Nearshore Ecology of Grand Canyon Fish


Executive Summary Nearshore Ecology Project

Introduction- Management actions in aquatic ecosystems are frequently directed at restoring or improving specific habitats to improve fish growth and survival.  In the Grand Canyon reach of the Colorado River experimental flow operations as part of the Glen Canyon Dam Adaptive Management Program impact the creation of habitat types (i.e., sandbars and associated backwaters), water temperatures, or flow fluctuations and magnitude which are critical for juvenile native fish conservation.  One of the objectives of a recent experiment evaluating steady flow operations from Glen Canyon Dam was to understand how river discharge, through its interaction with physical habitat structure, influences the growth, survival rates, and habitat use of juvenile native fish in the Colorado River in Grand Canyon.  The key fish species of interest was humpback chub Gila cypha, currently listed as “Endangered” under the US Endangered Species Act. Population recovery of humpback chub is of keen interest to numerous federal, state, and tribal entities.  The “Nearshore Ecology” (NSE) project was designed to address key fundamental research questions to improve our knowledge of humpback chub population ecology.


(1) Do steadier flows during late summer and early fall increase survival, abundance, and/or growth rates of juvenile native fish?

(2) Do juvenile humpback chub select specific habitat types and if so, does this selection change under different river flow regimes?

(3) What is the provenance of juvenile humpback chub in the mainstem Colorado River and is there evidence for mainstem spawning and rearing?




Update August 2013                                                                                                                                                                                                                                                                                                                                   

We have completed the final report for this project and it is available here:


Nearshore Ecology of Grand Canyon Fish Final Report*

*Updated 8.27.2013 to correct missing figure (see Errata below)


Questions about the final report can be directed to Bill Pine (


A supplemental file of water chemistry data collected as part of the project is available here as an Excel spreadsheet. If you have questions about the water chemistry data please email Karin Limburg (


All field data from the NSE project are uploaded in the USGS-GCMRC database.


We are working to submit the sections of this report for publication in peer-reviewed journals and will continue to keep our agency partners up-to-date on the status of these publications.




Papers accepted or published to date:


Hayden, T. A., K. E. Limburg, and W. E. Pine, III.  2012.  Using Otolith Chemistry Tags and Growth Patterns to Distinguish Movements and Provenance of Native Fish in Grand Canyon.  River Research and Applications. DOI 10.1002/rra.2627


K. E. Limburg, T. A Hayden, W. E. Pine, III, M. D. Yard, R. Kozdon, and J. W. Valley.  2013.  Of Travertine and Time: Otolith chemistry and microstructure detect provenance and demography of endangered humpback chub in Grand Canyon USA.  PLoS One 8(12), E84235


Gerig, B. S., M. J. Dodrill, and W. E. Pine, III.  In-Press.  Habitat Selection and Movement of Adult Humpback Chub in the Colorado River in Grand Canyon during an Experimental Steady Flow Release.  North American Journal of Fisheries Management


Finch, C., W. E. Pine, III, K. E. Limburg.  In-press.  Do hydropeaking flows alter juvenile fish growth rates? A test with juvenile humpback chub in the Colorado River.  River Research and Applications. DOI 10.1002/rra.2725



We are very appreciative of the opportunity to work with a large group of dedicated natural resource managers, scientists, tribal representatives, boatmen, volunteers, and the general public on this project. We hope that the results from this project will be useful in informing the operation of Glen Canyon Dam and in promoting the conservation of native fish populations in Grand Canyon.



Background- Glen Canyon Dam is operated primarily as a load-following hydropower facility, increasing and decreasing dam discharge to match power demand. This periodic “flushing” of the river reduces the residence time of water as well as the availability of certain shoreline habitat types. In contrast, steady flows can increase the retention time of water in littoral areas such as backwaters and low-angle shorelines, and if discharge volume and ambient temperature are appropriate, can locally increase water temperatures. The NSE project evaluated experimental steady flows that occurred from 1 September- 31 October in each year 2009-2011. This study took place between river km 102-106 just downstream of the confluence of the mainstem Colorado and Little Colorado rivers where most prior research on humpback chub in Grand Canyon has occurred. The timing and magnitude of the steady flow experiment was developed by resource managers independent of the NSE team. Experimental flow regimes were about 10% of the unregulated (pre-Glen Canyon Dam) annual fluctuations. 

