Spatiotemporal population genomics of marine species : invasion, expansion, and connectivity

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2017Every genome tells a story. This dissertation contains four such stories, focused on shared themes of marine population dynamics and rapid change, with an emphasis on invasive marine species. Biological invasions are often characterized by a range expansion, during which strong genetic drift is hypothesized to result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. In this dissertation, population genetic and genomic tools are used to approach complex and previously intractable fundamental questions pertaining to the non-equilibrium dynamics of species invasions and rapid range expansions in two invasive marine species: the lionfish, Pterois volitans; and the shrimp, Palaemon macrodactylus. Using thousands of loci sequenced with restriction enzyme associated DNA sequencing in these two systems, this research tests theoretical predictions of the genomic signatures of range expansions. Additionally, the first chapter elucidates patterns of population genetic connectivity for deep-sea invertebrates in the New Zealand region demonstrating intimate relationships between genetics, oceanographic currents, and life history traits. Invasive shrimp results extend our understanding of marine population connectivity to suggest that human-mediated dispersal may be as important— if not more important—than oceanographic and life history considerations in determining genetic connectivity during specific phases of marine invasions. In invasive populations of lionfish, measures of genomic diversity, including a difference between observed and expected heterozygosity, were found to correlate with distance from the point of introduction, even in the absence of spatial metapopulation genetic structure. These results indicate a signal of rapid range expansion. The final study in this dissertation uses an innovative temporal approach to explore observed genomic patterns in the lionfish. In all, this dissertation provides a broad perspective through the study of multiple species undergoing superficially parallel processes that, under more intense scrutiny, are found to be mechanistically unique. It is only through comparative approaches that predictable patterns of population dynamics will emerge.I was privileged to receive support through a National Science Foundation (NSF) Graduate Research Fellowship (Grant No. 1122374), a Woods Hole Oceanographic Institution (WHOI) Fellowship administered through the Academic Program Office, funding from NSF award OCE-1131620, and the National Oceanic and Atmospheric Administration (NOAA OER #NA08OAR4600757). Research funding for sample collection, laboratory materials, sequencing, and analysis was provided by the WHOI Coastal Ocean Institute, WHOI Ocean Ventures Fund, WHOI James Education Fund for Ocean Exploration, WHOI Biology Educational Fund, Woods Hole Sea Grant New Initiative Award, Massachusetts Office of Coastal Zone Management, Northeast Sea Grant Consortium, and the PADI Foundation (Grant No. 14904). Additional research support was provided by the NSF (OCE- 1131620) to Timothy M. Shank