Genomic Islands of Divergence Show Strong Signatures of Selection among Three Ecotypes of Sockeye Salmon

Genomic islands of divergence are thought to play a significant role in the early stages of speciation and population differentiation.  However, the prevalence and importance of these islands in natural populations is largely unknown.  Here we used data from thousands of SNPs aligned to a linkage map to investigate genomic divergence among three ecotypes of sockeye salmon.  Neutral population structure was relatively low and was not partitioned by ecotype (F_ST = 0.01).  The majority of the genome reflected this neutral pattern, however we found five genomic islands displaying extremely high levels of divergence among ecotypes.  The most prominent genomic island contained six loci with F_ST values greater than 0.14.  Alignments to the Atlantic salmon genome and other resources revealed that the peak of this island contained a non-synonymous mutation in the TULP4 gene.  This gene is involved in growth and size, a trait that varies significantly among ecotypes.  Our results illustrate the importance of genomic islands in the early stages of ecologically driven divergence among populations and represent a significant advance towards linking genotypes and phenotypes in non-model organisms.