The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. In this thesis, a genotyping-by-sequencing (GBS) approach was used to examine genomic variation in an early life stage of the Dungeness crab (Cancer magister), which constitutes the most valuable single-species commercial fishery in the CCE. Previous population genetic studies of adult benthic stage Dungeness crab are expanded upon through genomic examination of the last pelagic larval stage of the species life history, the megalopae. Variation in abundance and timing of megalopae recruitment has been extensively studied for over two decades in Coos Bay, Oregon, and has been found to vary with ocean conditions. The aim of this fine-scale temporal and spatial genomic analyses of megalopae recruits was to better understand how ocean conditions influence larval transport and the ultimate population connectivity of the Dungeness crab within and between the marine ecosystems along the west coast of North America: the California Current Ecosystem (CCE), the Salish Sea Ecosystem (SSE), and the Gulf of Alaska Ecosystem (GOA). Using the same genomic methods across two studies, over 1,000 presumably neutral loci and two putatively adaptive loci were identified within each study. Genetic differences among Dungeness crab megalopae recruits were not detected based on presumably neutral loci across three years (2014, 2017, and 2018), and this finding was consistent across two sites along the Oregon coast (Coos Bay and Yaquina Bay). However, evidence was found for intra-annual genetic differences based on putatively adaptive loci. Moreover, the magnitude of intra-annual genetic differentiation based on putatively adaptive loci (quantified by FST estimates) differed between years (greater in 2017). The observed intra- and inter-annual genetic differentiation among megalopae recruits supports the current understanding that variation in CCE ocean conditions influence the larval dispersal and, ultimately, the population connectivity of Dungeness crab. Population connectivity within and between marine ecosystems is important to examine when considering how future changes in ocean conditions may impact fishery harvests.
Lee, E.M.J. (2019). Big Fishery, Big Data, and Little Crabs: Using a Genomic Approach to Examine Larval Recruitment Patterns of Dungeness Crab (Cancer magister) in the California Current Ecosystem (Master's thesis).