Larval dispersal of nearshore rockfishes
Larval dispersal is consequential for the structure and dynamics of populations and the distribution of species. Most benthic marine species inhabit patchily distributed habitat and larval dispersal is often the primary means of population connectivity. Studies suggest that gene flow is the product of conduits and barriers to dispersal, including oceanic and geographic features and a combination of physical and behavioral mechanisms that effect the relationship between larval supply and settlement. Tracking larval dispersal in the ocean is considered one of the great logistical challenges in marine ecology, with a substantial history of using genetic markers to study dispersal. Although most studies apply indirect methods that integrate information across generations, in highly dispersive populations and across fine spatial scales, genetic parentage analysis has seen increasing use, but with limited examples from temperate environments or along open-coastlines where currents dominate and larvae may be advected offshore. Here, I describe larval dispersal of nearshore rockfishes across a network of marine reserves along the open-coastline of central California, a temper- ate current-driven ecosystem and the site of a network of marine protected areas (MPAs). Rockfishes of the genus Sebastes form a marine species flock of more than 100 species and are a prominent component of the ichthyofauna in temperate ecosystems. Kelp rockfish (S. atrovirens) are part of this species flock and one of >50 species present in the Monterey Bay, California region. In Chapter 1, I describe the development of a novel set of statistically powerful microhaplotype markers for efficiently performing pedigree relationship inference in the kelp rockfish and demonstrate that the false positive rates for single parent-offspring and full-sibling analyses are orders of magnitude lower than relying on the most informative single nucleotide polymorphism (SNP) in the same short-read sequence. In Chapter 2, I apply these new genetic markers to identify eight single parent-offspring pairs and 25 full siblings from thousands of samples of adult and juvenile rockfishes collected inside and outside of marine reserves. Dispersal between reserves and areas where fishing is allowed demonstrates the efficacy of the MPA network. Chapter 3 applies these microhaplotype markers to species identification of >50 rockfishes from the Northeast Pacific. Genetic assignment accuracy exceeds 99% and the species for which accuracy does not reach 100% are gopher (S. carnatus) and black-and-yellow (S. chrysomelas) rockfishes, sister species with evidence of ongoing gene flow. Phylogenetic analyses recovers relationships among species and subgenera concordant with previous studies. Finally, in Chapter 4, I analyze additional species of rockfishes obtained for the larval dispersal study and identify full siblings among juvenile gopher/black-and-yellow and copper rockfishes. Combining these data with results from Chapter 2, I compare the proportions of full sibling pairs among the species, finding the greatest proportion of full siblings sampled in the kelp rockfish. Collectively, these chapters provide valuable new genetic resources for studying rockfishes, describe the first direct observations of dispersal in rockfishes, and provide insight into the efficacy of a network of MPAs along an open-coastline.