U.S. Dept Commerce/NOAA/NMFS/NWFSC/Publications
NOAA Technical Memorandum NMFS F/NWC-201

Status ReviewforSnake River Fall Chinook Salmon       

by Robin S. Waples1, Robert P. Jones,       Jr.2,Brian R. Beckman1, and George A.       Swan1 

1National Marine Fisheries       ServiceNorthwest Fisheries Science CenterCoastal Zone and       Estuarine Studies Division2725 Montlake Blvd. E.Seattle WA       98112-2097(206) 860-3270 

2National Marine Fisheries       ServiceEnvironmental and Technical Services Division911       NE 11th Ave., Rm. 620Portland, OR 97232 

June 1991

NOAA NMFS F/NWC-201: Status Review for Snake River Fall Chinook Salmon

NOAA Technical Memorandum NMFS Series

The Northwest Fisheries Science Center of the National Marine Fisheries Service, NOAA, uses the NOAA Technical Memorandum NMFS series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible due to time constraints. Documents published in this series may be referenced in the scientific and technical literature. 

The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest & Alaska Fisheries Science Center, which has since been split into the Northwest Fisheries Science Center and the Alaska Fisheries Science Center. The NMFS-AFSC Technical Memorandum series is now being used by the Alaska Fisheries Science Center. 

Reference throughout this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA.

This document should be cited as follows:

Waples, R.S., R.P. Jones, Jr., B.R. Beckman, and G.A. Swan. 1991. Status Review for Snake River Fall Chinook Salmon. U.S. Dep. Commer., NOAA Tech. Memo. NMFS F/NWC-201. 73 p.

This document is available to the public through:

National Technical Information ServiceU.S. Department of Commerce5285 Port Royal RoadSpringfield, VA 221611-800-553-8647orders@ntis.fedworld.gov
CONTENTS
List of Figures

List of Tables

Summary

Acknowledgments

Introduction

Key Questions in ESA Evaluations
The "Species" Question
Thresholds for Threatened or Endangered Status

Hatchery Fish and Wild Fish 

Summary of Biological and Environmental Information
Life History Characteristics 
Past and Present Distribution and Abundance 

Straying 

Artificial Propagation 

Ocean Distribution 

Phenotypic Characters 

Environmental Features 

Genetics 

Discussion and Conclusions 
Differences in Run-timing 
Distinct Population Segments 
Reproductive Isolation 
Ecological/Genetic Diversity 

Species Determination 

Status of the ESU 

Citations 

Glossary
SUMMARY
This report summarizes biological information gathered in conjunction with an Endangered Species Act (ESA) status review for Snake River fall chinook salmon (Oncorhynchus tshawytscha). As amended in 1978, the ESA allows listing of "distinct population segments" of vertebrates as well as named species and subspecies. National Marine Fisheries Service (NMFS) policy is that a population will be considered "distinct" for purposes of the ESA if it represents an evolutionarily significant unit (ESU) of the species as a whole. The ESA evaluation of Snake River fall chinook salmon is complicated by the presence of spring- and summer-run chinook salmon in the Snake River. According to NMFS policy, those groups that are reproductively isolated from groups with other run-times should be considered separately for ESA purposes; fish of different run-times for which reproductive isolation cannot be established should be considered as a unit. Because of compelling evidence that fall chinook salmon are reproductively isolated from spring- and summer-run fish in the Snake River, this status review is confined to Snake River fall chinook salmon [see Matthews and Waples (1991) for the status review for Snake River spring and summer chinook salmon].

Prior to 1900, fall chinook salmon were widely distributed in the Snake River and supported important commercial and tribal fisheries. In this century, construction of 12 dams on the main-stem Snake River has reduced spawning habitat to a fraction of its former extent. With completion of the Hells Canyon Dam and Lower Snake River dam complexes between 1958 and 1975, the most productive areas were inaccessible or inundated, and only about 165 kilometers of habitat in the main-stem Snake River remains. Since 1975, the estimated number of wild fall chinook salmon passing Lower Granite Dam on the Snake River has been less than 1,000 per year, and in 1990 the estimate was less than 100.

A brood-stock program designed to preserve the genetic integrity of and enhance production of Snake River fall chinook salmon was initiated in the late 1970s. This program has been operated from Lyons Ferry Hatchery since its completion in 1984. Brood stock is composed of fish returning to the hatchery and hatchery and wild adults taken at Ice Harbor Dam.

