Phylogeographic analysis of rainbow trout in Alaska.

Genetic population structure of Alagnak River rainbow trout.

This study is testing genetic relationship among different population segments of rainbow trout identified with unique life histories in our recent Alagnak River telemetry study .Preliminary analyses show limited genetic differentiation among trout populations with unique life histories within this basin.  This investigation adds to our speculation on the extent to which reproductive isolation follows ecomorphological divergence among lineages of Oncorhynchus mykiss.

Genetic population structure of Sashin Creek steelhead and lake resident rainbow trout in southeast Alaska.

This study is looking at populations of rainbow trout supplemented in lakes in southeast Alaska 30 years ago that were derived from one anadromous steelhead population in Sashin Creek.  We are investigating the extent to which genetic diversity found in the current anadromous populations is found in the isolated lake populations.  We have also investigated one lake population (Deer Lake) where genetic profiles indicate that recent subsequent supplementation from other trout stocks has occurred.

Genetic population structure of steelhead and rainbow trout of the Aleutian Islands.

In this study we are working cooperatively with Aleutian Tribal members to collect samples of fin tissue for genetic analyses of steelhead and rainbow trout in this area. These samples will be to study the relationship between resident rainbow trout and anadromous steelhead in different populations. We will also use these data to compare the evolutionary genetics of Aleutian steelhead with steelhead in other parts of Alaska, the Pacific Northwest, California, and the Kamchatka Peninsula in a broader biogeographic analysis of steelhead in the Pacific.

Investigations on antifreeze genes and population structure in Alaska blackfish (Dallia pectoralis).

In this study we are looking at the unique physiological adaptation found in Alaska blackfish that allows survival at very cold temperatures. Antidotal evidence suggests that these fish can be frozen for long periods of time and recover fully. We plan to search the blackfish genome for genetic surrogates for antifreeze genes already depicted in other coldwater fishes such as Atlantic cod, flounder, and several Antarctic fishes. If antifreeze genes are found, we will compare their sequence with currently described fish antifreeze genes to test the hypotheses of co-evolution and a marine origin for this adaptation.

Investigations on population genetics of Pacific halibut in Alaskan waters.

We are investigating the genetic population structure of Pacific halibut found in the Gulf of Alaska and in Glacier Bay by amplifying microsatellite loci from different populations. This study will tell us about the local population structure, gene flow and migrations patterns in Pacific halibut and is linked to out test of satellite pop-up tags for defining critical marine habitat.

Genetic analyses of coho colonization events in Glacier Bay.

This study incorporated genetic analyses of recently colonized coho populations in Glacier Bay. We have developed a coho microsatellite database that allow us to test correlations between the time a stream was free from glaciation and the genetic diversity found among the coho in that stream. Preliminary results from this study show significant correlations among geographic distance, time since de-glaciation of a stream, and coho allelic diversity. These results hold significant inference for restoration of salmonids in natural systems by demonstrating how a single colonization event can promote rapid population diversification in a few generations despite threats of genetic bottlenecks and/or founder effects within the basin if adequate, high quality habitat is available.

Genetics of Pacific Salmonids

Genetic population structure of steelhead populations in the Snake River, Idaho.

This project will use microsatellite analyses to look at hatchery and wild populations of steelhead in the Snake River. The Snake River is a tributary of the Columbia River and wild steelhead in this system are endangered. The issue of dams on the Columbia River and their impact on wild salmonid populations is highly controversial. This study will help address some of this controversy by allowing us to define remnant wild stock of steelhead, the proportion of genetic diversity remaining in specific hatchery populations and the effects these hatchery programs have had on wild fish gene pools, and the degree of introgression by other salmonid species found in putative wild steelhead in the Snake River.

Molecular systematics and evolutionary status of the trout of the Sierra Madre, Mexico.

This project has identified unique genetic diversity in populations of freshwater trout in the Sierra Madre Mountains of north central Mexico. These fish appear quite ancient and are genetically distinct from other populations of trout found in the Pacific Ocean and interior freshwater systems of the southwest. Recent microsatellite analyses have supported earlier findings from mtDNA that these fish deserve unique species status in Oncorhynchus.

Sequence analysis of microsatellite loci in chinook salmon.

In this study we are analyzing sequence variation and cryptic nucleotide substitutions in commonly used microsatellite loci for chinook salmon in the Central Valley in California. These data will allow us to evaluate conservation and management decisions made using size-class data alone in microsatellites. This type of research is important in our understanding of the evolutionary history of microsatellite loci and in the weight we give to genetic factors in analyses of stock structure and population viability.

Genetic population analysis of Lahontan cutthroat trout in Nevada, California, Utah and Oregon.

This study looked at the evolutionary relationships between hatchery and wild populations of Lahontan cutthroat trout in the Great Basin and their evolutionary history. These data are assisting in management decisions made by the Department of the Interior for the restoration of trout in Lake Tahoe, the Truckee River, and Pyramid Lake. Preliminary data indicate that there are at least two geographic lineages of Lahontan trout in this area. One lineage is associated with populations from the East Carson River in the western basin and the other is associated with populations thought to be derived from an original Pyramid Lake strain that was transferred to the Pilot Peak drainage before the original Pyramid Lake population of cutthroat trout went extinct.

Allelic standardization for microsatellites loci in Pacific salmonids.

ASC-BSO is a participant in the organizational effort to standardize allelic signatures for salmonid microsatellite loci across different laboratory platforms, different amplification equipment, and among different laboratories. This is a very important step in the development of microsatellite systems in molecular genetics and in its use for identification of stock structure, and the conservation and management of fisheries.

Forensic analyses of southern steelhead.

California steelhead at the southern extent of their range were listed as an endangered species in 1997. Our lab assists the National Marine Fisheries Service by providing forensic tests on mitochondrial DNA amplified from salmon tissues that are thought to represent a “take” under the U.S. Endangered Species Act.