Abernathy Fish Technology Center
Pacific Region

Applied Research Program in Conservation Genetics

Capability/Technical Service - Standardization of genetic markers and tissue banking/sample archiving.

Standardization of genetic markers.
Federal and State governments as well as tribal organizations, and universities commonly use genetic data to improve our understanding of genetic diversity in fish populations. Use of non-standardized genetic methods and markers make results obtained by one group difficult or impossible for other groups to use or validate. In the past this lead to redundant work by several laboratories. Personnel in the Applied Program in Conservation Genetics have provided leadership and continued support for coastwide standardization of genetic markers in Chinook salmon and steelhead salmon. In species for which standardized markers are not yet available, we take measures to adopt markers and methods that render data generated by AFTC comparable with those generated in other laboratories.

Tissue banking/sample archiving.
We archive tissue samples and extracted DNA for samples in the Pacific Region. This repository allows any results generated by our laboratory to be examined further or validated in the future. It also allows archiving of samples that are collected opportunistically in cases where no funding presently exists for anallysis of those samples. Archived samples are made available to other tribal, agency and university laboratories on request, under the conditions that they are returned following analysis and that results of analyses of the samples are made available.

Sample Projects

1) Conservation Genetics of Endangered Modoc Suckers
The Modoc Sucker, Catostomus microps, was listed as endangered under the federal Endangered Species Act in 1985. Due to relatively small population sizes and potential genetic bottlenecks, there remains concern that the current populations may lack the genetic diversity to maintain their long-term viability. Restricted distribution, small population sizes, habitat conditions and hybridization with the sympatric native Sacramento Sucker, C. occidentalis, are considered the principal threats to Modoc Suckers. Recent genetic research has confirmed that the two species do hybridize and that there has been some level of unresolved historic introgression. Our objective was to 1) determine the genetic diversities in all ten known Modoc Sucker populations and compare them with local populations of sympatric Sacramento Suckers; and 2) estimate genetic similarity and gene-flow between the two species and among Modoc Sucker populations. Eight microsatellite loci were genotyped in 95 samples of Modoc and Sacramento suckers. Individual fish were assigned to one of the two species based on multi-locus genotypes. All fish were assigned correctly, suggesting that these 8 loci are sufficient for species identification and should be useful in identifying hybrids.
Partners USFWS Pacific Region, Ecological Services

2) Current and Future Applications of Genetic Stock Identification (GSI) to Ocean Salmon Management
Several stocks of Pacific salmon are listed or being considered for listing under the U.S. Endangered Species Act (ESA) or Canada’s Species at Risk Act (SARA). As such it is critical to monitor the impact of harvesting on multi-species populations. Several possible methods exist for applying genetic data to improve harvest monitoring by the PSC. The Pacific Salmon Commision needs specific guidelines and recommendations on optimal ways to incorporate genetic data into their applications. Thus the Pacific Salmon Commission needs to develop recommendations for integration of Genetic Stock Identification information into a coordinated coast-wide management system to improve the ability of ocean fisheries to access abundant stocks within impact constraints established for other specific stocks and, to identify and quantify costs, implementation steps and timeframes to incorporate the recommendations. We were invited to participate in the Pacific Salmon Commission's Invited Workshops: Current and Future Applications of Genetic Stock Identification (GSI) to Ocean Salmon Management. Abernathy Fish Technology Center scientists have a lead authorship role in writing a comparison of genetic marker types for use by the Pacific Salmon Commission and in presenting this comparison to the Commission. Results from these workshops will be used by the Pacific Salmon Commission to make recommendations regarding GSI.
Partners Pacific Salmon Commission

3) Genetic Stock Identification of Adult Spring/Summer Chinook Salmon at Lower Granite Dam
Currently managers rely on coded wire tag program (CWT) and redd counts to estimate population abundance of endangered Chinook salmon populations in the Snake River. These methods have limitations for monitoring wild stocks and within river harvest. Our objective is to develop genetic based methods to assign mixtures of fish back to their geographic origins in the Snake River. To accomplish this objective genetic mixture analysis was used to estimate natural and hatchery contribution to the Snake River aggregate escapement at Lower Granite Dam. Scales taken from stratified-random sample of Chinook at Lower Granite Dam (n=2000) were genotyped at 13 microsatellite loci. Fish were also aged to determine the population composition and age structure of the aggregate run. Multi-locus genotypes for these 1000 fish plus the 1000 fish analyzed in FY06 were standardized to those used by the GAPS Consortium and then used to assign fish individually and proportionally to the Columbia River baseline.
Partners Columbia River Inter Tribal Fish Commission, Idaho Fish and Game, NOAA Fisheries Northwest Science Center

Lower Granite Dam Chinook salmon dendrogram
Last updated: September 23, 2014
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