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Understanding how agricultural and land management practices affect amphibian biodiversity is essential for conservation efforts in farmland. We investigated the impact of farm dam enhancement on tadpole abundance and growth in a highly modified farming landscape in south-eastern Australia. We completed detailed surveys on 52 farm dams (artificial ponds or agricultural reservoirs). These dams were categorized into two groups: enhanced ( n  = 28), which had undergone management activities such as fencing to prevent livestock access and facilitate revegetation, and control ( n  = 24), which had not received any intervention and were subject to standard management practices similar to adjacent paddocks. Our findings revealed a notable increase in tadpole abundance across all species in enhanced dams, with 92% of all observed tadpoles recorded in these dams. Factors such as higher dissolved oxygen and greater riparian vegetation cover were positively associated with tadpole abundance, while high pH levels showed a negative association. We found no evidence that tadpole growth was influenced by dam enhancement. Concerningly, when the invasive fish Gambusia holbrooki was present, tadpoles were smaller and at earlier developmental stages. Our findings highlight the potential benefits of strategic farm dam management for improving tadpole presence in agricultural landscapes., Competing Interests: The authors declare no conflicts of interest., (© 2025 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Pathogens that infect multiple host species have an increased capacity to cause extinctions through parasite-mediated apparent competition. Given unprecedented and continuing losses of biodiversity due to Batrachochytrium dendrobatidis (Bd), the causative fungus of the amphibian skin disease chytridiomycosis, a robust understanding of the mechanisms driving cross-species infection dynamics is essential. Here, we used stage-structured, susceptible-infected compartmental models to explore drivers of Bd-mediated apparent competition between two sympatric amphibians, the critically endangered Litoria spenceri and the non-threatened Litoria lesueurii. We additionally simulated the impact of plausible L. spenceri conservation management interventions on competitive outcomes between these two species. Despite being more susceptible to disease than its competitor, a high relative rate of recruitment allowed the non-threatened L. lesueurii to reach substantially higher densities than L. spenceri in our baseline models, applying a strong absolute force of infection on L. spenceri as an amplifying host. However, simulated management interventions which bolstered L. spenceri recruitment (i.e., captive breeding and release, removal of predatory non-native trout) spurred strong recoveries of L. spenceri while simultaneously (1) increasing the force of Bd infection in the environment and (2) reducing L. lesueurii population density. At high and moderate elevations, combined captive breeding/release and non-native trout removal were sufficient to make L. spenceri the most abundant species. Overall, our results demonstrate the importance of recruitment in moderating pathogen dynamics of multi-host amphibian chytridiomycosis systems. While infection-based parameters are undoubtedly important in Bd management, modifying relative rates of recruitment can substantially alter pathogen-mediated competition between species of an amphibian community., (© 2025 The Ecological Society of America.)

Quantifying temporal changes in species occurrence has been a key part of ecology since its inception. We quantified multidecadal site occupancy trajectories for 18 bird species in four independent long-term, large-scale studies (571 sites, ~1000 km latitude) in Australia. We found evidence of a year × long-term study interaction in the best-fitting models for 14 of the 18 species analysed, with differences in the temporal trajectories of the same species in multiple studies consistent with non-stationarity. Non-stationarity patterns in occupancy were not related to the distance from a species niche centroid; species in locations further from their niche centroid did not demonstrate differing temporal trajectories to those closer to their niche centroid. Furthermore, temporal trajectories of species were not associated with climatic values for each study relative to their niche. Our findings demonstrate the need for multiple long-term studies across a species range, especially when tailoring conservation decisions for populations., (© 2024 The Author(s). Ecology Letters published by John Wiley & Sons Ltd.)

