Sienna Hatfield, John H. Neddermeyer

Title:

Genomic and Ecological Insights into Amphibian Evolution and Conservation

Abstract:

The recent availability of amphibian genomes provides a unique opportunity to investigate the interplay between ecological, climatic, and phenotypic factors and their influence on genetic variation. This study aims to explore these relationships. We seek to determine how environmental and phenotypic traits correlate with amphibian genomic variation, and whether the association of these factors can predict conservation status. By integrating bioinformatics, phylogenomics, and ecological statistical modeling, we analyze publicly available amphibian genomes alongside ecological and phenotypic datasets. To estimate genomic variation, we clustered orthologous genes with Orthofinder and estimated nonsynonymous and synonymous substitution rates with HyPhy. We also quantified transposable element activity using RepeatModeler and Repeatmasker. We obtained species range maps and bioclimatic variables from online climate databases and processed them using QGIS. We then used Rstudio and Monsoon to determine the overlap between species distributions and climatic variables, calculate summary statistics, and perform principal components analysis (PCA) to quantify environmental niche space for each species. We then used Phylogenetic Least Squares (PGLS) regression to determine the association between the environmental principal components and genomic features, conservation status, and cancer prevalence. By identifying genomic regions associated with extinction risk and disease outcomes, this research will provide insights into biodiversity conservation and potential applications for understanding cancer resistance in humans.