ddRADseq Analysis of Genomic Divergence Patterns in Six Pacific Rockfishes (Genus Sebastes)

Pacific rockfishes, are comprised of over 120 different species, a majority of which are clustered in coastal waters between Alaska and Baja California. An open question in evolutionary biology is what type and how many changes occur within genomes at different stages of the speciation process. To explore how rockfish genomes have diverged during speciation, a double digestion restriction enzyme associated DNA sequencing (ddRADseq) protocol was used to randomly sequence 100,000 different loci from three species pairs of rockfishes that differ in time since speciation, and proposed speciation mechanism.  Data was analyzed using the Stacks pipeline, and reads were mapped to a reference genome from another rockfish. Divergence times were estimated for highly divergent regions using the Isolation with Migration program to identify genes that diverged earliest in the speciation process.  Genome wide patterns of diversity and divergence are also contrasted among the three species pairs.