A Quest for Adaptive Variation from RNA-Seq and Genomic Shotgun Sequencing Among Brook Trout (Salvelinus Fontinalis) Populations Exhibiting Prodigious Genetic Differentiation at Neutral Loci

Given that both neutral drift and natural selection govern the variance of traits among demographically distinct entities, we are employing a research framework that involves quantifying neutral (i.e., differentiation due to genetic distance) and adaptive genetic variation (measured by mass gene expression profiling) among ecologically and evolutionarily distinct S. fontinalis.  As a first step, the U.S. Geological Survey and National Park Service has collaborated in an extensive survey of neutral allelic variation at 13 microsatellite DNA loci in over 17,000 S. fontinalis sampled from 400 collections comprising the species’ native range.  Traditional population genetic analyses identified prodigous levels of genetic differentiation at all spatial scales.  Coalescence-based analyses also illuminated previously undetected demographic histories and evolutionary relationships among populations.  Subsequent steps to identify the adpative genetic variation consist of the quantification of comparative gene expression profiles generated from deep sequencing (RNAseq) to identify genes exhibiting baseline (control) differential expression in S fontinalis representing the three life history forms (salter, coaster, and riverine), a broad latitudinal distribution (Labrador Sea to southern Appalachian Mountains), and a vast elevational differential (sea-level to mountaintop).  Comparisons of expression differences among these life history forms include miRNAs, metabolically variable genes/gene systems; and immunologically critical gene systems.