As freshwater systems and biota are rapidly declining globally, conservation efforts will require assessment of the adaptive capacity of populations to rapid environmental change. Small populations with limited connectivity may have reduced adaptive potential and difficulty responding to current and future environmental change. Assessing genetic health and determining population units is a crucial component for successful conservation management, particularly in sensitive and threatened species. No other taxa is at greater risk than amphibians—over a third of all amphibian species globally are at risk of extinction—yet utilizing recent genomic advancements for conservation has been difficult due to the typically large amphibian genome sizes and lack of existing sequence data. One tool for addressing ecological genomics questions at scales that were previously impossible is restriction site-associated DNA sequencing (RADSeq). Furthermore, a new method called RAPTURE (RAD-Capture) adapts RADSeq to target desired loci and allows highly efficient genotyping across large number of individuals. We test the application of this method in several different ecological questions across different spatial scales using a suite of different frog species (within the genus Rana) native to Western North America, including multiple endangered, threatened and sensitive species.
Results/Conclusions
Genomic analysis of thousands of genetic markers distributed throughout the genome can detect changes in population size, connectivity, and overall genetic health. We show RAPTURE can be successfully used to investigate a variety of ecological and molecular questions including detection of hybridization in closely related species with overlapping ranges, landscape genetics assessment of genetic isolation and health in frogs impacted by river regulation, and fine scale differentiation of over a dozen Rana species. Rana boylii populations from regulated watersheds throughout the Northern Sierra Nevada in California show an elevated pattern of genetic isolation and loss of genetic diversity as compared to populations from unregulated watersheds. A rare hybridization event was detected between the endangered R. sierrae and R. boylii in the only location the two species’ ranges overlap. Furthermore, implementing a single marker set for multiple species to efficiently assess population structure, genetic variation, and contemporary effective population sizes across many individual samples provides a potent tool for genetic monitoring and conservation management.