Paul Hime: Leveraging anchored hybrid enrichment to reveal genomic correlates of amphibian species richness.

One of the most salient and tantalizing features of the Tree of Life is that lineage diversification rates vary greatly across its branches, leading to asymmetric patterns of contemporary species richness1. Elucidating the underlying causes of this variation in organismal diversity and disparity is a central and challenging focus of modern evolutionary biology. While much is known about the ecological correlates of macroevolutionary change2,3, substantial progress remains to be made in understanding its genomic bases. Many studies have suggested a fundamental link between rates of molecular evolution and rates of lineage diversification over macroevolutionary timescalese.g.4,5. However, the extent to which this pattern is borne out across different regions of the genome, across different functional classes of genes, and across different organismal groups remains unknown. To date, research on the genomic underpinnings of species richness has employed concatenation-based tree reconstruction methods which discount discordant gene histories and consider disparate genomic regions in aggregate. Such methods obfuscate the underlying relationships between genomic architecture and lineage diversification and in some cases may even lead to highly precise, highly supported inferences that are nonetheless inaccurate6. Accordingly, I propose new methods to study the genomic correlates of contemporary species richness and advocate their application across extant amphibians, a diverse group comprising over 7,000 species with extreme variation clade density. I will generate sequence data from hundreds of informative and well characterized genomic regions using an amphibian-specific capture method that I have helped to develop. I will combine coalescent methods for species tree reconstruction with a recent method for taxonomic rank-independent diversification through time analysis to reveal the history of amphibian lineage accumulation. I will then use a novel analytical method which I propose for gene-by-gene and node-by-node analyses of gene trees within a species tree to address several long-standing hypotheses about the genomic correlates of macroevolutionary change in general and diversification dynamics of amphibians specifically.