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Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex,more » « less
Rana muscosa andRana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in theR. muscosa clade, we also found evidence of some admixture across cluster boundaries in theR. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southernR. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.Free, publicly-accessible full text available September 29, 2024 -
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Abstract World‐wide, infectious diseases represent a major source of mortality in humans and livestock. For wildlife populations, disease‐induced mortality is likely even greater, but remains notoriously difficult to estimate—especially for endemic infections. Approaches for quantifying wildlife mortality due to endemic infections have historically been limited by an inability to directly observe wildlife mortality in nature.
Here we address a question that can rarely be answered for endemic pathogens of wildlife: what are the population‐ and landscape‐level effects of infection on host mortality? We combined laboratory experiments, extensive field data and novel mathematical models to indirectly estimate the magnitude of mortality induced by an endemic, virulent trematode parasite (
Ribeiroia ondatrae ) on hundreds of amphibian populations spanning four native species.We developed a flexible statistical model that uses patterns of aggregation in parasite abundance to infer host mortality. Our model improves on previous approaches for inferring host mortality from parasite abundance data by (i) relaxing restrictive assumptions on the timing of host mortality and sampling, (ii) placing all mortality inference within a Bayesian framework to better quantify uncertainty and (iii) accommodating data from laboratory experiments and field sampling to allow for estimates and comparisons of mortality within and among host populations.
Applying our approach to 301 amphibian populations, we found that trematode infection was associated with an average of between 13% and 40% population‐level mortality. For three of the four amphibian species, our models predicted that some populations experienced >90% mortality due to infection, leading to mortality of thousands of amphibian larvae within a pond. At the landscape scale, the total number of amphibians predicted to succumb to infection was driven by a few high mortality sites, with fewer than 20% of sites contributing to greater than 80% of amphibian mortality on the landscape.
The mortality estimates in this study provide a rare glimpse into the magnitude of effects that endemic parasites can have on wildlife populations and our theoretical framework for indirectly inferring parasite‐induced mortality can be applied to other host–parasite systems to help reveal the hidden death toll of pathogens on wildlife hosts.
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Abstract Pathogen persistence in host communities is influenced by processes operating at the individual host to landscape‐level scale, but isolating the relative contributions of these processes is challenging. We developed theory to partition the influence of host species, habitat patches and landscape connectivity on pathogen persistence within metacommunities of hosts and pathogens. We used this framework to quantify the contributions of host species composition and habitat patch identity on the persistence of an amphibian pathogen across the landscape. By sampling over 11 000 hosts of six amphibian species, we found that a single host species could maintain the pathogen in 91% of observed metacommunities. Moreover, this dominant maintenance species contributed, on average, twice as much to landscape‐level pathogen persistence compared to the most influential source patch in a metacommunity. Our analysis demonstrates substantial inequality in how species and patches contribute to pathogen persistence, with important implications for targeted disease management.