Globally, species are increasingly at risk from compounding threatening processes, an increasingly prominent driver of which is environmental disturbances. To facilitate effective conservation efforts following such events, methods that evaluate potential impacts across multiple species and provide landscape-scale information are needed to guide targeted responses. Often, the geographic overlap between a disturbance and species' distribution is calculated and then used as a proxy for potential impact. However, such methods do not account for the important influence of environmental heterogeneity throughout species' ranges. To address this shortcoming, we quantified the effects of environmental disturbances on species' environmental niche space. Using the Australian 2019 and 2020 Black Summer fires as a case study, we applied a niche-centric approach to examine the potential impacts of these fires on 387 vertebrate species. We examined the utility of established and novel niche metrics to assess the potential impacts of large-scale disturbance events on species by comparing the potential effects of the fires as determined by our various niche measures to those derived from geographic-based measures of impact. We examined the quality of environmental space affected by the disturbance by quantifying the position in niche space where the disturbance occurred (center or margin), the uniqueness of the environmental space that was burned, and the degree to which the remaining, unburned portion of the niche differed from a species' original prefire niche. There was limited congruence between the proportion of geographic and niche space affected, which showed that geographic-based approaches in isolation may have underestimated the impact of the fires for 56% of modeled species. For each species, when combined, these metrics provided a greater indication of postdisturbance recovery potential than geographic-based measures alone. Accordingly, the integration of niche-based analyses into conservation assessments following large-scale disturbance events will lead to a more nuanced understanding of potential impacts and guide more informed and effective conservation actions., (© 2024 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Metapopulations often exist in a fragile balance between local extinctions and (re)colonisations, in which case emerging threats that alter species vital rates may drastically increase metapopulation extinction risk. We combined empirical data with metapopulation simulations to examine how demographic shifts associated with amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) have altered metapopulation viability for threatened amphibians in Australia. Comparing the ages of museum specimens collected before Bd emerged in Australia with individuals from geographically matched remnant populations revealed significant truncation of age structures post-Bd, with a halving of annual adult survival probabilities. Spatially realistic metapopulation modelling demonstrated that reduced adult survival led to major reductions in the parameter space over which persistence was possible for the focal species, with contractions to landscapes with higher landscape connectivity, lower environmental stochasticity and considerably higher recruitment rates. Metapopulation persistence post-Bd required greater landscape connectivity than pre-Bd. This arises from a landscape-level analogue of compensatory recruitment at the population level, in which higher (re)colonisation rates can offset more frequent local extinctions, enabling persistence of amphibians susceptible to Bd. Interactions between recruitment rate, environmental stochasticity and landscape connectivity were also more important for metapopulation persistence post-Bd. Higher recruitment was required to mitigate the impacts of environmental stochasticity, and higher landscape connectivity was required to mitigate the impacts of environmental stochasticity and poor recruitment. Increased reliance on these interdependencies shrunk the parameter space over which metapopulations could persist post-Bd. Our study demonstrates that emerging threats that alter species vital rates can drastically reduce the capacity of certain environments to support metapopulations. For our focal species, reductions in adult survival rates due to Bd produced major reductions in the conditions under which persistence was possible, providing a mechanistic insight into the processes underpinning observed range and niche contractions of amphibians impacted by this pathogen. More broadly, our study illustrates how environmentally mediated host resilience can enable persistence following the emergence of novel pathogens. This pathway to persistence is worthy of greater attention on both conceptual and applied grounds., (© 2024 The Author(s). Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Biodiversity is in rapid decline globally with agriculture being one of the leading causes. Within agricultural landscapes, some features provide a benefit to biodiversity that is disproportionate to their spatial area. An interesting example is artificial ponds-or farm dams-which can support a large variety of taxa. Here, we present a global review of farm dam research related to biodiversity conservation objectives to provide an overview of the topics, key research insights, and the characteristics of current research. We used a three-stage process to screen literature and identified 104 relevant papers across 27 countries encompassing studies of 13 different taxa. Most of the studies were short-term (less than 5 years) with small sample sizes (less than 20 sites). Of the 104 papers, 88 were focussed primarily on ecological outcomes, such as species richness or abundance, and 15 on primary production outcomes, such as crop and livestock yield, despite addressing or measuring ecological metrics. Only one study measured both ecological and primary production outcomes. Studies frequently examined how the features of dams (79 studies) and attributes of the surrounding landscape (47 studies) impact particular species and communities. Terrestrial mammals (1 study) were under-represented in the literature with macrophytes (28 studies), macroinvertebrates (26 studies), and amphibians (19 studies) receiving the most attention. Our results reveal a growing trend towards recognizing farm dams as habitats for various taxa, including amphibians, beetles, dragonflies, and other macroinvertebrates within agricultural environments. Significant knowledge gaps exist in understanding how dam age, invasive species, and effective management practices impact the biodiversity conservation values of farm