Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing

Genomics has great potential to advance understanding of amphibian evolution, ecology, and behavior, as well as to improve conservation of this highly imperiled class of vertebrates. However, application of new massively parallel sequencing technology to amphibians lags behind its application to other vertebrates, due in part to their large, repetitive genomes, making genome assembly challenging. The goal of our chapter is to outline ways in which population genomics – coupled with field biology, experiments, and modeling – can deepen our understanding of basic and applied questions in amphibian evolutionary ecology and conservation. We start by discussing potential applications of genomics to several long-standing questions in amphibian evolution, ecology, and behavior, including phylogenetic relationships, phylogeography, sex chromosome evolution, population structure and demography, local adaptation, and mating systems and sexual selection. We then highlight opportunities for improving amphibian conservation with genomics, focusing on hybridization, disease evolution and ecology, and captive breeding programs. Next, we provide strategies for moving amphibian genomics forward in the face of challenges such as few available reference genomes and large repetitive genomes, including a bold proposal for whole genome sequencing of a minimum of one species per amphibian family. We conclude by providing suggestions for maximizing the potential of genomics to advance understanding of amphibian evolutionary ecology and conservation and recommendations for getting started in genomics.