Collaborative Research: The Genomic Basis of Evolutionary Innovations in the Squamate Tree of Life

Throughout the history of life on Earth, organisms have evolved multiple adaptations to a constantly changing environment. In many instances, key innovations arise coincident with the origins of groups and provide the opportunity for the diversification of many species. However, the evolution of the underlying genetic mechanisms responsible for these important adaptations across the tree of life are not well known, leaving a major gap in our knowledge about the evolution of key innovations. This research will combine information from complete genomes with anatomical data from both living and fossil species of squamates (lizards and snakes) to pinpoint the timing of major evolutionary changes in anatomy, and determine areas of the genome associated with such changes. This project will also provide training opportunities for students and early career scientists, yield new open access databases, and contribute to the education of underrepresented groups in STEM through outreach about research on squamates and genomics. Squamates are an excellent model for studying evolutionary innovations, with ~11,000 living species and a rich fossil record spanning over 240 million years. An understanding of the genomic basis of evolutionary innovations across all major groups of squamates has been historically limited by the lack of whole genomes, comprehensive trait data, and appropriate analytical tools. To address these limitations, the project will compile comprehensive phenotypic data for 370 living and fossil squamate species and build a database of complete genomes representing >90% of living squamate families, resulting in the most complete database for squamate reptiles ever assembled. Using emerging tools for comparative genomics and phylogenetics, this research will provide two broadly interesting products: 1) the first whole-genomic squamate tree of life with a precise timeline of squamate evolution; 2) a detailed understanding of how evolutionary rates across multiple regions of the squamate genome and phenome have changed across time, and their correlation with each other. The latter will reveal the genomic changes associated with key adaptations in squamate evolution, such as the origin of highly mobile snake skulls and body elongation across various lineages. Collectively, the research will determine whether changes in protein-coding genes or non-coding regulatory regions of the genome are responsible for evolutionary innovations in the tree of life; identify the genetic pathways involved in organismal growth, development, and other life functions that have driven species diversification; and provide discoveries and tools widely applicable to evolutionary biologists across diverse fields of specialization. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.