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 discussed

Barotrauma - injury induced by changes in pressure - is a widespread challenge for successfully releasing fishes following capture. We used acoustic telemetry to examine the long-term post-release survival and behaviour of four rockfish species (genus Sebastes) suffering from barotrauma following capture using recreational fishing techniques. We placed particular emphasis on examining Cowcod (Sebastes levis) and Bocaccio (Sebastes paucispinis), two historically overfished species along the United States West Coast that serve as good model species representing different ecological lifestyles. We show that fish survival was species specific and that 40% of observed mortality occurred more than 48 h post release - a typical time period used in many short-term survivorship studies. Cowcod survival was correlated with fish length, sea surface temperature, and dissolved oxygen concentration at the mean depth of capture. Generalized additive mixed models of Cowcod and Bocaccio behaviour showed that surviving individuals were negatively affected by capture and barotrauma for at least 30 d post-release. Our findings demonstrate the need for extended observations to accurately quantify the mortality of fishes suffering from barotrauma and show how such data can be successfully implemented into fisheries management through engagement between managers, scientists, and the fishing community.

In April and May of 2020, a large phytoplankton bloom composed primarily of the dinoflagellate Lingulodinium polyedra reached historic levels in geographic expanse, duration, and density along the coast of southern California, United States, and Baja California Norte, Mexico. Here, we report the water quality parameters of dissolved oxygen and pH over the course of the red tide, as measured by multiple sensors deployed in various locations along San Diego County, and document the extent of mass organism mortality using field surveys and community science observations. We found that dissolved oxygen and pH corresponded with bloom dynamics, with extreme hypoxic and hyperoxic conditions occurring at multiple locations along the coast, most notably within select estuaries where dissolved oxygen reached 0 mg L−1 and hypoxia occurred for up to 254 consecutive hours, as well as along the inner shelf of the open coast where dissolved oxygen dropped as low as 0.05 mg L−1. Similarly, pH ranged widely (6.90–8.79) across the bloom over both space and time, largely corresponding with dissolved oxygen level. Extreme changes in dissolved oxygen and pH, in addition to changes to other water parameters that affect organismal health, ultimately led to documented mortalities of thousands of demersal and benthic fishes and invertebrates (primarily within estuarine and inner-shelf environments), and long-term surveys within one lagoon showed protracted changes to benthic infaunal density and species composition. In addition to field observations, we also quantified water quality parameters and organism mortalities from four local aquarium facilities, with varying levels of filtration and artificial oxygenation, and documented the morphological changes in the gills of captive-held Pacific sardine in response to the red tide. We show that multiple factors contributed to organismal stress, with hypoxia likely being the most widespread, but not the only, cause of mortality.