Statement of Work for FY 2006 Funding

Contract Title: Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts

BPA Proposal Number: 2001-025-00 (Gorge Province)

BPA Project Number: 0003882

Existing Contract Number: 00005068

Principal Investigator: Patrick J. Connolly, Ph.D.
U.S. Geological Survey
Western Fisheries Research Center
Columbia River Research Laboratory
5501-a Cook-Underwood Road
Cook, WA 98605
509-538-2299 x269; FAX 509-538-2843
patrick_connolly@usgs.gov

Project Leader: James H. Petersen, Ph.D.
(address same as above)
509-538-2299 x236; FAX 509-538-2843
jim_petersen@usgs.gov

Submitted to: John Baugher
Bonneville Power Administration
Division of Fish and Wildlife
905 NE 11th Avenue
P.O. Box 3621
Portland, OR  97208-3621

USGS Administrative Contact: Michele Beeman
U.S. Geological Survey
Western Fisheries Research Center
Columbia River Research Laboratory
5501-a Cook-Underwood Road
Cook, WA 98605
509-538-2299 x263; FAX 509-538-2843
michele_beeman@usgs.gov

Contract Period: May 1, 2006 through September 30, 2006

Date Submitted: March 31, 2006

Below is the Statement of Work for U.S. Geological Survey's Columbia River Research Laboratory (USGS-CRRL) portion of a project on Rattlesnake Creek (White Salmon Subbasin, WA) for FY2006.  The objectives that appear below are exactly as stated in the original proposal for FY2001 funding submitted to BPA in April 2000.  Because of reduced funding in 2006, we will not conduct habitat and fish surveys.  Our field efforts in 2006 will be limited to maintaing our PIT-tag detector and flow gage.  We expect that thermographs will be maintained by UCD, and the resulting data will be available for our analyses.  Our focus will be on analysis of data collected during 2001-2006 and preparation of a technical report and journal articles.  The methods have been altered to reflect the analysis and writing focus of the project for 2006.

If a question or need for information arises that is specific to CRRL's portion of this project, please contact Patrick J. Connolly (phone: 509-538-2299 ext. 269, email: patrick_connolly@usgs.gov) or James H. Petersen (phone: 509-538-2299 ext. 236, email: jim_petersen@usgs.gov).


Objectives, Tasks, and Methods

OBJ-1.  Characterize stream and riparian habitat conditions in Rattlesnake Creek drainage.

Task 1-a.  Analyze water quality, water quantity, stream habitat, and riparian conditions.  (UCD, YN, USGS)

Methods:  To characterize stream and riparian habitat conditions, we will use information from the habitat surveys of Rattlesnake Creek and its tributaries that we conducted in 2001-2005.  These habitat surveys quantified key stream habitat components and indicators of aquatic health including: 1) large woody debris, 2) frequency and depth of pools, 3) substrate composition, 4) stream gradient, 5) floodplain connectivity, and 6) riparian vegetation characteristics (e.g., species composition, age structure, shading).  
Stream discharge measurements were taken in major tributaries and several mainstem Rattlesnake Creek sites.  Flow measurements were taken periodically during May through October and an automated stage height gage has been taking 15 minute measurements since 2003.  As done in 2001-2004 and reported in Allen et al. (2003a, 2003b, 2006), these data will be used to characterize temporal and spatial patterns of flow along the stream continuum.


OBJ-2.  Determine the status of fish populations in the Rattlesnake Creek drainage.

Task 2-a.  Derive and analyze estimates of salmonid population abundance.  (USGS)

Methods:  To determine the status of fish populations, we will use estimates of population density and biomass of resident salmonids in selected portions of Rattlesnake Creek that we obtained in 2001-2005.  To obtain these estimates, we first conducted intensive habitat surveys of sampling sites during summer low-flow conditions.  These surveys identified and measured dimensions (e.g., length, weight, and depth) of stream habitat units (e.g., pools, glides, riffles, etc.) as described in Allen et al. (2006), which generally follows methods of Bisson et al. (1982) and Bain and Stevenson (1999).  Soon after these habitat surveys, fish sampling was conducted by electrofishing.  We electrofished a systematic sample of habitat units with block nets within strata of specific habitat types (e.g., pools, glides, riffles).  A backpack electrofisher was used to conduct two or more passes using the removal-depletion methodology (Zippin 1956, Bohlin et al. 1982, White et al. 1982).  The field guides of Connolly (1996) were used to insure that a pre-determined level of precision for the population estimate is achieved (generally, coefficient of variation no greater than 25%) within each sampling unit for each salmonid species.  These methods were chosen to minimize sampling error while minimizing the number of units sampled by electrofishing and the number of electrofishing passes conducted, thereby lessening the numbers of fish that will be exposed to the potentially harmful effects of electroshocking.  These results will be analyzed and summarized so that the effects of anadromous fish re-introduction to the resident fish population may be evaluated.


