USFWS
Fisheries & Ecological Services
Alaska Region   

 

Conservation Genetics Laboratory
Selected Projects

These projects are a sample from a larger body of projects that are managed by the Conservation Genetics Laboratory. More information on projects is available on request
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Landscape Genetics
This study will combine landscape genetics with a comparative analysis of population structure to address the question “what are some of the spatial, environmental, ecological and life history factors influencing genetic diversity of Chinook, chum, and coho salmon in western Alaska?”, as there is currently a paucity of information what factors are influencing genetic variation in Chinook, chum, and coho salmon in western Alaska.  A Geographic Information Systems (GIS) will be used to measure broad and fine scale environmental (e.g. stream gradient) and ecological (e.g. ecoregion) variables.  A combination of statistical methods will be used to evaluate the influence of these variables on the spatial distribution of genetic diversity in each species.  A multispecies comparison of these results will be used to infer the extent to which demographic and life history differences among the species influence the distribution of genetic diversity.  The results will be useful for defining conservation units and for predicting how genetic diversity may change in the face of small scale (e.g. localized habitat destruction) and large scale (e.g. global warming) environmental perturbations.

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Genetic detection of Canadian-origin Chinook salmon in U.S. tributary streams
Chinook salmon are the most valued subsistence and commercial fishery resource in the Yukon River. About half of the Chinook salmon run is headed for Canada, and these fish account for 47 to 67% of the harvest. Monitoring projects are usually focused on ensuring adequate escapement of adult salmon to spawning grounds. Less monitoring is conducted on juveniles, but ensuring that juveniles have adequate rearing habitat is equally important to maintaining the health and productivity of Chinook salmon.

After emergence from river gravel, juveniles Chinook salmon feed and grow in tributary streams of the Yukon River throughout their first summer, over-winter in freshwater, and usually leave rearing areas for marine waters during the second spring or summer. The importance of freshwater rearing areas to juvenile Chinook salmon, including non-natal streams, is well documented in the upper Canadian portion of the Yukon River drainage. Data from mainstem and tributary trapping studies in Canada suggest that many juveniles leave their natal streams after emergence, drift downstream for several days in the mainstem current, and then seek out clear freshwater habitats to feed and possibly over-winter. The extent to which juveniles leave their natal streams is not well known.

Little information is available on juvenile Chinook salmon use of non-natal stream habitat in the upper U.S. portion of the Yukon River, above any known U.S. spawning populations. Because the extent to which Canadian juvenile Chinook salmon leave their natal habitat is unknown, it is necessary to study this section of the river. Without this documentation, the value of these habitats to juvenile salmon can not be determined and habitat protection or rehabilitation can not be initiated, which could negatively impact this resource. In this study, in collaboration with the Fairbanks Fish and Wildlife Field Office, we will sample juvenile Chinook salmon from non-natal streams in a 260 kilometer segment of the Yukon River between the Circle, Alaska and the U.S./Canada border. Our goals are to: 1) document presence and length-weight relationships of juvenile Chinook salmon; 2) determine their genetic population origin; and 3) describe non-natal stream rearing characteristics. These results will provide an initial assessment of the importance of this habitat for rearing and the extent to which Canadian juvenile Chinook salmon rear in U.S. non-natal streams.

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Yukon River Chum Salmon – Rapid Response
Multiple stocks and two seasonal races of chum salmon spawn in the Yukon River, which flows 3,200 kilometers through Alaska and Canada. Chum salmon are an important resource for subsistence users in both countries.  A major goal of harvest management is to ensure that sufficient numbers of fish return to their spawning grounds, while providing harvest opportunities. Furthermore, fishery managers have additional obligations to conserve and equitably share fall chum salmon with Canada pursuant to the Pacific Salmon Treaty. While essential for effective management, this is a difficult task in such a large system where harvests consist of mixtures from many stocks, up to thousands of miles from spawning grounds and months prior to spawning.  However, genetic mixed-stock analysis allows us to provide in-season stock composition estimates of Pilot Station test fishery harvests. With the assistance of the Office of Subsistence Management, and the Alaska Department of Fish and Game, we provide State and Federal fishery managers allocation information from the test fishery at this lower river position, within a day or two of receiving the test fishery samples.  This provides unique, timely, stock-specific information to assist fishery managers in meeting conservation, allocation, and harvest goals.

