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Evolutionary and Ecological Genomics in Deep-Sea Ogranisms

Santiago Herrera Monroy, Ph.D., 2015
Tim Shank, Advisor

Hydrothermal vents and coral ecosystems are conspicuous biological hotspots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species’ relatedness, diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomics and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. These tools are then applied to test global- and regional-scale biogeographic hypotheses of vent fauna using barnacles as model. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa. Finally, I explore the adaptive potential of deep-sea corals to environmental changes by examining a case of adaptation to shallow water from the deep sea. Overall, these results constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems.