Whole Genome Analysis of Divergent Natural Selection Between Depth-Partitioned Sibling Species in the Sebastes Marine Species Flock

Detailed examination of adaptation and reproductive isolation at the molecular level is very challenging in most species, yet to achieve a full understanding of these processes we must determine the genomic underpinnings of population divergence.  The genus Sebastes boasts over 100 species worldwide and presents a natural evolutionary laboratory within which one may pursue hypotheses with the rare advantage of phylogenetic replication.  There are a series of depth segregated sister species within the Sebastes, allowing for replicate studies to identify loci that are likely linked to genes that produced and/or maintain species boundaries through reproductive and ecological differentiation.  We performed ddRAD-seq reduced representation whole genome population genomic analysis between individuals of two depth-segregated sister species, and one allopatrically separated pair with a known reference divergence time.  RAD-tags and their interspecific divergence levels were mapped against the draft Sebastes nigrocinctus genome, which itself was mapped against the finished three-spined stickleback genome to establish approximate gene order.  Three regions on the order of 0.5Mbp were divergent among S. carnatus and S. chrysomelas.  Only one such region was divergent between S. miniatus vs S. crocotilis, which was also in common between S. carnatus and S. chrysomelas and is estimated to contain 43 genes.  The region in common contained candidate genes that may be related to prezygotic reproductive isolation and niche partitioning.