This project implements Genetic Stock Identification (GSI) methodologies within the Snake River basin for wild Chinook salmon and steelhead passing Lower Granite Dam. The SNP genotype data generated in this project is standardized with Columbia River genetic baselines overseen by CRITFC (project 200890700).  

Project 2010-026-00 contributes directly to the monitoring of “viable salmonid population” (VSP) criteria as described in McElhany et al. 2000.

This includes:
Development, maintenance, and reporting of Columbia River basinwide SNP genetic baselines for steelhead and Chinook salmon.
Development, maintenance, and reporting of Genetic Stock Identification Techniques for Snake River steelhead and Chinook salmon monitoring.
Reporting of spawner abundance, productivity, and genetic diversity of ESA listed steelhead and Chinook salmon in the Snake River basin.

Snake River GSI baseline-
NOAA specifically recommends that to demonstrate ESU/DPS viability a long-term strategy for monitoring genetic diversity be implemented that involves the development of a SNP baseline for each population within each MPG and ESU/DPS (Recommendation 16; Crawford and Rumsey 2011). These SNP baselines will also provide the known origin, reference population data necessary for Genetic Stock Identification (GSI). Snake River steelhead and Chinook salmon SNP baselines will be refined and maintained through annual population sampling and genotyping. Ultimately, annual sampling plans will be based on resolution of initial baselines and manager’s specific needs.

Snake River steelhead and Chinook salmon stock composition estimates-
NOAA recommends that to demonstrate ESU/DPS viability, annual documentation of a variety of biological parameters (including adult and juvenile abundance, age distribution, sex ratio, length, and run timing) is needed at the population, major population grouping, and ESU/DPS level for each listed species (Crawford and Rumsey 2011). Genetic stock identification (GSI) of steelhead and Chinook salmon adults and juveniles at Lower Granite Dam should be able to provide estimates of these parameters annually at the MPG and ESU/DPS level. GSI uses multi-locus genotype data from reference populations (presumably representing all contributing stocks) as a baseline and a complimentary set of genotype data from mixtures of fish of unknown origin to estimate stock proportions within the mixture (Shaklee et al. 1999; Anderson et al. 2008). In the Snake River basin, studies have indicated that both Chinook salmon and steelhead exhibit significant genetic structure at the watershed (or subbasin) level (Moran 2003; Narum et al. 2007; Nielsen et al. 2009). Previously, researchers have made use of this genetic structure to identify the stock origin of kelt steelhead at Lower Granite Dam (Narum et al. 2008b) and to estimate the stock composition of wild and hatchery Chinook salmon over Lower Granite Dam (Smith 2007). This project expands and evaluates GSI technologies to estimate genetic stock contributions of wild and juvenile Snake River steelhead and Chinook salmon as they migrate past Lower Granite Dam. This project also provides several measures of genetic diversity and life history characteristics for adult steelhead and Chinook salmon detected at PIT tag arrays in the Snake River basin.