Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms

Local adaptation is facilitated by loci clustered in relatively few
regions of the genome, termed genomic islands of divergence. The
mechanisms that create and maintain these islands and how they contribute
to adaptive divergence is an active research topic. Here, we use sockeye
salmon as a model to investigate both the mechanisms responsible for
creating islands of divergence and the patterns of differentiation at
these islands. Previous research suggested that multiple islands
contributed to adaptive radiation of sockeye salmon. However, the
low-density genomic methods used by these studies made it difficult to
fully elucidate the mechanisms responsible for islands and connect
genotypes to adaptive variation. We used whole genome resequencing to
genotype millions of loci to investigate patterns of genetic variation at
islands and the mechanisms that potentially created them. We discovered 64
islands, including 16 clustered in four genomic regions shared between two
isolated populations. Characterization of these four regions suggested
that three were likely created by structural variation, while one was
created by processes not involving structural variation. All four regions
were small (< 600 kb), suggesting low recombination regions do not
have to span megabases to be important for adaptive divergence.
Differentiation at islands was not consistently associated with
established population attributes. In sum, the landscape of adaptive
divergence and the mechanisms that create it are complex; this complexity
likely helps to facilitate fine-scale local adaptation unique to each
population.