Prior to the NSE project, our understanding of juvenile humpback chub ecology in the mainstem Colorado River was deficient compared with our knowledge of adult humpback chub primarily because of limited sampling of mainstem habitat for juvenile life stages.  The NSE project developed a sampling and analytical framework to directly assess juvenile humpback chub survival, abundance, individual growth, and habitat use.  These analyses used spatially referenced mark-recapture experiments with multiple gear types and determined provenance (birth river) through otolith microchemistry.  This direct assessment of key vital rates complements indirect approaches used to estimate survival through population modeling efforts. For example, age-structured-mark-recapture (ASMR, Coggins et al. 2006) reconstructs juvenile abundance and survival through time from adult population numbers (estimated from mark-recapture) and assumes survival relationships based on life-history characteristics and growth rates.  In contrast, the NSE project directly estimates juvenile fish population metrics in terms of abundance, survival, growth, or habitat use, which is useful for rapidly assessing how juvenile humpback chub respond to management actions such as experimental flows.  


Results and Discussion- The NSE project found that annual apparent survival of juvenile humpback chub (size at tagging < 100-mm total length, TL) did not differ significantly between the extant fluctuating flows and the experimental steady flow treatments (Finch et al. in-review A).  The NSE project also documented that juvenile humpback chub were able to survive and rear in the mainstem Colorado River even at small sizes of 40-100 mm TL (Finch et al. in-review B).  A somewhat surprising finding was that growth in juvenile humpback chub declined during these short-term steady flows versus fluctuating flows even though water temperatures were generally similar (Finch et al. in-review B).  Reasons for this counterintuitive growth response are not known, but Finch (et al. in-review B) hypothesizes that food availability in the drift (primarily aquatic insects) is higher in fluctuating flows than in steady flows. 

In Grand Canyon the creation, maintenance, and persistence of specific habitat types are considered critical for the persistence and recovery of native fish populations, including humpback chub. Backwaters are thought to be more similar to the Colorado River ecosystem prior to river modification because they are generally warmer and may be less influenced by river stage and dam operations than other mainstem habitat types.  The NSE study compared abundance, density and habitat selection patterns between shoreline habitats (cliff, talus, debris fan, sand, backwater) and found that abundance of juvenile humpback chub was consistently highest in talus habitats and lowest in backwater habitats (Dodrill et al., in-review).  Juvenile humpback chub showed positive selection for backwater habitats, but the spatial extent of backwater habitats in the NSE study reach was small compared to other habitat types.  Additionally, ultrasonic telemetry of larger juvenile humpback chub (about 180-190-mm TL) found that habitat selection and daily movements did not change between fluctuating conditions and the steady flow experiment (Gerig et al., in-review).  This suggests that, at least in this reach of the Colorado River, management actions directed at manipulating backwater habitat type will affect only a small proportion the habitats, and the population, of humpback chub.  The NSE study reach is in a section of Grand Canyon with steep bank angle, thus the available habitat in this reach is relatively unaffected by changes in river stage associated with the range of flows observed from 2009-2011.  Future work could assess whether juvenile humpback chub are similarly robust to changes in a river reach where available habitats are more flow sensitive.

We successfully developed a framework to address humpback chub growth and provenance through the analysis of humpback chub otoliths (ear-stones).  Otoliths form part of the hearing and balance system in fishes and grow incrementally as fish grow.  Made of calcium carbonate, otoliths absorb trace elements and isotopes from the environment. If these differ amongst environments, analysis of otolith chemistry can shed light on provenance and lifetime habitat use of fishes.  Direct querying of this sort permits deeper insight into population ecology and habitat use, because individual fish life histories are tracked retrospectively.  Data from tagging programs, on the other hand, are limited to the locations in which fish are captured and recaptured.

Using information on water and humpback chub otolith chemistry we asked:

(1)  Do different parts of the mainstem Colorado River system in Grand Canyon, including its tributaries, differ in terms of dissolved water chemistry?

(2)  In particular, are there trace elemental and/or isotopic markers that can distinguish the Little Colorado River tributary from the mainstem?  If so, then

(3)  At what age and size do juvenile humpback chub emigrate from the Little Colorado to the mainstem Colorado River?

(4)  Is humpback chub recruitment to the mainstem Colorado River population dependent on reaching a certain size before emigration?

(5)  Are any humpback chub spawned in the Colorado mainstem and if so do they survive?


