactions of the American Fisheries 

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Bestgen, K.R., D.W. Beyers, J.A. Rice and G.B. Haines. 2006. Factors affecting recruitment of 

young Colorado pikeminnow: Synthesis of predation experiments, field studies and individualbased modeling. Transactions of the American Fisheries Society 135:1722–1742. 

Bestgen, K.R., R.T. Muth and M.A. Trammell. 1998. Downstream transport of Colorado 

squawfish larvae in the Green River drainage: temporal and spatial variation in abundance and 

relationships with juvenile recruitment. Final report of Colorado State University Larval Fish 

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Beyers, D.W., R.T. Muth and M.S. Farmer. 1994. Experimental evidence of competition 

between larvae of Colorado squawfish and fathead minnow. Final report of Colorado State 

University Larval Fish Laboratory to Upper Colorado River Endangered Fish Recovery Program, 

Lakewood, Colorado. 

Blinn, D.W. and G.A. Cole. 1991. Algal and invertebrate biota in the Colorado River: 

Comparison of pre-and post-dam conditions. Pages 102–123 in Colorado River Ecology and 

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Washington, DC. 

Blinn, W., J.P. Shannon, L.E. Stevens and J.P. Carder. 1995. Consequences of fluctuating 

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suckers. Transactions of the American Fisheries Society 112:601–607. 

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cyprinacea in a stream fish population. Transactions of the American Fisheries Society 108: 

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Service, Hualapai Tribeand SWCA Environmental Consultants, Flagstaff, Arizona. 

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Green River, 1994 and 1995. Final report of Utah Division of Wildlife Resources to Upper 

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Collins, K.P. and D.K. Shiozawa. 1996. The effects of fish predation on backwater invertebrate 

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Converse, Y.K. 1995. Use of geomorphology to predict subadult humpback chub distribution in 

the Colorado River. Proceedings of the Desert Fishes Council. 

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Converse, Y.K., L.D. Lentsch and R.A. Valdez. 1999. Evaluation of size-dependent overwinter 

growth and mortality of age-0 Colorado squawfish. Final report of Utah Division of Wildlife 

Resources to Upper Colorado River Endangered Fish Recovery Program, Lakewood, Colorado. 

Day, K. S., K. D. Christopherson, and C. Crosby. 2000. Backwater use by young-of-year chub 

(Gila spp.) and Colorado pikeminnow (Ptychocheilus lucius) in Desolation and Gray Canyons of 

the Green River, Utah. Report B in Flaming Gorge studies: reproduction and recruitment of Gila 

spp. and Colorado pikeminnow (Ptychocheilus lucius) in the middle Green River. Final report of 

Utah Division of Wildlife Resources to Upper Colorado River Endangered Fish Recovery 

Program, Lakewood, Colorado. 

Day, K.S., K.D. Christopherson and C. Crosby. 1999. An assessment of young-of-year Colorado 

pikeminnow Ptychocheilus lucius use of backwater habitats in the Green River, Utah. Report B 

in Flaming Gorge Studies: Assessment of Colorado pikeminnow nursery habitat in the Green 

River. Final report to Upper Colorado River Endangered Fish Recovery Program. Utah Division 

of Wildlife Resources, Salt Lake City, Utah. 

DeMarais, B.D. and T.E. Dowling. 1993. Introgressive hybridization and evolution of Colorado 

River basin Gila (Teleostei: Cyprinidae). Proceedings of the Desert Fishes Council 24:67. 

Didenko, A.V., S.A. Bonar and W.J. Matter. 2004. Standard weight (Ws) equations for four 

rare desert fishes. American Journal of Fisheries Management 24(2):697–703. 

Douglas, M.E. 1993. An analysis of sexual dimorphism in an endangered cyprinid fish (Gila 

cypha Miller) using video image technology. Copeia 1993:334–343. 

Douglas, M.E. and P.C. Marsh. 1993. Monthly population estimates of endangered humpback 

chub (Gila cypha) in the Little Colorado River of Arizona. Proceedings of the Desert Fishes 

Council 24:65-66. 

Douglas, M.E. and P.C. Marsh. 1996. Endangered humpback chub (Gila cypha) as prey of 

introduced fishes in the Little Colorado River, Arizona. Section 2 in M.E. Douglas and P.C. 

Marsh, eds. Ecology and Conservation Biology of Humpback Chub (Gila cypha) in the Little 

Colorado River. Bureau of Reclamation, Salt Lake City, Utah. 

Douglas, M.E. and P.C. Marsh. 1996. Population estimates/population movements of Gila 

cypha, an endangered cyprinid fish in the Grand Canyon region of Arizona. Copeia 1996:15–28. 

Douglas, M.E. and P.C. Marsh. 1996. Survivability of an endangered species (Gila cypha) 

within the Grand Canyon region of Arizona. Section 4 in M.E. Douglas and P.C. Marsh, eds. 

Ecology and Conservation Biology of Humpback Chub (Gila cypha) in the Little Colorado 

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