GENETICS MANAGEMENT PLAN

for 

HUMPBACK CHUB (Gila cypha)

Prepared by

Thomas E. Czapla

Upper Colorado River Endangered Fish Recovery Program

U.S. Fish and Wildlife Service

Denver, Colorado

DRAFT 1

April 22, 2005
DRAFT HBC Genetics Management Plan-1

INTRODUCTION

A perceived decline in the Grand Canyon humpback chub population in 2002 raised concern over

genetic viability, and a possible need was identified to take the species into a refuge or captive

propagation program. There was also concern expressed regarding genetic ramifications when 

creating small founder populations by translocations into tributaries to the Grand Canyon. In

response to concerns about the status of humpback chub, Glen Canyon Dam Adaptive

Management Work Group formed an Ad Hoc Committee to consider actions to implement a

comprehensive research and management program for the humpback chub. Although the

comprehensive plan is still in draft, it identifies a genetics management plan for humpback chub

to determine genetic relationships within and among populations of the endangered Gila cypha

(humpback chub) in the Colorado River ecosystem

(http://137.77.133.1/uc/envprog/amp/amwg/mtgs/04oct25/HBC_Projects.pdf), further genetics

research on humpback chub gentics is being conducted at Colorado State University and is due

out by the end of this year. The U.S. Fish and Wildlife Service was requested to develop a

genetics management plan for humpback chub in the Colorado River Basin in order to identify

and direct research and management actions needed to ensure current genetic diversity and

viability of humpback chub are preserved as actions are taken to recover the species. 

HUMPBACK CHUB SPECIES STATUS

Six extant populations of humpback chub exist (Yampa Canyon, Desolation/Gray canyons, Black

Rocks, Westwater Canyon, Cataract Canyon, and Grand Canyon). Similar morphometric and

meristic characteristics among the six populations of Gila cypha (Douglas et al. 1998, 2001;

McElroy and Douglas 1995; McElroy et al. 1997) and lack of genetic differentiation among the

six populations suggest panmixis and extensive introgression with sympatric Gila species

(Dowling and DeMaris 1993).

The most current estimates of the mean number of wild adult humpback chub (greater than 200

mm total length) are provided below. Information on Upper Colorado River Basin populations

was gathered from presentations at the August 2004 population estimates workshop. Many of

these estimates are preliminary (analyses ongoing), and some are contained in draft reports

undergoing peer and Biology Committee review. These data indicate recent downward trends in

the abundance of humpback chub in Black Rocks, Westwater Canyon, and Desolation/Gray

Canyons. Information on the Grand Canyon population in the Lower Colorado River Basin is

provided by Grand Canyon Research and Monitoring Center, through the use of an AgeStructured Mark Recapture program.
DRAFT HBC Genetics Management Plan-2

Table 1. Current humpback chub population estimates with confidence intervals.

Population Year Estimate Confidence Interval Author/Method

Yampa Canyon 1998–

2000

400 100–2000 B. Haines & T.

Modde, Likelihood

Density Function

Desolation/Gray

canyons

2001

2002

2003

1,254*

2,612*

937*

733–2,697*

1,477–8,509*

636–1,520*†

J. Jackson et al.,

Closed MarkRecapture

Black Rocks 1998

1999

2000

2003

764

921

539

500*

512–1,206

723–1,208

223–1,497

221–1,176*

C. McAda, Closed

Mark-Recapture

Westwater Canyon 1998

1999

2000

2003

4,744

2,215

2,201

2,413*

37,60–14,665

1,608–7,508

1,335–4,124

1,500–4,396*

J. Jackson, Closed

Mark-Recapture

Cataract Canyon 2003 150* 71–407* P. Badame, et al.,

Closed MarkRecapture

Grand Canyon 2004 2,000–4,000 L. Coggins, Age

Structure-Mark

Recapture

* Preliminary data.

† Sampling season switched to fall from summer.

The recovery goals for humpback chub (U.S. Fish and Wildlife Service 2002) discuss the concept

of redundancy and core populations:

“Humpback chub occur as multiple, demographically independent populations in widely

distributed regions of the Colorado River Basin; distances of 17–394 km separate adjacent

populations. This widely clumped distribution pattern contributes to redundancy as species

protection against threats and catastrophic events. The five populations in the upper basin occur

in discrete regions of three subbasins, including three populations in the Colorado River, and one

population each in the Green River and Yampa River. The lower basin population in Grand

Canyon exists independently downstream of Glen Canyon Dam, where it has been

geographically isolated from upper basin populations since dam construction in 1963. This

pattern of geographic separation among all six populations provides population redundancy and

greatly reduces the likelihood of a catastrophic event simultaneously affecting the majority of

populations.
DRAFT HBC Genetics Management Plan-3

It is recognized that the six populations of humpback chub vary considerably in size, from about

400 to 5,000 adults. The larger populations are considered “core populations”. A core population

is an independent self-sustaining population sufficiently large to maintain genetic and

demographic viability. A core population may serve as a center of dispersal from which new

populations are established or existing populations are augmented. Core populations are

sufficiently large and viable to protect against extreme demographic and environmental

variability. A core population may consist of two or more geographically proximate populations

(e.g., Black Rocks and Westwater Canyon). In case of a catastrophe, multiple or redundant core

populations preserve species viability.”