We developed a geochemical atlas of the Grand Canyon reach of the Colorado River, analyzing a suite of trace elements and stable isotopic ratios.  Our sampling was limited primarily to summer and fall months in 2009 – 2012.  We assayed otoliths of juvenile humpback chub as well as any available adult chub that had been collected as incidental mortalities.  

We found that the ratio of a few trace elements to calcium – primarily strontium, barium, and selenium, along with the stable isotopic ratios of carbon, oxygen, and hydrogen/deuterium could, as an ensemble, serve to discriminate between the mainstem and the Little Colorado River, which was the focus of the study (Hayden et al., 2012; Limburg et al., in review).  Carbon stable isotopic ratios (d13C) were particularly good discriminators because of the substantial fractionation during travertine formation within the Little Colorado River.  We also found that the chemical signature of the mainstem was maintained throughout the entire reach of Grand Canyon, with little variation, such that this signature was readily distinguished from many of the tributaries. 

We measured lapillar otoliths of humpback chub and derived a relationship between otolith size and fish total length.  Using this relationship, we back-estimated the size, as well as age (in days) when humpback chub egressed from the Little Colorado to the mainstem (Limburg et al., in-review).  In addition to this evidence from changes in otolith chemistry we discovered changes in the otolith microstructure itself.  Daily growth increments of otoliths reduced in width markedly upon fish entry into the mainstem due to the temperature differential which strongly affects otolith growth. 

We determined a range of sizes and ages at egress amongst juvenile humpback chub captured in the mainstem.  However, this range was reduced in adult chub, suggesting that successful recruitment (i.e. survival) is favored by remaining longer in the Little Colorado.  We also found that fish captured in the Little Colorado tended to be larger on their first birthdays (determined retrospectively by otolith analysis) than fish in the mainstem.  These fish also showed a bimodal distribution of size at age-1 suggesting differential growth within the birth cohort. 

We analyzed a small number of juvenile humpback chub that had been captured many kilometers upstream of the Little Colorado confluence with the Colorado mainstem.  These individuals turned out to be much older than comparably sized juveniles collected in the Little Colorado River.  Chemical analysis of their otoliths suggested a different natal source; one source appears to be in the 30-Mile Spring reach and another may have been an unidentified spring or tributary (Hayden et al. 2012).  Such small fish (20-25 mm) for their age (e.g., 70-80 days old) are unlikely to survive and recruit to adulthood in the mainstem Colorado River. 


Conclusions- The NSE project developed a sampling and analytical framework to directly assess juvenile humpback chub population responses to management actions at smaller fish sizes than were previously possible. This framework is important, as the key outcome from many different types of management actions in the Colorado River is to improve survival of juvenile humpback chub, increasing overall abundance and accelerating the population to recovery.  The NSE project also documented that small juvenile humpback chub can survive and rear in the mainstem Colorado River.  This information is important because adult humpback chub numbers (age 4+) have increased over the past decade, possibly due to improved survival in the mainstem Colorado River (Coggins and Walters 2009). 

We identified chemical markers that can distinguish fish use of Little Colorado River from mainstem use.  Humpback chub in this reach of Grand Canyon originate overwhelmingly from the Little Colorado.  Mainstem adult otoliths showed evidence that longer rearing in the Little Colorado promotes better growth and recruitment.  The combination of otolith chemistry and growth increment analysis together produced a good natural marker that could be used as a tag to follow fish movements between the mainstem and Little Colorado River.  Further work will be needed to extend this methodology to other humpback chub aggregations within Grand Canyon and possibly to other native fish species assessments.

The results of the NSE project suggest that juvenile humpback chub survival, growth, abundance, and habitat use are robust to the fall steady flows observed during 2009-2011. It is likely that more extreme flow treatments (e.g. higher or lower discharges, longer duration) are required before changes in these metrics would be observed. This research demonstrates the apparent flexibility of juvenile humpback chub in habitat selection regardless of fluctuating or steady river flows.   Our development and application of methods to assess the growth, survival, and persistence of juvenile humpback chub in the mainstem Colorado River are key new additions to the body of knowledge available for managing the Colorado River and understanding how juvenile fish populations respond to hydropower operations in regulated rivers globally.





Coggins, L. G. Jr., W. E. Pine III, C. J. Walters, D. R. Van Haverbeke, D. Ward, and H. C. Johnstone. 2006. Abundance trends and status of the Little Colorado River population of humpback chub. 

            North American Journal of Fisheries Management 26:233-245.


