Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 to 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction incl...