Genomic data have the potential to revolutionize the delineation of conservation units (CUs) by allowing the detection of adaptive genetic variation, which is otherwise difficult for rare, endangered species. In contrast to previous recommendations, we propose that the use of neutral versus adaptive markers should not be viewed as alternatives. Rather, neutral and adaptive markers provide different types of information that should be combined to make optimal management decisions. Genetic patterns at neutral markers reflect the interaction of gene flow and genetic drift that affects genome-wide variation within and among populations. This population genetic structure is what natural selection operates on to cause adaptive divergence. Here, we provide a new framework to integrate data on neutral and adaptive markers to protect biodiversity.

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Landscape features such as mountains, rivers, and ecological gradients may strongly affect patterns of dispersal and gene flow among populations and thereby shape population dynamics and evolutionary trajectories. The landscape may have a particularly strong effect on patterns of dispersal and gene flow in amphibians because amphibians are thought to have poor dispersal abilities. We examined genetic variation at six microsatellite loci in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. We were particularly interested in addressing three questions: (i) do ridges act as barriers to gene flow? (ii) is gene flow restricted between low and high elevation ponds? (iii) does a pond equal a 'randomly mating population' (a deme)? We found that mountain ridges and elevational differences were associated with increased genetic differentiation among sites, suggesting that gene flow is restricted by ridges and elevation in this species. We also found that populations of Columbia spotted frogs generally include more than a single pond except for very isolated ponds. There was also evidence for surprisingly high levels of gene flow among low elevation sites separated by large distances. Moreover, genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation. Our results show that landscape features have a profound effect on patterns of genetic variation in Columbia spotted frogs.

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Inventory, monitoring, and experimental studies have been the primary approaches for documenting and understanding the problem of amphibian declines. However, little attention has been given to placing human-caused perturbations affecting one or more life-history stages in the context of the overall population dynamics of particular species. We used two types of ecological sensitivity analysis to determine which vital rates have the strongest influence on the population dynamics of western toads ( Bufo boreas ), red-legged frogs ( Rana aurora ), and common frogs ( Rana temporaria ), pond-breeding amphibians that have declined in all or portions of their ranges. Our results suggest that post-metamorphic vital rates and highly variable vital rates both have a strong influence on the population dynamics of these species and therefore deserve more research and management attention. Ecological sensitivity analysis should be more widely applied to the issue of amphibian declines in order to identify the most plausible mechanisms of decline and prioritize which lifehistory stages should be the focus of research and management efforts. Future experimental studies of perturbations in one or more life-history stage should attempt to link the magnitude of the perturbation measured with the overall population-level consequences. Finally, current research, inventory, and monitoring efforts should be supplemented with demographic studies so that quantitative analyses can be applied to a wider range of species and life-history groups.