Despite a current downward trend (not statistical) in adult humpback chub population estimates

in the past few years, if the estimates of all humpback chub populations were summed there

would be between 5,000 and 10,000 adults in the Colorado River Basin. The current population

trend may be caused by recent drought during the late 1990's and early part of 2000, although

there is some indication that some of the population declines may have been occurring before the

drought conditions. Reduced streamflows have also allowed for an expansion of nonnative fish

species which compete with and prey upon the native fishes.

UPPER COLORADO RIVER BASIN GENETICS MANAGEMENT PLAN

The Upper Colorado River Endangered Fish Recovery Program (Recovery Program) philosophy

and mission for genetics management of endangered fishes are to: 

1. Maintain the genetic integrity of wild endangered fish stocks in the upper basin;

and

2. Maintain genetic diversity in captive broodstocks that is similar to the stock used

as founders. 

The goals of this genetics management plan are to:

1. Conserve genetic diversity of wild endangered fish populations while

implementing recovery efforts that will maintain, enhance, or reestablish viable

wild populations by removing or significantly reducing factors that caused

population declines; 

2. Maintain genetic diversity in captive-reared endangered fish broodstock that is

similar to that of the wild population used as founders; and 

3. Produce genetically diverse fish for augmentation efforts. 

According to the current Genetics Management Plan (Czapla 1999), the humpback chub was

assigned “Priority 3” among the four endangered species because the populations were

considered stable but small and localized in deep canyon river reaches. Within the species,
DRAFT HBC Genetics Management Plan - 4

populations were prioritized as follows (the Grand Canyon population was not considered in the

plan): 

Priority Population - Reason

1 Desolation-Gray Canyon - because of small numbers of fish, morphological

variation, and remoteness in the upper basin.

2 Yampa Canyon - because it is located in the relatively unaltered Yampa River. 

Concern of nonnative fish predation impacting this population is currently under

investigation.

3 Cataract Canyon - because the phenotypes indicate the population is not as variable

as the Yampa River and Desolation-Gray Canyon population and is less likely to be

impacted from human activities.

4 Black Rocks - because the phenotypes indicate a pure humpback chub population. 

Westwater Canyon - because the phenotypes appear to be pure humpback chubs like

the Black Rocks Canyon population. Black Rocks and Westwater Canyon

populations were considered relatively large and stable and assigned the lowest

priority.

SERVICE POLICY ON CAPTIVE PROPAGATION

A joint policy with U.S Fisha and Wildlife Service and National Maine Fisheries Service

regarding controlled propagation of species (U.S Office of Federal Register 65:183 [2000]:

56916–56922) “addresses the role of controlled propagation in the conservation and recovery of

species listed as endangered or threatened under the Endangered Species Act of 1973 (as

amended) (Act). The policy provides guidance and establishes consistency for use of controlled

propagation as a component of a listed species recovery strategy. This policy will help to ensure

smooth transitions between various phases of conservation efforts such as propagation,

reintroduction and monitoring, and foster efficient use of available funds. The policy supports

the controlled propagation of listed species when recommended in an approved recovery plan or

when necessary to prevent extinction of a species. Appropriate uses of controlled propagation

include supporting recovery related research, maintaining refuge populations, providing plants or

animals for reintroduction or augmentation of existing populations, and conserving species or

populations at risk of imminent extinction or extirpation.”
DRAFT HBC Genetics Management Plan - 5

The policy further states: “Controlled propagation is not a substitute for addressing factors

responsible for an endangered or threatened species’ decline. Therefore, our first priority is to

recover wild populations in their natural habitat wherever possible, without resorting to the use

of controlled propagation. This position is fully consistent with the Act.”

There is no mention in this policy that when wild populations fall to a certain level or number

that they must be brought into captivity.

Status of Captive Propagation of current endangered fish species:

The captive propagation policy clearly states “Our policy is that the controlled propagation of

threatened and endangered species will be: 1. [First] Used as a recovery strategy only when other

measures employed to maintain or improve a listed species' status in the wild have failed, are

determined to be likely to fail, are shown to be ineffective in overcoming extant factors limiting

recovery, or would be insufficient to achieve full recovery. All reasonable effort should be made

to accomplish conservation measures that enable a listed species to recover in the wild, with or

without intervention (e.g., artificial captivity provisioning), prior to implementing controlled

propagation for reintroduction or supplementation.” [emphasis is by author] 

Another reason for this reluctance to advance a controlled propagation program is to avoid risks

associated with hatchery products: 1) avoid reducing genetic variability within naturally

occurring populations; 2) an increased level of inbreeding that would likely result from the

enhancement of only a portion of the gene pool; and 3) diminishing a listed species’ natural

capacity to survive and reproduce in the wild through exposure to selection regimes in controlled

environments. Identifying a critical number of individuals in the wild that would require a listed

species to be brought into captivity or prepared for controlled propagation depends on speciesspecific demographic and environmental factors, and would have to be established on an

individual basis.

