Population Structure in Puget Sound Rockfishes (Sebastes spp.): Using Genetics To Inform Management Of A Vulnerable Species Complex

Abstract

Successful management relies on the correct identification of management units. Quantifying the connectivity between populations is a critical factor in defining management units and improving fishery plans. Despite stock recoveries along the US West Coast, rockfish populations in Puget Sound continue to decline, and three species were listed under the Endangered Species Act. These management measures were primarily based on data from a hybridizing species complex (Brown-Copper-Quillback Rockfish), which identified Puget Sound as a distinct population from the Washington Coast. It is unknown whether the population structure identified in previous studies is due to extensive hybridization in the region. Additionally, recent studies have suggested that there is species specific population structure for rockfish in Puget Sound. Population structure in the remaining species, and the factors determining population differentiation within Puget Sound are therefore unknown. Therefore, the overall goal of this thesis was to investigate population structure and the extent of hybridization of Puget Sound rockfishes. To accomplish this goal, fin clips from eight rockfish species (Brown (Sebastes caurinus), Copper (S. auriculatus), Quillback Rockfish (S. maliger), Black (S. melanops), Yellowtail (S. flavidus), Redstripe (S. proriger), Greenstriped (S. elongatus), and Puget Sound (S. emphaeus)) were sequenced using reduced representation sequencing (RADseq), resulting in over 10,000 loci per species. First, we identified the geographic and genetic extent of hybridization for the Copper-Quillback-Brown species complex. We found that hybridization is low-level, asymmetric from Quillback into Copper and Brown, and localized in south Puget Sound. Hybridization inflated estimates of species-specific population structure in Brown and Copper rockfish. Second, we estimated population structure and connectivity for five common species of rockfish. We identified no structure in Black and Puget Sound Rockfish, temporal structure in Redstripe Rockfish and geographic structure in Yellowtail and Greenstriped Rockfish. There was no clear effect of life history on geographic structure, but oceanography and temporal variation were evident in our results. Of the eight species analyzed, no species followed the current DPS boundaries that they are managed by. Finally, we discuss the management implications of these studies and suggest future directions for management of this species complex.