Management of sea urchin fisheries is hampered by a lack of understanding of recruitment processes.

Over the past three decades, we have witnessed dramatic declines of abalone stocks along the southern California coast. What was once an important fisheries resource (commercial and recreational) has completely disappeared and there is now a moratorium on all abalone harvesting in the region (California Department of Fish and Game 2002). Populations of white, red, black, pink and green abalone have all been impacted; the former species, Haliotis sorenseni, has become the first marine invertebrate to be listed as an endangered species. Both anthropogenic (overexploitation and habitat destruction) and natural (disease and predation) processes have contributed to the decline in abalone abundance. Attempts to develop effective conservation and recovery strategies for abalone require understanding many aspects of the biology of these species. The primary question is: can reproduction in remnant populations provide the recruits necessary for recovery of abalone populations that have gone locally extinct? Two factors are important in answering this question. First, there is the question of fertilization success in low abundance populations of broadcast spawning invertebrates; can males and females locate one another and successfully produce fertilized eggs? The second issue regards the level of "connectivity" of abalone populations; can success in one part of the species range provide a natural reseeding in other parts of the range? This project used population genetic methods to address the latter question.

Using seven microsatellite markers, scientists examined the “connectivity” of red sea urchins (Strongylocentrotus franciscanus) along the West Coast of North America and found Canadian and California populations to be genetically differentiated. This is the first research project to find evidence of population structure for this species across its range. Some genetic structure was also detected among different sizes of urchins (recruits and adults) at a single site off San Diego. California populations overall, however, appear genetically the same, or “homogenized.” It should be emphasized that this apparent lack of genetic structure does not preclude the possibility of significant local recruitment within populations.

The history of California’s abalone fisheries has become an object lesson in the potential for traditional fisheries management to fail in protecting species from over-harvesting and even the threat of extinction. Over the course of four decades, five species of abalone (red, green, pink, white and black) were sequentially exploited in California. Despite management efforts, based on minimum-size limits, landings of each species sequentially crashed. In 1997, after years of debate among fishing interests, managers and biologists on the severity, meaning and cure for the declines, the California Department of Fish and Game (CDFG) closed all commercial abalone fishing and relegated sport diving to the cold, rough waters of Northern California, where inaccessibility of the shoreline and prohibitions on using SCUBA gear have created defacto refugia for sexually mature abalones. On top of this, the only abalone species that can be recreationally harvested is the relatively abundant red abalone.

Sea urchins are what are known as “broadcast spawners.” Adults release their gametes into seawater, and fertilization occurs if there is a high enough density of gametes to ensure that female and male gametes meet. What happens after fertilization is something of a mystery. Scientists do not, for instance, know how far, on average, larvae travel during the six-week period it takes for them to develop and settle onto the seafloor. And, they do not know the degree to which ocean waves and currents mix larvae originating from different geographic locales.

With the warming trend due to climate change, conservation of species requires knowledge in ecological and evolutionary aspects of thermal tolerance and adaptation. In this dissertation, I use tidepool copepod, Tigriopus californicus, as a model for studying both aspects of thermal tolerance. For ecological aspect, identifying the most sensitive life stage can help us predict future responses especially in marine organisms with complex life history. I examined different survivorship to acute heat stress among life stages and across populations of T. californicus. Results revealed early life stages of T. californicus survived acute heat stress at higher temperatures than adults in contrast to popular belief. However, heat stress during larval stage of T. californicus resulted in developmental delay. Survivorship in larval and juvenile stages across populations also conform with a pattern previously observed in adults with more heat tolerant populations toward southern range of the species. In order to uncover the evolutionary basis underlying thermal tolerant in T. californicus, I examined allele specific expression in F1 hybrid between populations from San Diego (SD) and Santa Cruz (SC). RNA sequencing revealed regulatory divergence in several gene ontology categories that potentially contribute to thermal tolerance including, electron carrier genes, genes involved in muscle and cuticle assembly, genes involved in proteolysis and Heat Shock Protein (HSP) genes. Heat Shock Protein Beta 1 (HSPB1) is one of the highest expressed HSPs in response to heat stress. HSPB1 Allelic imbalance suggested divergence in cis regulatory element underlying heat stress induced expression. HSPB1 promotor sequencing revealed polymorphisms in the Heat Shock Elements (HSEs), a binding site for Heat Shock Transcription Factor (HSF), where heat tolerant southern populations contain 2 canonical HSEs while northern populations have substitutions in the conserved motif of HSEs. Allele specific expression in more F1 crosses confirmed biased expression favoring alleles from populations with 2 canonical HSEs. Functional assays comparing recombinant SD and SC HSPB1 demonstrated that SD HSPB1 has a better capacity for preventing protein aggregation and preserving enzymatic function under high temperature. Overall, results from this dissertation provide insights on both ecological and evolutionary perspectives of thermal tolerance.

