The Added Value of Large-Scale Genomic Data in Conservation
Large-scale genomic datasets have transformed the way we approach problems in biology. While genomic data are now common in studies of human disease and variation, they are rarely used in molecular ecology and conservation genetics. In this dissertation I investigate the added value of genomic-scale data to answer conservation-relevant questions for threatened and endangered amphibians and reptiles. The first chapter is a synthetic literature review of recent studies that used genetic data to learn about the ecology of amphibian species to aid in conservation. This review reveals that genomic studies in amphibians, likely due to their extremely large and complex genomes, have lagged behind other taxa, and includes future directions aimed squarely at large-genome analyses. Chapter two addresses this deficiency empirically by optimizing a genomic data collection strategy for amphibians with large genomes. This study shows that target capture is feasible in large-genome amphibians and experimentally examines two specific modifications that greatly improve efficiency and substantially reduce cost when gathering population-scale genomic data. Chapter three makes use of advancements from chapter two, and presents empirical results from a genomic exon capture dataset of endangered tiger salamanders (Ambystoma tigrinum) on Long Island, NY. This chapter demonstrates the substantial benefits and insights derived from our genomic dataset for answering conservation-relevant questions compared to a previous study of the same system using traditional microsatellite analyses. The final chapter attempts to elevate conservation genomics to the next level by using whole genomes to quantify the impacts of alternative solar energy development scenarios on gene flow of the Mojave desert tortoise (Gopherus agassizii). We generated 270 low-coverage whole genome tortoise sequences to build a historical map of gene flow for the species across the Mojave Desert, modeled the effects on gene flow of a set of proposed renewable energy development alternatives, and supplied management agencies with a ranked list of impacts of the green energy alternatives. Overall, this dissertation provides context for the current use of genomic tools in conservation biology, methodological advances for their application to large-genome amphibians, and two examples of large-scale studies that showcase the added value of genomic datasets in conservation.