This project will develop and implement GSI methodologies within the Snake River basin for wild Chinook salmon and steelhead passing Lower Granite Dam. Project leads will ensure that all SNP genotype data generated from this project will be standardized and available for Columbia River genetic baseline expansions (CRITFC 200890700-objective 2).  In addition, side by side comparisons of Parentage Based Tagging datasets (BPA project #201003100) and GSI datasets, will allow the identification of a single set of SNPs that can be used for both technologies.  This will allow the integration of sampling programs at Bonneville and Lower Granite Dam and in Columbia River and Snake River mainstem fisheries such that any sampled wild adult can be included in mixture analyses to determine stock composition and any sampled Snake River hatchery adult can be assigned to a stock and cohort. Once standardized SNP marker sets have been developed and tested, this project will genotype 2000 adults and 2000 juveniles (for each species) annually as they migrate past Lower Granite Dam on the Snake River.  An additional 1000 samples (for each species) will be genotyped annually as part of generational genetic baseline development and maintenance.  This sampling and genotyping will provide a robust baseline from which GSI mixture analyses can be performed, and will also provide temporal monitoring of genetic diversity/structure across the basin allowing estimation of gene flow and effective population size. Incorporating age and sex information collected simultaneously from migrating adults and juveniles will provide data on abundance and biodiversity of Snake River Chinook salmon and steelhead that have previously been unavailable for managing wild stocks in the basin.

In the ISRP review of Proposal 201002600: Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam, they suggested that three items be addressed in contracting and future proposals:

1.) They suggested that while the GSI methodology was established in the proposal that the analytical framework for including this information in status and trends analysis and reporting for steelhead and Chinook salmon was not provided.  

Specifically this project will provide managers working on population viability assessments and recovery efforts for Snake River steelhead and Chinook salmon (e.g.  NOAA Fisheries Service salmon recovery team):
a. More detailed descriptions of genetic population structure for steelhead and Chinook salmon in the Snake River basin than what has been previously available.  This will allow better information for delineating extant populations of listed Chinook salmon and steelhead within the Snake River ESU.  Currently, independent populations are defined for VSP purposes using a definition that is equivalent to Ricker’s (1972) characterization of a stock, that is, “an independent population is a group of fish of the same species that spawns in a particular lake or stream (or portion thereof) at a particular season and which, to a substantial degree, does not interbreed with fish from any other group”.
b. Annual, stock specific estimates of adult and juvenile abundance in the Snake River basin above Lower Granite Dam.  This will allow estimates of abundance and productivity statistics including:  Number of natural origin spawners and natural origin recruits, lambda (median annual population growth rate based on four-year running), Number of recruits per spawner.
c. Diversity estimates on a stock specific basis including life history traits (run-timing, size and age at return, sex ratios, etc.), estimates of effective population size, and measures of genetic differentiation/similarity of hatchery populations to wild populations.

2.) They suggested that the rationale for sampling 2000 individuals at LGD needs to be justified.  

Sampling of juveniles and subsequent stock specific estimates of juvenile abundance will be required to estimate the statistics described above (mean of natural origin recruits, mean of recruits per spawner, etc.).  The sample size of 2000 was selected because this sample size should allow us to partition the run by sex and most abundant age classes, while maintaining sample sizes needed for mixture analyses between 400-600.  These sample sizes should be adequate to ensure that stock proportion estimates are within ±5 percentage points of the true values 90-95% of the time (Thompson 1987).

3.) They suggested that it may be useful to consider ways to integrate and coordinate projects 201002600, 201003100 and 200890700 under an umbrella proposal that clearly identifies the  responsibilities of the individual projects.

Due to the size of these projects, the fact that project 200890700 was initiated in 2008, and the fact that each project has very specific goals and objectives, we do not feel that it would be efficient or practical to attempt to combine these projects under one umbrella proposal.  These projects will be highly integrated and coordinated however.  Not just among themselves but with other genetic labs and projects throughout the Columbia River basin.  Both IDFG and CRITFC scientists have substantial experience collaborating with other coastwide genetic labs to standardize microsatellite loci for both steelhead and Chinook salmon (GAPS-Seeb et al. 2007; SPAN-Stephenson et al. 2008).  Both IDFG and CRITFC scientists are already involved in coordination efforts to sample baseline populations and standardize SNP loci for both species (SNP Workshop III, March 22-24, 2010 and Coastwide Salmonid Genetics Meeting Jun 2-4, 2010).