A Quest for Adaptive Variation among Brook Trout (Salvelinus fontinalis) Populations Exhibiting Prodigious Genetic Differentiation at Neutral Loci

Neutral drift and natural selection govern the variance of traits among demographically distinct populations.  We have employed a research framework that quantifies neutral and adaptive genetic variation among ecologically and evolutionarily distinct populations. We have collaborated in an extensive survey of putatively neutral allelic variation at 13 microsatellite DNA loci in over 27,000 S. fontinalis sampled from 700 collections comprising the species’ native range.  Traditional population genetic analyses identified prodigous levels of genetic differentiation at all spatial scales. Our recent efforts have focused on transitioning S. fontinalis from population genetics to population genomics by employing genotype by sequence and RNA-Seq analyses.  This massively parallel sequencing has allowed: 1) Identification and screening of large numbers of single and physically linked single nucleotide polymorphisms (SNP) within and among populations; 2) Determining each markers selective status (i.e., neutral or naturally selected (directional and balancing)); 3) Contrasting patterns and rates of gene flow between the two classes of markers; 4) Establishing surrogate SNP loci to more accurately delimit units of conservation, patterns of divergence, and metapopulation assemblages; and 5) Identifying markers exhibiting adaptive variation indicative of resiliency and persistence signatures (e.g., SNPs associated with metabolically variable genes/gene systems; and immunologically critical gene systems).