Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification
Understanding the evolutionary factors underlying the disparity in species richness across groups is a fundamental challenge in fish evolutionary biology. A difficulty in investigating this field lies in the paucity of robust, well-sampled phylogenies that act as a necessary framework to test hypotheses about the affects of ecology on fish evolution. In chapter one I use molecular sequence data to generate a time-calibrated hypothesis of surgeonfish (Family: Acanthuridae) relationships. I found strong support that the gizzard-like stomach, an important morphological trait for benthic grazing species including some Acanthurus and all Ctenochaetus, evolved only once, contrary to a previous hypothesis of multiple, independent origins. The timetree also shows that the subfamily Nasinae (genus Naso) experienced high turnover since originating in the Miocene, and that the extant species arose much more recently (~17 Ma) than previous hypotheses. To abet creating robust phylogenies across a diverse set of species and at multiple phylogenetic levels, I developed a new genomic method capturing ultraconserved elements (UCEs). UCEs are highly conserved regions of the genome that are flanked by more variable regions, making them ideal for target enrichment. I created custom probes targeting 500 loci across fishes and used massively parallel sequencing to obtain a phylogenomic dataset both efficiently and economically. I validate this method by resolving the higher-level relationships among ray-finned fishes. The well-supported topology reveals monophyly of Amia and Lepisosteus (Holostei), and suggests that elopomorphs, then osteoglossomorphs were the first teleost lineages to diverge. The results show that sequence capture of UCE loci and their flanking regions provides an excellent approach to resolve the fish Tree of Life. In chapter three, I use molecular data to generate the most comprehensive, time-calibrated phylogeny for the sharks. This framework is then used to understand the influence of ecology (e.g. habitat preference) on the diversification of these fishes. My results show that deepwater radiations and transitions to coral reefs have played an important role in generating extant biodiversity. Coral reefs, therefore, have greatly influenced species richness across multiple fish trophic levels, from algivores to top predators like sharks.