Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparativ...