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Genetics Tools:

Much of our work depends on determining genotypes of fish. In 2003, we set up an genetics laboratory here at the Conte Anadromous Fish Research Center that now forms an integral part of the Ecology Section. Capabilities include DNA extraction, PCR amplification, and genotyping on a sequencer. The genetics capability is used to analyze samples in Ecology Section projects and to support cooperative efforts.

Development and application of genetics tools for natural resources management: A major goal of the Ecology Section is the development and application of genetics tools to management and research. The application of genetics tools began in 1996 when the USFWS established that the top two research priorities for Region 5 were a fry mark for stocked fry and genetics-based brood stock management. In response, we initiated and developed a large-scale, innovative approach to using genetics tools to simultaneously address both research priorities. This program has completely reorganized Atlantic salmon hatchery practices in the Connecticut River and similar programs have been initiated in the Maine Atlantic salmon hatcheries. In the Connecticut River, the program has been underway since 1997 and starting in2004 the marking program allowed assignment of outmigrating smolts to tributary of stocking on a full Connecticut River watershed scale.

Brood stock management: In small captive populations, like the Connecticut River Atlantic salmon brood stock (< 100 individuals), it is critically important to manage matings to avoid inbreeding and to maintain existing genetic diversity. We established protocols for mating that use genotypes of adults to determine relatedness and avoid matings of closely related individuals. Working with hatchery managers, we developed software and tools to simplify the procedure, although there were some fairly major changes required. We are now over a decade into this program and the continued low numbers of fish have recently required the incorporation of complex factorial mating designs in an attempt to balance maintenance of genetic diversity with the potential loss of rare alleles. This has been a collaborative effort with state fisheries managers, USFWS hatchery managers, and other program personnel.

Fry marking: Approximately 9 million Atlantic salmon fry are stocked annually in the Connecticut River basin. In concert with project the brood stock management program, we have established a fry marking program to allow determination of location of stocking a large proportion of the stocked fry. The basic premise is that we can create identifiable F2 families (grandchildren of adult returns mated) that can be stocked in known locations. As the fish from various stocking locations combine in the mainstem during outmigration or as returning adults, we take a fin clip, determine family membership and can therefore establish location of stocking. This allows a watershed-scale assessment of relative productivity of the stocking locations. In 2002 and 2003 approximately two-thirds of the stocked fry in the Connecticut River and most of the fry above the dam in Turners Falls were part of the marking program. In the spring of 2004, age-2+ smolts were sampled at mainstem dams as they left the river (analysis of these data is ongoing). In addition to the relative productivity of stocked basins, we will also be able to determine timing of migration and sizes of fish from the various basins. Combining these data with environmental data from the basins (e.g., temperature profiles, numbers of dams) we should be able to determine factors that limit freshwater salmon production.

Brook trout spatial population structure: According to the Nature Conservancy (TNC), the top two science needs for freshwater fish in the Northeast are understanding the effects of habitat fragmentation and flow alteration on population structure. We are involved with three studies examining brook trout population structure. In Virginia, we are working with US Forest Service personnel to identify subpopulation structure and effective population size in streams containing brook trout. In Connecticut, we are working with a graduate student who is estimating the effects of thermal barriers to brook trout population substructure. An important part of this effort, is scaling our model up to a large enough spatial scale to be useful for managers. In a third and much broader study (across four New England states), we are collecting nested data at the catchment and sub-watershed spatial scale to explore population connectivity in the context of scaling up our population persistence models. With close collaboration with TNC, we have developed models of connectivity as well as flow and temperature effects. Once finalized, TNC will incorporate model results into a GIS tool to allow managers prioritize barriers for removal/repair given limited resources.

Gene expression of alternative life history strategies in Atlantic salmon: Working with Nadia Aubin-Horth, we have identified differences in gene expression among Atlantic salmon with different life history strategies. The results help understand mechanisms involved with life history expression and evolution and maintenance of alternate life histories.

Publications:

Aubin-Horth, N. C. Landry, B. H. Letcher, and H. A. Hofmann. 2005. Alternative life-histories shape different brain gene expression profiles in males of the same population. Proc. R. Soc. B., 272:1655-1662.

Aubin-Horth, N. B. H. Letcher, and H. A. Hofmann. 2005. Interaction of rearing environment and reproductive tactic on brain gene expression profiles in Atlantic salmon. J. Hered. 96:261-278.

Letcher, B.H, and T.L. King. 2001. Parentage and grandparentage assignment with known and unknown matings: application to the Connecticut River Atlantic salmon restoration. Can. J. Fish. Aquat. Sci., 58: 1812-1821.