Coggins, L.G., Jr., and C. J. Walters. 2009. Abundance trends and status of the Little Colorado River population of humpback chub; an update considering data from 1989-2008: U.S. Geological Survey Open-File Report 2009-1075, 18 p.


*Dodrill, M. J., B. S. Gerig, C. B Yackulic, W. E. Pine, C. Finch, and J. Korman.  In-Review.  Nearshore habitat use patterns of juvenile and small-bodied native fish in the Colorado River, Grand Canyon.  Canadian Journal of Fisheries and Aquatic Sciences


*Finch, C., W. E. Pine, III, C. B. Yackulic, M. Yard, B. S. Gerig, L. G. Coggins, Jr., and J. Korman.  In-review A.  Assessing juvenile fish population demographic responses to a steady flow experiment in a highly regulated large river ecosystem: A test in the Colorado River below Glen Canyon Dam.  Journal of Fish and Wildlife Management.


*Finch, C., W. E. Pine, III, and K. E. Limburg. In-Review B. Differential growth of humpback chub in regulated and unregulated portions of the Colorado River basin. River Research and Applications.


*Gerig, B. S., M. J. Dodrill, and W. E. Pine, III.  In-review.  Habitat selection and movement of sub-adult humpback chub in the Colorado River in Grand Canyon, Arizona during experimental steady flow releases.  North American Journal of Fisheries Management.


*Hayden, T. A., K. E. Limburg, and W. E. Pine, III.   2012.  Using otolith chemistry tags and growth patterns to distinguish movements and provenance of native fish in the Grand Canyon.  River Research and Applications. DOI: 10.1002/rra2627.


*Limburg, K. E., T. A. Hayden, W. E. Pine, III, M. D. Yard, R. Kozdon, J. W. Valley.  In-review.  Of Travertine and Time: Otolith Chemistry and Microstructure Detect Provenance and Demography of Endangered Humpback Chub in Grand Canyon (USA).  Public Library of Science. July 2013.


*Available in this report



August 27, 2013. We uploaded a new version of the report that corrected a missing figure in the otolith microchemistry section. 






Update November 2012


We have provided annual project reports and updates to our cooperators for the 2009, 2010, and 2011 field seasons.   These reports are archived below.  All project data are also provided to USGS-GCMRC for archiving in their database.  While these reports are written as annual reports, ultimately the deliverables from this work are a synthesis of the three years of field work both related to the NSE project and other ongoing research in Grand Canyon.  Our final deliverables in terms of peer reviewed manuscripts and final report will reflect this synthesis.  These annual reporting documents should be considered draft, and are not suitable to be referenced because they have only undergone agency peer-review.  All information in these documents are developed in cooperation with the NSE core research team, USGS-GCMRC, and all cooperators of the GCDAMP.  We thank the various funding agencies, cooperators, and river users including AZGF, BOR, USFWS, NPS, WAPA, Navajo Nation Department of Fish and Wildlife, and the Colorado River rafters and hikers who provided information, logistical assistance, and field help.


2009 NSE Project Report

2010 NSE Project Report

2011 NSE Project Report


A key aspect of the NSE project has been education of three MS degree students at the University of Florida.  Three students (Brandon Gerig, Mike Dodrill, and Colton Finch) have completed their degree requirements and their theses are available for review below.  Note these documents are currently being revised for submittal to peer reviewed journals.


Brandon Gerig -    

"Site occupancy and habitat selection of endangered humpback chub during experimental flow releases from Glen Canyon Dam in the Colorado River in Grand Canyon, Arizona"


Mike Dodrill-

"Habitat relationships of small bodied fish in the Grand Canyon reach of the Colorado River, Arizona: Emphasis on native fish and evaluation of backwater habitats"


Colton Finch-

"Manipulation of fish vital rates through ecosystem experimentation in a regulated river"



