Abernathy Fish Technology Center
Pacific Region

Applied Research Program in Conservation Genetics

Capability/Technical Service - Characterization of genetic diversity within and among natural populations.

Definition. Populations of a species may diverge from one another when geneflow (migration) between populations is limited and when environments that populations are in differ in the selective pressures on those populations. This commonly results in the genetic resources off the species being distributed among several populations. Panmixia, a state of unlimited geneflow between all populations, limits the potential for adaptation to different environments in which individuals of the species are distributed. Pacific salmon and freshwater fish species generally do not exhibit panmixia and more often exist as a series of populations between which geneflow is limited (i.e. sub-populations). Decisions regarding conservation priorities and conservation actions can be difficult to make in the absence of knowledge of geneflow among populations. This can be true on a recent temporal scale, such as determination of the degree of interbreeding between wild and hatchery fish with in a system, or over a longer temporal scale, such as designation of the evolutionary units important to that species.

Sample Projects

1) Genetic Analyses of Bull Trout in Mount Rainier National Park, WA
Bull trout are listed as threatened throughout their range. Genetic data is seen as an important piece of information to guide conservation and management activities for local populations such as those in Mt. Rainier National Park. Prior to this study, no genetic data existed for this local bull trout population, however. The objective of this project was to examine levels of genetic diversity among local spawning populations of bull trout in three watersheds in Mt. Rainier National Park. This information will be used to guide conservation and management decisions for bull trout found within the park.We used a set of 12 standardized genetic markers to examine genetic variation both within and among bull trout populations within Mt. Rainier National Park. We performed genetic analyses on 100 bull trout from three watersheds within Mt Rainier National Park. We compared the levels we observed to other populations found throughout the species range. We found that that genetic diversity was significantly lower above contemporary barriers. We also observed significant genetic differentiation between populations located above barriers compared to populations located below barriers.
Partners National Park Service

Bull trout habitat in Mt Rainier National Park, WA, NPS Photo

2) Genetic Analyses of Bull Trout in the Deadwood and Payette Rivers, ID
Bull trout populations have become fragmented throughout the species range due to the construction of barriers. Population fragmentation often results in a reduction in genetic diversity. In this study we examined the effects that barriers and fragmentation had on bull trout populations in the Deadwood/Payette River system, ID. Our objective was to examine the genetic effects that historical and contemporary barriers have on levels of genetic diversity within bull trout populations. We examined levels of genetic diversity within population both above and below barriers as well as the level of differentiation between populations isolated above and below barriers. Genetic samples were taken from bull trout populations above and below barriers throughout the Deadwood/Payette River system. We used 12 nuclear DNA markers to examine how genetic diversity was partitioned. We found that that genetic diversity was significantly lower above contemporary barriers. We also observed significant genetic differentiation between populations located above barriers compared to populations located below barriers.
Partners U.S. Forest Service, U.S. Bureau of Reclamation, USFWS, Pacific Region, Ecological Services

Lake habitat in Deadwood River basin, ID, USFWS Photo

3) Genetic Analyses of Coho Salmon Populations in Hood Canal, WA
The Hatchery Scientific Review Group (HSRG) recommended that the current coho stock at the Quilcene NFH be replaced with a new broodstock derived from an existing natural population in Hood Canal, Big Beef Creek. These fish were chosen in part to reduce the genetic risks of straying of returning hatchery-origin adults from Port Gamble Bay. Hood Canal co-managers felt that the HSRG lacked enough scientific information to make the recommendations for coho stocks used for on station release and tribal net pens. The Service wanted to secure data to scientifically evaluate those recommendations and then act on them. The objective of this study was to determine the genetic relationship of USFWS Quilcene National Fish Hatchery (NFH) stock relative to natural populations within Hood Canal and then use this genetic information to help determine if Quilcene NFH coho are straying and spawning in Hood Canal tributaries. We used DNA markers to genetically compare 11 hatchery and 17 natural populations of coho salmon in Hood Canal. Out-of-basin populations served as genetic “outgroups” for quantifying the genetic similarity of hatchery and natural populations within Hood Canal. A report describing the results of this work was distributed to the co-managers, and an oral presentation of the results was given to staff at both Quilcene NFH and Quinault NFH. This effort provided information that helped the co-managers decide to maintain the current Quilcene NFH broodstock and to include 20% two year old males in their broodstock in order increase gene flow among years.
Partners NOAA Fisheries Manchester Laboratory, Northwest Indian Fish Commission, Point No Point Treaty Council, Washington Department of Fish and Wildlife, USFWS Quilcene National Fish Hatchery, USFWS Western Washington Fish and Wildlife Office.

Map of coho salmon populations in Hood Canal, WA. USFWS Graphic

4) Population Structure sand Genetic Characteristics of Summer Steelhead in the Deschutes River, OR
In identifying independent populations of ESA listed steelhead in the Deschutes River basin the Interior Columbia River Technical Recovery Team identified a number of important information gaps that needed to be addressed for effective steelhead trout management and recovery. This project will address those gaps. Limited information exists on the genetic differences between steelhead occupying the tributaries on the east and west sides of the lower Deschutes River below the Pelton Dam complex. Over half of the returning steelhead to the system have been out of basin strays and little is known about the reproductive success of these fish in the basin. Our objective is to describe population structure and genetic variability among steelhead occupying tributaries and the main stem downstream of the Pelton Round Butte Dam, evaluate the effect of out-of-basin strays on natural populations, and help select a broodstock source for reintroducing steelhead to currently inaccessible portions of the middle and upper basin. Nine hundred steelhead and redband trout were genotyped at 13 microsatellite loci from over 17 locations in the basin. Stray fish will be sampled at the Shears Falls trap. Genetic population structure will be determined and mixture analysis will be used to determine the genetic contribution of stray fish to the natural populations.
Partners The Confederated Tribes of the Warms Springs Indian Reservation, Columbia River Inter-Tribal Fish Commission, NOAA Fisheries, Northwest Science Center, Oregon Department of Fish and Wildlife, USFWS Columbia River Fisheries Program Office.

Last updated: July 29, 2014
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