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Chinook Heritability
Many Chinook salmon in the Kuskokwim River are harvested using “large mesh” (8 inches or larger) gillnets that preferentially capture older and larger fish.  There is interest in determining if this selective fishery has a population-level impact on traits such as adult size and age.  In order to fully evaluate this issue realistic estimates of trait heritability are needed.  This selective fishery may also indirectly influence abundance if reproductive success (number of adult progeny) is greater for larger fish.  In order to evaluate this issue estimates of family size for a sample of parents of known length are needed.  In this study we examine both issues in Chinook salmon from the Tuluksak River.  Our objectives are to 1) estimate the heritability of adult size, growth rate, and age and the genetic covariance among these traits, in males and females, and 2) determine if family size is related to size of adult parent.  We will use recently developed pedigree reconstruction methods to identify full-sib and half-sib groups from the 2003 cohort (adults born in 2003).  These groups will be used to estimate heritability and evaluate family size.  The results of this study will provide salmon fishers and fishery managers a better understanding of0 the possible impacts of a size selective harvest on Chinook salmon.

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Migration patterns of Kuskokwim River coho salmon
Coho salmon are the second most abundant salmon in the Kuskokwim River and provide the largest commercial harvests, making them a mainstay to the ecology and economy of the region. The preponderance of enumeration projects for coho salmon in the Kuskokwim River are distributed in the lower and middle portion of the drainage. Little is known about the abundance of coho salmon in the upper portion of the drainage, yet these fish are genetically distinct and likely represent an important component of the genetic and life history variation. In this project, we will obtain run timing and relative abundance information for this stock by estimating the stock composition of coho salmon sampled from the Bethel test fishery located in the lower Kuskokwim River in order to provide a complete picture of the way the genetic diversity of coho salmon is structured in this large system to inform both management and conservation efforts alike.

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Behm Canal Eulachon Genetics
Recent runs of eulachon in tributaries to Behm Canal (Unuk, Klahini and Eulachon Rivers) have been extremely low (USFS, unpublished data), raising conservation concerns. In 2005 and 2006, nearly total run failures resulted in no subsistence or personal use harvest in these rivers.  In Alaska, eulachon are considered to be an important subsistence and personal use fishery. In Canada and the lower contiguous U.S., run strength of eulachon populations and spawning distributions between and within rivers can vary dramatically. This variability has been observed in Alaska as well, making management of these populations difficult..

Population discreteness for eulachon within and among river systems in Alaska and Behm Canal is unknown.  In fact, very little information exists on eulachon in general.  Initial, pilot genetic studies focused on eulachon from British Columbia and Washington observed little population structure, suggesting that eulachon exist as large metapopulations with low levels of genetic diversity. However, a more recent and thorough study of eulachon from this area found that eulachon exhibit much higher levels of genetic diversity than originally thought with significant differences occurring among eulachon from different inlets areas. These contradictory results further complicate management. It is clear that an understanding of eulachon genetic population structure is necessary to identify appropriate management units for maintenance of biodiversity and productivity. In this study, in collaboration with the U.S. Forest Service, we propose to investigate the population discreteness of eulachon across Alaska..

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Southwest Dolly Varden
Dolly Varden are an important subsistence resource in southwest Alaska, where some communities harvest more than 10,000 fish annually. Dolly Varden abundance in the Togiak National Wildlife Refuge (TNWR) is monitored through subsistence catch data from the Togiak River and through weir counts on the Kanektok and Goodnews rivers, which can vary greatly across years. These three systems represent approximately 85% of the production of Dolly Varden in the TNWR. Counts include fish returning to spawn, but also include fish entering freshwater to overwinter, making it impossible to interpret trends in these data because poor returns of some ocks may be masked by greater production in other. In collaboration with TNWR staff, we are collecting genetic data from Dolly Varden sampled from rivers in southwestern Alaska to assemble a baseline for use in future mixed-stock analysis studies to estimate stock-specific abundance. Using genetic analyses to estimate the origin of Dolly Varden in various aggregates will allow us to develop a much clearer picture of critical parameters, such as the movement patterns and abundance, for this ecologically, economically and culturally important species.

