The impacts of pathogen emergence in naïve hosts can be catastrophic, and pathogen spread now ranks as a major threat to biodiversity. However, pathogen impacts can persist for decades after epidemics and produce variable host outcomes. Chytridiomycosis in amphibians (caused by the fungal pathogen Batrachochytrium dendrobatidis, Bd) is an exemplar, with impacts ranging from rapid population crashes and extinctions, to population declines and subsequent recoveries. Here, we investigate long-term impacts associated with chytridiomycosis in Australia. We conducted a continent-wide assessment of the disease, reviewing data collected since the arrival of Bd in about 1978, to assess and characterize mechanisms driving past, present and future impacts. We found chytridiomycosis to be implicated in the extinction or decline of 43 of Australia's 238 amphibian species. Population trajectories of declined species are highly variable; six species are experiencing ongoing declines, eight species are apparently stable and 11 species are recovering. Our results highlight that while some species are expanding, Bd continues to threaten species long after its emergence. Australian case-studies and synthesis of the global chytridiomycosis literature suggests that amphibian reservoir hosts are associated with continued declines in endemically infected populations, while population stability is promoted by environmental conditions that restrict Bd impact, and maintenance of high recruitment capacity that can offset mortality. Host genetic adaptation or decreased pathogen virulence may facilitate species recovery, but neither has been empirically demonstrated. Understanding processes that influence Bd-host dynamics and population persistence is crucial for assessing species extinction risk and identifying strategies to conserve disease-threatened species.

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Aim Population viability analysis (PVA) is used to quantify the risks faced by species under alternative management regimes. Bayesian PVAs allow uncertainty in the parameters of the underlying population model to be easily propagated through to the predictions. We developed a Bayesian stochastic patch occupancy model (SPOM) and used this model to assess the viability of a metapopulation of the growling grass frog (Litoria raniformis) under different urbanization scenarios.Location Melbourne, Victoria, Australia. MethodsWe fitted a Bayesian model that accounted for imperfect detection to a multiseason occupancy dataset for L. raniformis collected across northern Melbourne. The probability of extinction was modelled as a function of effective wetland area, aquatic vegetation cover and connectivity, using logistic regression. The probability of colonization was modelled as a function of connectivity alone. We then simulated the dynamics of a metapopulation of L. raniformis subject to differing levels of urbanization and compensatory wetland creation. Uncertainty was propagated by conducting simulations for 5000 estimates of the parameters of the models for extinction and colonization.Results There was considerable uncertainty in both the probability of quasiextinction and the minimum number of occupied wetlands under most urbanization scenarios. Uncertainty around the change in quasi-extinction risk and minimum metapopulation size increased with increasing habitat loss. For our focal metapopulation, the analysis revealed that significant investment in new wetlands may be required to offset the impacts of urbanization.Main conclusions Bayesian approaches to PVA allow parametric uncertainty to be propagated and considered in management decisions. They also provide means of identifying parameters that represent critical uncertainties, and, through the use of informative priors, can easily assimilate new data to reduce parametric uncertainty. These advantages, and the ready availability of software to run Bayesian analyses, will ensure that Bayesian approaches are used increasingly for PVAs.

Metapopulation persistence in fragmented landscapes depends on habitat patches that can support resilient local populations and sufficient connectivity between patches. Yet epidemiological theory for metapopulations has largely overlooked the capacity of particular patches to act as refuges from disease, and has suggested that connectivity can undermine persistence. Here, we show that relatively warm and saline wetlands are environmental refuges from chytridiomycosis for an endangered Australian frog, and act jointly with connectivity to sustain frog metapopulations. We coupled models of microclimate and infection probability to map chytrid prevalence, and demonstrate a strong negative relationship between chytrid prevalence and the persistence of frog populations. Simulations confirm that frog metapopulations are likely to go extinct when they lack environmental refuges from disease and lose connectivity between patches. This study demonstrates that environmental heterogeneity can mediate host-pathogen interactions in fragmented landscapes, and provides evidence that connectivity principally supports host metapopulations afflicted by facultative pathogens.