Data from: Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss

Next generation sequencing and the application of population genomic and
association approaches have made it possible to detect selection and
unravel the genetic basis to variable phenotypic traits. Using the two
approaches in parallel is an especially attractive approach in non-models
organisms that lack a sequenced and annotated genome, but only works well
when population structure is not confounded with the phenotype of
interest. Herein, we use population genomics in a non-model fish species,
rainbow trout (Oncorhynchus mykiss), to better understand adaptive
divergence between migratory and non-migratory ecotype, and to further our
understanding about the genetic basis of migration. RAD tag sequencing was
used to identify Single Nucleotide Polymorphisms (SNPs) in migrant and
resident O. mykiss from two systems, one in Alaska and the other in
Oregon, USA. A total of 7,920 and 6,755 SNPs met filtering criteria in the
Alaska and Oregon, data sets respectively. Population genetic tests
determined that 1,423 SNPs were candidates for selection when loci were
compared between resident and migrant samples. Prior linkage mapping
studies using RAD tag SNPs were available to determine the position of
1,990 markers. Several significant SNPs are located in genome regions that
contain QTL for migratory related traits, reinforcing the importance of
these regions in the genetic basis of migration/residency. Annotation of
genome regions linked to significant SNPs revealed genes involved in
processes known to be important in migration (such as osmoregulatory
function). This study adds to our growing knowledge on adaptive divergence
between migratory and nonmigratory ecotypes of this species; across
studies, this complex trait appears to be controlled by many loci of small
effect, with some in common, but many loci not shared between populations
studied.