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Prince of Wales Steelhead
A limited Federal subsistence fishery for Steelhead was approved in Southeast Alaska in 2002.  However, lack of accurate information on population structure and population abundance hampers efforts to assess the impacts of this fishery on individual populations and population complexes.  The steelhead populations on Prince of Wales Island (POW) are particularly vulnerable because logging roads built during the 1980s provide access to many of the island streams.  In this study, we partner with the Bureau of Indian Affairs, and the Alaska Department of Fish and Game Division of Sportfish, to examine the population abundance and genetic diversity within and among selected streams on POW.  The results of the study will provide managers estimates of the level of population structure that may be used to evaluate and adjust harvest management strategies.  In a related issue, the genetic data will provide the beginning of a baseline that may be used to assess the origin of steelhead by-catch in the various fisheries..

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Katmai National Park Sockeye and Kokanee
Sockeye salmon diversity within the Katmai National Park and Preserve (KATM) is poorly understood.  This lack of knowledge hinders the ability of the U.S. Park Service to manage this resource in accordance with agency goals and congressional mandate.  Of particular interest is the rare presence in this region of the freshwater resident form of sockeye, called kokanee.  In this study we partner with the U.S. Park Service to examine the level of genetic diversity within and among populations of sockeye salmon and examine the genetic relationship between sockeye and kokanee.  The results will help the U.S. Park Service achieve it’s goal of preserving diversity within the KATM..

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Coastal cutthroat trout and Dolly Varden in SE AK, persistence of isolated populations
The health and persistence of coastal cutthroat trout populations throughout their range have been repeatedly called into question over the past two decades.  Populations in Alaska are assumed to be healthy, but little evidence is available on their genetic diversity. Furthermore, the effects of isolation and small population sizes on genetic diversity on any species is a major area of concern in conservation genetics.  Here, along with University of Montana and University of Alaska Southeast, we are exploring the population structure of coastal cutthroat trout from multiple small streams in Southeast Alaska and the persistence of those isolated above natural migration barriers, asking questions such as, how are populations related (within and between streams) and how should they be managed? What affect does isolation (5-10 thousand years) have on genetic variability and how is adaptive variation maintained? And do above barrier populations augment the genetic diversity of the below barrier populations?.

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Yukon River chum telemetry
In 1999, a radio telemetry study was conducted on Yukon River chum salmon wherein 1050 fish were radio tagged and sampled for genetic analysis. Of the tagged fish, 629 ended up in terminal locations or were harvested, leaving the fate of large percentage of the fish in question. Tagging effects and previously unknown mainstem Yukon River Flats spawning may explain these results. In this study, we are conducting genetic mixed-stock analysis to estimate origin of the samples to compare the results with the radio tag estimates to evaluate tagging effects, and assess the existence of a Yukon River Flats spawning stock..

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Fountain Darter Genetics
Etheostoma fonticola is a small endangered percid native only to the upper San Marcos and Comal rivers in central Texas. Critical habitat is strongly influenced by the amount of spring water emerging from the Edwards Aquifer at the headwaters of each river.  Spring discharge is affected by the amount of precipitation on aquifer recharge areas and the amount of water pumped from the aquifer. Droughts in central Texas occur approximately every 5 years and during the severe drought of the 1950s, the Comal Springs ceased flowing for 5 months, possibly extirpating E. fonticola from this location.  Fish were reintroduced by Southwest Texas State University personnel in 1975 and 1976 using 457 fish from the San Marcos River.  Groundwater pumping rates have greatly increased from the 1950s, and if another substantial drought were to occur, the Comal River could go dry for months or even years.  The contingency plan calls for adequate numbers of darters to be removed from the wild to establish a genetically representative founding broodstock.  Although numbers of breeding pairs are outlined in the contingency plan, these numbers are not based on the genetic needs of the species, but rather, on feasibility of animal care and housing.  We do not know if the numbers outlined in the contingency plan will adequately cover a reasonable percentage of the genetic diversity reflected in the wild populations.  Genetic variability needs to be reflected in refugium population, so that in the event of drought and future reintroduction, those darters introduced will have a better chance at maintaining enough variability and genetic flexibility to be able to respond to future selective pressures.  In this study, we are collaborating with the USFWS Austin Ecological Services Field Office to examine population structure and genetic variability in E. fonticola and determine if the current contingency plan is adequate for protection of the species.  Furthermore, the known history of bottlenecking and reintroduction into the Comal provides a unique opportunity to examine short-term genetic divergence under a variety of demographic circumstances.  .

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Last updated: March 8, 2011