Estimating Abundance and Life History Characteristics of Threatened Wild Snake River Steelhead Stocks by Using Genetic Stock Identification

Abstract

Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single contribution of 36.1% (95% confidence interval [CI] = 30.2–39.7%). Other large contributions were 15.4% (12.8–18.7%) from the upper Clearwater River reporting group and 13.9% (12.5–18.7%) from the lower Salmon River reporting group. Smaller contributions came from the other six reporting groups (Imnaha River: mean = 9.5%, 95% CI = 6.8–13.6%; upper Salmon River: 9.2%, 5.1–11.3%; South Fork Clearwater River: 7.6%, 4.3–8.9%; Middle Fork Salmon River: 5.1%, 3.5–6.4%; South Fork Salmon River: 2.7%, 1.3–3.6%; Elk Creek: 0.5%, 0.0–1.2%). Significant differences in reporting group contributions were observed when samples were grouped according to length, age, and run timing differences. Of the samples analyzed, 372 (34.9%) were identified as males and 694 (65.1%) were identified as females. Our results demonstrate that the GSI methodologies applied to Snake River steelhead have the potential of providing an efficient, minimally intrusive tool for obtaining stock-specific abundance of this threatened distinct population segment. This technology can assist future viability status assessments of Snake River steelhead by contributing to refinements in population delineations, productivity calculations, and annual stock-specific estimation of life history characteristics (e.g., age structure, sex ratio, and run timing).

Received November 15, 2011; accepted April 24, 2012

ACKNOWLEDGMENTS

We thank Eric Tretter, Kelly Heindel, and Amanda Boone (Idaho Department of Fish and Game [IDFG]) and Lori Maxwell, Vanessa Morman, and Jeff Stephenson (Columbia River Inter-Tribal Fish Commission) for laboratory contributions. We are also grateful to Kristin Ellsworth and Scott Putnum (IDFG) and Jerry Harmon (National Oceanic and Atmospheric Administration Fisheries) for organizing sample collection at Lower Granite Dam. Thanks are extended to Lynn Schrader for inventorying the incoming samples. We especially thank all IDFG, Oregon Department of Fish and Wildlife, Washington Department of Fish and Wildlife, U.S. Fish and Wildlife Service, and Nez Perce Tribe staff and volunteers who contributed to the sampling of baseline collections. Finally, we appreciate Paul Bunn for providing GIS assistance and Lani Clifford for help with formatting and editing earlier drafts of this manuscript.