Available evidence indicates that, at least through the early 1980s, Snake River fall chinook salmon met both of the requirements to be considered an ESU (Waples 1991)-reproductive isolation and ecological/genetic distinctness. Several lines of evidence indicate that the population with the closest affinity to Snake River fall chinook salmon is fall-run fish in the upper Columbia River. Tagging data suggest that the rate of natural straying of upper Columbia River fall chinook salmon into the Snake River is very low. Consistent genetic differences between upper Columbia and Snake River fish, documented over several years in the late 1970s and early 1980s, also indicate significant, long-term reproductive isolation of the two groups.

The main-stem upper Columbia and Snake Rivers differ ecologically in a number of ways, including water temperature, turbidity, total alkalinity, and pH. High summer water temperatures may prevent rearing of juvenile fall chinook salmon after July in many areas of the main-stem Snake River. Significant differences in average size have been reported between adults from the two areas, and tagging data indicate that Snake River fall chinook salmon have a more southerly ocean distribution than fish of similar run-timing from the upper Columbia River. In conjunction with the genetic data, these results suggest that, historically, fall chinook salmon in the Snake River contributed substantially to ecological/genetic diversity of the biological species. Utter et al. (1982) reached a similar conclusion in an earlier ESA evaluation of Snake River fall chinook salmon.

Information that has only recently become available casts doubt on the present status of the Snake River population. In recent years, strays from hatcheries producing upper Columbia River fall chinook salmon have appeared in the Snake River in increasing numbers; it is estimated that in 1989, such strays constituted almost 40% of the adults used for brood stock at Lyons Ferry Hatchery. A high percentage of adults taken at Lower Granite Dam and on spawning grounds in 1990 were estimated to be of hatchery origin, including strays from hatcheries using upper Columbia River fall chinook salmon. Protein electrophoretic data confirm that introgression of upper Columbia River genes into Lyons Ferry Hatchery brood stock has occurred, but there is no direct information about the genetic effects of hatchery strays on the wild Snake River population.

Although the NMFS Biological Review Team (BRT) concluded that, historically, Snake River fall chinook salmon were an ESU, it is not so clear whether this is still the case. One viewpoint is that introgression from Columbia River hatchery strays has caused the Snake River population to lose the qualities that made it "distinct" for ESA purposes. Evidence in support of this viewpoint includes genetic and tagging data documenting effects of straying on Lyons Ferry Hatchery brood stock, estimates that in 1990 a high proportion of fish passing Lower Granite Dam and found on nearby spawning grounds were hatchery strays, and the lack of any positive information documenting the continued existence of "pure" wild fish. However, given that 1) an ESU was present until at least the early 1980s, 2) substantial straying of upper Columbia River hatchery fish has occurred only within the last generation, and 3) no direct evidence exists for genetic change to wild fall chinook salmon in the Snake River, the BRT felt it would be premature to conclude that the ESU no longer exists. 

In addition, the BRT concluded that Snake River fall chinook salmon face a substantial risk of extinction if factors affecting the population remain unchanged. This conclusion was based on the following considerations: 1) substantial reductions in habitat for fall chinook salmon in the Snake River have occurred in this century; 2) the present abundance of wild fish is a small fraction of the historical abundance, and estimates for 1990 are the lowest on record; 3) application of a simple stochastic model to recent abundance data indicates extinction is likely if present conditions continue; and 4) current hatchery operations pose clear and immediate threats to the genetic integrity of Snake River fall chinook salmon. 
ACKNOWLEDGMENTS
This status review was conducted by the NMFS Northwest Region Biological Review Team. The extensive public record developed pursuant to this petition and discussions of that record by the ESA Technical Committee formed the basis for the review. Members of the BRT for fall chinook salmon were Brian Beckman, David Damkaer, Thomas Flagg, Elizabeth Garr, Lee Harrell, Orlay Johnson, Robert Jones, Conrad Mahnken, Gene Matthews, Desmond Maynard, Gerald Monan, Ben Sandford, Michael Schiewe, George Swan, Grant Thompson, Merritt Tuttle, Robin Waples, John Williams, Gary Winans, and Waldo Zaugg.

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