Genomic data uncover previously undetectable fragmentation effects in the endangered Eastern tiger salamander

A critical consideration when using molecular ecological methods to detect trends and parameterize models at very fine spatial and temporal scales has always been technical limits of resolution. Critical landscape features, including most anthropogenic modifications, can cause substantial, but very recent loss of metapopulation dynamics and restrictions of gene flow, but few studies have had the statistical power to genetically examine these effects. The problem is one of temporal scale: human change is rapid and recent, while genetic changes accumulate over many generations. We used DNA sequence data from thousands of nuclear loci to characterize the population structure of New York-endangered Eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. In stark contrast to a recent microsatellite study, we uncovered highly structured populations over an extremely small spatial scale (approximately 40 km2) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds were both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors are responsible for the observed patterns of genetic variation. All ponds supported small effective breeding populations, and pond surface area showed a strong positive correlation with salamander population size. Our study demonstrates the value of genomic approaches in molecular ecology, as none of these patterns emerged in an earlier study of the same system using microsatellite loci. Conservation assessments using earlier genetic techniques in other species may similarly lack the statistical power for small-scale inferences and benefit from reassessments using genomic tools.