The origin, evolution, and diversification of rockfishes of the genus Sebastes (Cuvier) : insights into speciation and biogeography of temperate reef fishes

Dispersal and speciation in the marine environment have long been key topics in evolutionary biology and more recently in conservation biology. The genus Sebastes, with approximately 110 species, is found throughout most of the world's cold-temperate seas. Their breadth of phenotypic and species diversity, ecological dominance, and importance to world fisheries has made them a focus of intensive study by countless researchers. In this dissertation, DNA sequence and microsatellite data were used to investigate patterns of speciation, distribution, and mating habits. In Chapter I, DNA sequence data from seven mitochondrial and two nuclear genes, were used to evaluate possible geographic origin, patterns and timing of dispersal, speciation patterns and drivers, and inter- species relationships. The data support a middle Miocene origin for Sebastes spp. in deep habitats of the Northwest Pacific followed by dispersal into the Northeast Pacific and eventually into the southern hemisphere, driven by progressive cooling and strengthening of major ocean currents. Previous hypothesized relationships, shown to be mostly poly- or para- phyletic, were revised in light of the findings. Chapter I provided evidence for two new "cryptic" species. In Chapter II, sequence of the mitochondrial cytochrome b gene, in combination with nine microsatellite loci, was used to evaluate the geographic and bathymetric range of the vermilion rockfish species complex, as well as test for reproductive isolation between the putative species. Genetic analyses supported the presence of two species, separated primarily by depth of adult occurrence. This finding, in association with distribution patterns of 12 recent species pairs, suggests a novel speciation mode based upon the loss/truncation of an ontogenetic migration phase. In Chapter III, DNA sequence data from Chapter II was used to evaluate patterns of population connectivity and gene flow within the vermilion rockfish. A range-wide analysis showed high levels of genetic heterogeneity, likely driven by limited larval dispersal and barriers to gene flow across major oceanographic features. Patterns of paternity and mating system were investigated in Chapter IV using microsatellite loci. Paternity analyses were performed on larvae from both captive and wild populations, representing most major lineages found in Chapter I. Ten of the 17 examined species, showed evidence for multiple sires within a single brood. The implications for genetic diversity produced by this polygynandrous mating system are discusse