Conservation Genetics and Genomics of Brook Trout (Salvelinus fontinalis) Populations: Identification of the Functional Unit of Management

While the current paradigm for conservation of species and associated habitats places emphasis on recognition and protection of irreplaceable evolutionarily distinct lineages, the identification of adaptive features must become a priority and may best be protected by maintaining evolutionary potential in the form of heterogeneous landscapes, migratory corridors, and viable populations rather than protecting specific phenotypes.  However, habitat restoration in the form of migratory corridors is frequently an unrealistic conservation goal for many range/habitat compressed brook trout populations.  Therefore, resource managers must plan for an evolutionary future for populations of this trust species, as such, ecological and evolutionary processes—those that maintain genetic diversity and provide the raw material for evolution and adaptation of populations—must be explicitly identified and represented in conservation and restoration efforts.LSC is employing a research framework that involves quantifying neutral (e.g., genetic drift) and adaptive (i.e., natural selection)genetic variation among ecologically and evolutionarilydistinct brook trout populations.  Phase I of this research has witnessed an extensive survey of genetic variation at 13 microsatellite DNA loci in over 15,000 brook trout sampled from 420 collections comprising the species’ native range.  Analyses have identified prodigous levels of genetic differentiation at all spatial scales with nearly all geographic populations existing as discrete populations (i.e., a punctuated distribution) often isolated by unacceptable habitat (e.g., natural and man-made barriers, unacceptable water temperature).In addition to traditional population genetics analyses, retrospective monitoring (i.e., coalescent simulations) of brook trout populations has illuminated previously undetected demographic histories and evolutionary relationships among populations and shed light on past and future evolutionary trajectories of populations at previously intractable scales. Phase II is designed to identify a suite of physiologically and immunologically relevant genes and consists of de novo transcriptome assembly and annotation for brook trout (currently underway).  This will be followed by the quantification of whole-genome comparative gene expression profiles generated from deep sequencing (e.g., RNA-seq) to identify genes exhibiting differential expression in fish representing a broad latitudinal and elevational distribution.  Populations exhibiting superior capabilities (e.g., genes contributing to adaptive variation) will be identified and this information can be used to assist in prioritizing restoration and conservation efforts.