RECOMMENDATIONS

1. At this time, bringing humpback chub into captivity or developing a controlled

propagation program does not appear prudent. With 2–3 wild core populations available

for redundancy as insurance in case of a catastophic event, emphasis and resources should

be placed on removing or minimizing threats to the species. Establishing a refuge or a

captive propagation program for humpback chub could result in reduced numbers of

recruits or adults in the wild, reducing genetic variability; enhancing only a portion of the

gene pool; and developing selection regimes in controlled environments.

2. Existing genetic characteristics and variability of humpback chub are currently unknown,

but are being investigated at Colorado State University. These studies should continue in

order to assess the genetic status of the humpback chub. The existing genetic effective

population size (Ne

) should be determined for the species and for individual populations,
DRAFT HBC Genetics Management Plan - 6

if possible, and compared with historic Ne. This metric may be evaluated as a means to

determine critical population size for taking fish into captivity into a refuge or for captive

propagation.

Alternatives for the populations of Humpback Chub in the Upper Colorado River Basin (in

priority)

3. Continue to address threats to the species and translocate young-of-the-year (yoy; when

available) from nearest populations to river reaches where threats have been reduced or

minimized. For example, the Yampa Canyon population might be supplemented with

Desolation/Gray yoy once the control of nonnatives is affected in Yampa Canyon. 

Suggest the movement of no less than 100 yoy per year for at least 5 years.

4. Move yoy to a refuge, i.e., a hatchery such as Ouray or Grand Valley, and expect to add

yoy on an annual basis to minimize any genetic changes caused by genetic drift or

adaptations to hatchery conditions. In addition, funding will be required to provide

operation and maintenance of the fish held at the refuge. Identifying refuge, getting

permits lined up for signature, and other associated logistics of getting fish out of the wild

could be in place in case this is deemed necessary. 

5. If a precipitous decline in all populations occurs and is validated1, then breeding matrices

(e.g., 25x25 paired matings) should be developed that utilize many individuals from the

five diverse populations throughout the Upper Colorado River Basin, with the goal to

maintain genetic variation of the original wild populations.

6. Augmentation of the populations should not occur until the threats have been removed or

minimized to a level that reintroduced individuals can survive, mature, reproduce, and

their progeny do the same.

Alternatives for the Grand Canyon Population of Humpback Chub (in priority)

3. Continue to address threats to the species and translocate yoy (when available), that

would presumably be lost to the mainstem Colorado River, into tributaries where threats

have been reduced or minimized. This strategy of translocation has been preliminarily

successful in expanding the population in the Little Colorado River in an upstream

direction, past a natural fish barrier, Chute Falls (personal communication, Pam

Sponholtz, U.S. Fish and Wildlife Service). Suggest the movement of no less than 100

yoy per year for at least 5 years. Continue to explore other tributaries that may be suitable

for translocations.

4. Move yoy to a refuge, i.e., a hatchery such as Willow Beach or Wahweap, and expect to

add yoy on an annual basis to minimize any genetic changes caused by genetic drift or

adaptations to hatchery conditions. In addition, funding will be required to provide

operation and maintenance of fish held at the refuge. Identifying refuge, getting permits
DRAFT HBC Genetics Management Plan - 7

lined up for signature, and other associated logistics of getting fish out of the wild could

be in place in case this is identified. 

5. If a precipitous decline in the population occurs and is validated1

, then breeding matrices

(e.g., 25x25 paired matings) should be developed that utilize many individuals from

diverse congregations throughout the mainstem Colorado River and Little Colorado

River, with the goal to maintain genetic variation of the original wild population.

6. Augmentation of the population should not occur until the threats have been removed or

minimized to a level that reintroduced individuals can survive, mature, reproduce, and

their progeny do the same.

1

 The threshold that would require captivity should be determined by Recovery Team participants.
DRAFT HBC Genetics Management Plan - 8

LITERATURE CITED

Czapla, T.E. 1999. Genetics Management Plan (Revised). Recovery Implementation Program

for Endangered Fishes in the Upper Colorado River, Denver, Colorado.

Douglas, M.E., R.R. Miller, and W.L. Minckley. 1998. Multivariate discrimination of Colorado

Plateau Gila spp.: The “Art of Seeing Well” Revisited. Transactions of the American

Fisheries Society 127:163-173.

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 2001(2):389-400.

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

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

McElroy, D.M., and M.E. Douglas. 1995. Patterns of morphological variation among endangered

populations of Gila robusta and Gila cypha (Teleostei: Cyprinidae) in the Upper

Colorado River Basin. Copeia 1995(3):636-649.

McElroy, D.M., J.A. Shoemaker, and M.E. Douglas. 1997. Discriminating Gila robusta and Gila

cypha: Risk assessment and the Endangered Species Act. Ecological Applications

7(3):958-967.

U.S. Fish and Wildlife Service. 2002. Humpback chub (Gila cypha) Recovery Goals:

amendment and supplement to the Humpback chub Recovery Plan. U.S. Fish and

Wildlife Service, Mountain-Prairie Region (6), Denver, Colorado.