Genomic signatures of natural selection and population structure in West Coast and Alaskan sablefish (Anoplopoma fimbria)

Abstract

Previous population genetic studies have not been able to find clear population genetic structure across the range of the sablefish (Anoplopoma fimbria) in North America. They have focused on using a relatively small number of genetic markers that are presumed to be neutral to the effects of natural selection. Genomic approaches enable researchers to examine variation at thousands of genetic markers throughout the genome simultaneously. This allows for the detection of markers influenced by natural selection. Many marine species have large population sizes leading to low levels of genetic drift that often cause little or no differentiation to be observed at neutral genetic markers. On the other hand, there is potential for significant adaptive variation to be present between populations even when levels of genetic differentiation at neutral markers are low. In marine fish species, studies of adaptive variation may help resolve genetic structure that is weak at neutral loci. In the present study, traditional population genetic analyses were used to examine differentiation among sablefish collected in the Bering Sea, Gulf of Alaska and off the West Coast of the United States. Individual based methods were used to investigate the possibility of cryptic population structure, and a landscape genomics approach was used to examine adaptive variation in the sablefish genome by a testing for associations between environmental conditions and SNP genotypes. Restriction site associated DNA sequencing (RAD-seq) was used to identify and genotype single nucleotide polymorphism (SNP) markers throughout the sablefish genome. Low and insignificant levels of population differentiation among survey areas were observed and the individual based methods support a single genetic cluster of sablefish across their North American range. The results are suggestive of high rates of gene flow or movement of sablefish in the northeast Pacific Ocean. The landscape genomic analyses found two SNPs to be associated with depth.