Task 2-b.  Determine fish species composition, distribution, and life history attributes within the watershed.  (USGS)

Methods:  To document the distribution and abundance of individual fish species within the watershed prior to restoration activities and the potential removal of Condit Dam, we will use the data collected during the work associated with Task 2a.  In order to track movements, growth, and other life history attributes of resident salmonids, we will use the information gained from the recapture of PIT tagged age-1 or older fish that we captured during our stream surveys.  We will also use and the movement information gained from our remote PIT-tag detector that was established in 2001 (Jezorek and Connolly 2003a, 2003b) with cooperation with Earl Prentice, National Marine Fisheries Service.  This PIT-tag detector will be kept running at least through June 2006, but it will depend on our ability and streram flows to replace antennas that were damaged during winter 2005-06.  All PIT-tag data will be entered in the PITAGIS database, which is maintained by Pacific States Marine Fisheries Commission.

Task 2-c.  Determine existing kinds, distribution, and severity of fish diseases in the watershed.  (USFWS, USGS)

Methods:  The data obtained from 2001-2005 will provide an important baseline on the health of existing fish populations in the Rattlesnake Creek drainage.  Because the possible removal of Condit Dam would allow adult anadromous salmonids and other species access to Rattlesnake Creek from the mainstem Columbia River, these fish may introduce new pathogens or parasites into the watershed.  Knowledge of current conditions will help managers anticipate and weigh possible risks or threats to existing resident fish populations.  We have obtained fish specimens for disease sampling using a longitudinal and tributary sampling strategy.  This facilitated the development of a fish-health baseline for areas that would be accessible and inaccessible (above barriers) to anadromous salmonids in the future.  A subsample of fish captured during population studies and all fish incidentally killed during sampling under Tasks 2a and 2b were put on ice and delivered to the U.S. Fish and Wildlife Service's Lower Columbia Fish Health Center, which provided a thorough disease profile as part of the U. S. Fish and Wildlife Service's National Wild Fish Health Survey (contact: Dr. Susan Gutenberger, Director, all in-kind contribution of approximately $15,000).  


Task 2-d.  Obtain and archive tissue samples in a non-lethal manner for possible future genetic analysis.  (USGS)

Methods:  During 2001-2005, tissue samples (fin clip) from a subsample of salmonids captured during electrofishing for Tasks 2a and 2b were removed and preserved (95% ethanol) for future genetic analyses (an in-kind contribution will be sought to pay for this supplementary genetics work).  With the exception of introductions of hatchery fish (primarily rainbow trout, but also cutthroat trout) in the mainstem White Salmon River, resident salmonids have been reproductively isolated above Condit Dam for over 75 years.  These data will serve as a genetic reference point for rainbow trout and coastal cutthroat trout populations in the watershed prior to the reestablishment of congeneric anadromous salmonids.  In-kind genetic analysis will continue to be sought for these samples.


References

Allen, B.M., P.J. Connolly, and K. Martens.  2003a.  Characterization of flow, temperature, habitat conditions, and fish populations in the Rattlesnake Creek watershed.  Report A in P.J. Connolly, editor.  Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts.  2001 Annual Report.  Prepared for: Bonneville Power Administration, Portland, Oregon.  Project 2001-025-00.

Allen, B.M., P.J. Connolly, and K. Martens.  2003b.  Characterization of flow, temperature, habitat conditions, and fish populations in the Rattlesnake Creek watershed.  Report A in P.J. Connolly, editor.  Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts.  2002 Annual Report.  Prepared for: Bonneville Power Administration, Portland, Oregon.  Project 2001-025-00.

Allen, B.M., P.J. Connolly, C. S. Munz, and J. C. Charrier.  2006.  Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts.  2003-2004 Annual Report (May 2003-April 2004).  Prepared for: Bonneville Power Administration, Portland, Oregon.  Project 2001-025-00.

Bain, M. B., and N. J. Stevenson.  1999.  Aquatic habitat assessment: common methods.  American Fisheries Society, Bethesda, Maryland.

Bisson, P. A., J. L. Nielsen, R. A. Palmason, and L. E. Grove.  1982.  A system of naming habitat types in small streams, with examples of habitat utilization by salmonids during low streamflow.  Pages 62-73 in N.B. Armantrout.  1982.  Acquisition and utilization of aquatic habitat inventory information symposium.  American Fisheries society, Western Division, Bethesda, MD.

Bohlin, T.  1982.  The validity of the removal method for small populations -- consequences for electrofishing practice.  Institute of Freshwater Research Drottningholm Report 60:15-18.

Connolly, P. J.  1996.  Resident cutthroat trout in the central Coast Range of Oregon: logging effects, habitat associations, and sampling protocols.  Doctoral dissertation.  Oregon State University, Corvallis.
Jezorek, I.G., and P.J. Connolly.  2003a.  Instream PIT-tag detection system.  Report B in P.J. Connolly, editor.  Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts.  2001 Annual Report.  Prepared for: Bonneville Power Administration, Portland, Oregon.  Project 2001-025-00.

Jezorek, I.G., and P.J. Connolly.  2003b.  Instream PIT-tag detection system.  Report B in P.J. Connolly, editor.  Assess current and potential salmonid production in Rattlesnake Creek associated with restoration efforts.  2002 Annual Report.  Prepared for: Bonneville Power Administration, Portland, Oregon.  Project 2001-025-00.

White, G. C., D. R. Anderson, K. P. Burnham, and D. L. Otis.  1982.  Capture-recapture and removal methods for sampling closed populations.  No. LA-8787-NERP, UC-11.  Los Alamos National Laboratory, Los Alamos, New Mexico.

Zippin, C.  1956.  An evaluation of the removal method of estimating animal populations.  Biometrics 12:163-189.