Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii–Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.

Summary Wildfires are increasing in both frequency and intensity in many ecosystems, with climate change models predicting further escalations in fire‐prone environments. Set against this background is the global decline of amphibians, with up to 40% of species facing extinction from multiple additive threats. Despite these disturbing figures, it is currently unclear how increasing fire frequency may impact the long‐term persistence of frog populations. Following a severe wildfire in south‐eastern Australia in 2009, field surveys indicated healthy tree frog populations. However, the 2009 fire had significant impacts on genetic diversity, including increased levels of inbreeding and declines in effective population size. Using stochastic population modelling under a range of fire‐frequency scenarios, we demonstrate that amphibian populations in fire‐prone environments may be increasingly vulnerable to extinction, particularly where rates of immigration are low. Synthesis and applications. This study of amphibian population genetics before and after a major wildfire emphasizes the importance of integrating both ecological and genetic data into population models. This will help managers make more appropriate conservation decisions regarding fire management of natural environments, especially those containing threatened populations. Priorities for agencies involved in planning controlled burns should consider carefully the timing of controlled burns, along with maintaining habitat connectivity.