Evaluating Adaptive Divergence Between Migratory and Nonmigratory Ecotypes of a Salmonid Fish, Oncorhynchus mykiss

Abstract

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. The use of these two approaches in parallel is especially attractive in nonmodel 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 nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (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. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci 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.

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

“…Genome-wide association analysis suggested different genomic regions underlying different phenotypic components of the migratory phenotype (Hecht et al, 2012(Hecht et al, , 2013. Annotation of genome regions linked to significant SNPs indicated they were likely in regions associated with physiological processes important in migration (Hecht et al, 2013;Hale et al, 2013). The study identified a number of new loci associated with migratory traits and corroborated loci that had been identified in earlier QTL studies.…”

Genome‐wide nucleotide diversity of hatchery‐rearedAtlantic andMediterranean strains of brown troutSalmo truttacompared to wildMediterranean populations

“…A matrix of SNP variation in the variant call format (VCF) was produced with populations, using (1) a minimum percentage of 80% of genotyped individuals in a population to process a locus for that population, (2) a minimum number of six populations where a locus must be present to be processed ( i.e . a locus must be present in all samples), (3) a minimum minor allele frequency of 2% and (4), since only 10 individuals per population were considered (Table ), loci that were heterozygous at 90% were discarded in order to remove paralogous loci (Hale et al ., ). The loci passing these filters were exported in VCF.…”

Mechanisms of Thermal Tolerance in Reef-Building Corals across a Fine-Grained Environmental Mosaic: Lessons from Ofu, American Samoa

“…Data from Ofu indicate that thermal tolerance is a polygenic trait, where a number of alleles of small effect across many different cellular pathways are responsible for elevated thermal tolerance of the HV pool corals Palumbi et al, 2014). Polygenic traits are a common feature of high gene flow species and occur widely in marine populations (Limborg et al, 2012;Hale et al, 2013;Pespeni et al, 2013;Laporte et al, 2015;Barney et al, 2017).…”