In supralittoral splash pools, the copepod Tigriopus californicus is frequently exposed to environmental extremes, and synthesis and accumulation of the red ketocarotenoid astaxanthin from dietary precursors may be an important component of survival. To search for evidence of genes involved in the synthesis pathway and for potential further-reaching effects of the pigment, we evaluated the transcriptomic response to astaxanthin synthesis. By comparing RNA sequencing of copepods fed diets with varying amounts of astaxanthin precursors (Tetraselmis algae, spirulina, nutritional yeast) across two timescales (lifelong and raised on yeast but exposed for 16 hours to Tetraselmis), we found limited or mixed responses to the shift in carotenoids and other dietary antioxidants. Although we did not observe evidence in favor of any candidate carotenoid ketolases, the lack of differential expression in response to diet is not evidence against these candidates. A carotenoid oxygenase homologous to vertebrate BCO2 did shift in expression over a short-term exposure to carotenoids, potentially to prevent oxidative stress induced by carotenoid accumulation. Other changes in gene expression may relate to nutrient sensing and assimilation pathways. Both the upregulation of myosins in spirulina-fed copepods and shifts in neural signaling transcript levels in copepods exposed briefly to Tetraselmis may be related to the highly conserved ways that organisms sense, assimilate, and respond to nutrient changes. These include the TOR and IIS pathways. Protease and protease inhibitor levels could be influenced by multiple factors, including shifts in both antioxidant and nutrient assimilation systems.

As the climate warms, the response of organisms to rising temperatures has become an area of increasing interest. Much research is focused on understanding the basis for thermal tolerance, which can help us predict the capacity for adaptation or shifting range limits in response to changes in climate. Of particular interest are intertidal ectotherms, which experience highly variable environmental conditions. One such organism is Tigriopus californicus, a copepod found in high rocky tidepools along the west coast of North America. Its relatively low gene flow contributes to genetic isolation of populations, allowing the study of local adaptation along a latitudinal gradient. Previous studies have shown that southern populations have higher

survivorship following heat stress than northern populations, which is correlated with higher upregulation of important heat shock protein (HSP) genes. However, the physiological mechanisms and gene regulation patterns underlying thermal tolerance are not fully understood. In order to address these questions, thermal performance under acute and chronic thermal stress conditions and at abrupt and gradual ramping rates was assessed in three populations of T. californicus distributed from south to north. Additionally, gene regulation during the heat shock response was examined using knockdown of the heat shock transcription factor (HSF-1) gene. We found that at acute thermal exposures, survivorship and mitochondrial performance follow a latitudinal gradient. Chronic thermal performance is more complex, however, with the mid-latitude population showing decreased performance compared to both the southern and northern populations at lower temperatures. Gene regulation during the heat shock response is similarly crucial to organismal performance, and a knockdown of HSF-1 indicates a complex network of gene interactions. Finally, we found that a slower rate of thermal exposure similar to conditions in the intertidal allows organisms to more highly upregulate important HSPs, conferring protection and minimizing harmful effects of acute thermal stress. These findings allow us to better understand the mechanisms underlying thermal tolerance, determine why certain populations or species outperform others, and predict organismal responses to changing climatic conditions in the future.