Determinants of amphibian genomic diversity: Integrating traits, phylogeny, and geography

Genetic differences between individuals and populations of the same species are essential for organisms to adapt and survive in changing environments. Surveying genomic variation within species, and determining what factors influence that variation, are thus important goals for managing wildlife populations and conserving biodiversity. Amphibians are key contributors to many ecosystem processes, but they are one of the most threatened vertebrate groups.

They are also lacking from many comparative studies of genomic variation because they have large, complex genomes. This project will investigate the factors that influence genomic variation within amphibians and will produce new genome-scale data for several dozen frog species sampled across the United States. Broader impacts include training early-career scholars including a postdoctoral researcher, two graduate students, and six undergraduate students in field sampling, genomic sequencing, bioinformatics, and statistical analysis.

The project will also contribute to research infrastructure by archiving searchable, multi-purpose amphibian specimens and tissues at the Museum of Southwestern Biology for future uses. A new undergraduate course in Biodiversity Informatics will be developed to engage students with natural history collections and biodiversity databases, provide computational training, and offer hands-on research experiences through collaborative projects that leverage the amphibian genomic data produced by the project.

This research addresses key questions about the determinants of genetic diversity, thereby advancing knowledge about the origins, distribution, and evolutionary history of global biodiversity. Two complementary approaches to data collection encompass several complex factors that affect genetic diversity – life history and ecological traits, phylogenetic history, population history, and current environmental variation – and provide insights into the scale at which these factors influence diversity within species.

The first approach will combine data repurposing, machine learning, and phylogenetic comparative methods to identify important predictors of genetic diversity for global amphibians using open-access museum, trait, and genetic sequence databases. These results will shed light on the importance of species traits, phylogenetic history, and geographic range characteristics for predicting genetic diversity across hundreds of amphibian species.

The second approach will produce new high-resolution, genome-scale data for more than 40 frog species in the United States, sampled strategically across geographic space to test predictions about the influence of population history and current environmental variation on genetic variation within species. By integrating traits, phylogeny, and geography, this research will uncover the determinants of amphibian genomic diversity and establish a framework to address this fundamental aspect of biodiversity across different taxonomic and spatial scales.

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.