Background information on project and project personnel are below


The Team

This is a multi-collaborator project involving a diverse group of cooperators, collaborators, and friends.  A key collaborator on this project is Grand Canyon Monitoring and Research Center (GCMRC) based in Flagstaff, Arizona.  GCMRC scientists and staff are involved in every aspect of research planning, field work, logistics, analyses, presentations, and publications. Other cooperating groups will include the Florida Cooperative Fish and Wildlife Research Unit, Arizona Game and Fish, US Fish and Wildlife Service, and National Park Service.  Project Principal Investigators (PI) include private industry and academic institutions.  Josh Korman with Ecometric is a project PI who is able to provide tremendous analytical capabilities as well as extensive sampling experience in Grand Canyon.  Ecometric will be involved in every aspect of the project.  University of Florida faculty Bill Pine, Mike Allen, and Tom Frazer from the Department of Wildlife Ecology and Conservation and Fisheries and Aquatic Science Program, are all PIs who collectively provide a range of experience in basic ecology, food web mapping, and fish population dynamics in a wide range of arctic, sub-tropical, temperate, and desert freshwater and marine aquatic ecosystems.  Dr. Karin Limburg and Dr. Todd Hayden from SUNY-ESF are aquatic ecologists who has used innovative otolith microchemistry techniques to unlock new insights into life history characteristics of adult and juvenile anadromous and diadromous fishes in the US and Europe.  During this project we will certainly involve additional partners including long-standing collaborators from University of British Columbia, NC State University, USGS-FISC, and SWCA.  Students involved in this project will have the opportunity, and be expected, to actively engage and cooperate with all collaborators.


Large projects with large numbers of collaborators and cooperators such as this present special opportunity for graduate students.  In a system such as Grand Canyon, the assembled partner groups represent a tremendous amount of collective knowledge about the physical and ecological forces that shape the ecosystem.  This creates an excellent opportunity for the student to learn from this collective experience, while at the same time questioning long-held ideas, perceptions, and mis-conceptions that may be exist. 


The Location

The Colorado River Ecosystem (CRE) is defined as the Colorado River mainstem corridor, tributary streams, and adjacent terrestrial habitats, located between from an area below Glen Canyon Dam near Lee’s Ferry (river mile – 15) and the western boundary of Grand Canyon National Park (river mile 278), a distance of approximately 293 river miles that is punctuated by frequent rapids and over 1700 feet change in elevation.  Within the CRE, Grand Canyon is a deeply incised canyon (>1500-m deep in some areas).  The rock strata all have different erosive characteristics that affect the river channel morphometry.  Channel widths (40-120 m) and depths (4-15 m) vary, as do the shorelines that change from bedrock cliffs and alluvial sand bars to complex talus slopes.  Access to the river is extremely limited and consists of vehicle access only at the upper and lower end of the CRE (river miles 0 and 226), scattered trails that descend several thousand vertical feet into the Grand Canyon, or boat-based river trips that are launched from the upper end of the CRE and travel the entire 290+miles.  The remote nature and setting of the CRE creates a spectacular research site, but it also presents logistical challenges to river researchers.  A considerable amount of study and logistics planning is required to accommodate research within the CRE.  Fortunately for this project, expert GCMRC staff and partners including Humphrey Summit will provide logistics planning and support.  Each trip will generally by supported by two multi-tube “freighter” rafts to transport all gear (including food, water, fuel, sampling equipment, etc.) and two specially designed aluminum electrofishing boats.  On each trip it is likely that a base camp will be established (most often on a sand bar) near the sampling reaches for researchers to operate from for 12-15 day periods of time.  These base camps offer eating, sleeping, gear storage, and sample processing facilities that all comply with NPS wilderness camping requirements.   When working on the river, large daily fluctuations in discharge, cold water temperatures (10-13°C), and deep and powerful currents limit the areas of the CRE that can be sampled and create an environment in which all researchers must be alert and careful when working.  Total length of sampling trips, including boat travel time to sampling reaches and travel time from field camp to the boat take out location on Lake Mead is approximately 20 days.  For this project we anticipate participating in 4-5 sampling trips annually from approximately June-November.



Extensive background material, extracted from the original RFP written by USGS-GCMRC staff, can be found here.  Peer reviewed manuscripts of previous work with humpback chub in Grand Canyon we have authored are available here.


Humpback chub

The humpback chub (Gila cypha), a cyprinid endemic to the Colorado River basin, was described in 1945 from a specimen captured near the mouth of Bright Angel Creek in Grand Canyon, Arizona (Miller 1946).  This morphologically unique cyprinid has been characterized as the most specialized member of the genus Gila, and highly adapted to exist in turbulent canyon-bound reaches of the Colorado River basin (Minckley 1973).  This species was included in the federal list of endangered species in 1967 and is protected under the Endangered Species Act in 1973.  Presently, only six populations are known, five in the upper basin of the Colorado (i.e. above Lees Ferry on the Colorado River), and one in Grand Canyon (Valdez and Ryel 1995).  Our project will partially work with this population of humpback chub in Grand Canyon which is primarily concentrated in an area of the Colorado River near the mouth of the Little Colorado River.