dams. Future research should emphasize enhancing biodiversity by collaborating with landholders to increase habitat through strategic vegetation planning, minimizing runoff and nutrient inflow, and restricting stock access., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Littlefair et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Global change is causing an unprecedented restructuring of ecosystems, with the spread of invasive species being a key driver. While population declines of native species due to invasives are well documented, much less is known about whether new biotic interactions reshape niches of native species. Here we quantify geographic range and realized-niche contractions in Australian frog species following the introduction of amphibian chytrid fungus Batrachochytrium dendrobatidis, a pathogen responsible for catastrophic amphibian declines worldwide. We show that chytrid-impacted species experienced proportionately greater contractions in niche breadth than geographic distribution following chytrid emergence. Furthermore, niche contractions were directional, with contemporary distributions of chytrid-impacted species characterized by higher temperatures, lower diurnal temperature range, higher precipitation and lower elevations. Areas with these conditions may enable host persistence with chytrid through lower pathogenicity of the fungus and/or greater demographic resilience. Nevertheless, contraction to a narrower subset of environmental conditions could increase host vulnerability to other threatening processes and should be considered in assessments of extinction risk and during conservation planning. More broadly, our results emphasize that biotic interactions can strongly shape species realized niches and that large-scale niche contractions due to new species interactions-particularly emerging pathogens-could be widespread., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Reptiles are an important part of the vertebrate fauna in the temperate woodlands of south-eastern Australia. However, compared to birds and mammals, the long-term occurrence of reptiles across woodland growth types-old growth, regrowth, and replantings-remains poorly understood. Here, using 18-years of data gathered at 218 sites across 1.5 million hectares in New South Wales South West Slopes bioregion, we sought to quantify patterns of temporal change in reptile occurrence and determine if such changes varied between woodland growth types. Despite extensive sampling, almost 75% of our 6341 surveys produced no detections of reptiles. Significant survey effort exceeding 2000 surveys was needed over a prolonged period of time to record detections of 26 reptile species in our study area. Our analyses showed a temporal increase in estimated reptile species richness and abundance over 18 years. Such increases characterized all three vegetation structural types we surveyed. At the individual species level, we had sufficient data to construct models for five of the 26 species recorded. Three of these species were least commonly detected in replantings, whereas the remaining two were most often detected in replantings relative to old growth and regrowth woodland. We found evidence of a temporal increase in two skink species, a decline in one gecko species, and no change in the remaining two skink species. Although detections were consistently low, active searches were the best survey method, and we suggest using this method in habitats known to be hotspots for reptiles, such as rocky outcrops, if the aim is to maximize the number of individuals and species detected. Our findings highlight the value of all three broad vegetation structure types in contributing to woodland reptile biodiversity., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Lindenmayer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Deepening droughts and unprecedented wildfires are at the leading edge of climate change. Such events pose an emerging threat to species maladapted to these perturbations, with the potential for steeper declines than may be inferred from the gradual erosion of their climatic niche. This study focused on two species of amphibians- Philoria kundagungan and Philoria richmondensis (Limnodynastidae)-from the Gondwanan rainforests of eastern Australia that were extensively affected by the "Black Summer" megafires of 2019/2020 and the severe drought associated with them. We sought to assess the impact of these perturbations by quantifying the extent of habitat affected by fire, assessing patterns of occurrence and abundance of calling males post-fire, and comparing post-fire occurrence and abundance with that observed pre-fire. Some 30% of potentially suitable habitat for P. kundagungan was fire affected, and 12% for P. richmondensis . Field surveys revealed persistence in some burnt rainforest; however, both species were detected at a higher proportion of unburnt sites. There was a clear negative effect of fire on the probability of site occupancy, abundance and the probability of persistence for P. kundagungan . For P. richmondensis , effects of fire were less evident due to the limited penetration of fire into core habitat; however, occupancy rates and abundance of calling males were depressed during the severe drought that prevailed just prior to the fires, with the reappearance of calling males linked to the degree of rehydration of breeding habitat post-fire. Our results highlight the possibility that severe negative impacts of climate change for montane rainforest endemics may be felt much sooner than commonly anticipated under a scenario of gradual (decadal-scale) changes in mean climatic conditions. Instead, the increased rate of severe stochastic events places these narrow range species at a heightened risk of extinction in the near-term., Competing Interests: The authors declare no competing interests., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Agricultural practices have created tens of millions of small artificial water bodies ("farm dams" or "agricultural ponds") to provide water for domestic livestock worldwide. Among freshwater ecosystems, farm dams have some of the highest greenhouse gas (GHG) emissions per m 2 due to fertilizer and manure run-off boosting methane production-an extremely potent GHG. However, management strategies to mitigate the substantial emissions from millions of farm dams remain unexplored. We tested the hypothesis that installing fences to exclude livestock could reduce nutrients, improve water quality, and lower aquatic GHG emissions. We established a large-scale experiment spanning 400 km across south-eastern Australia where we compared unfenced (N = 33) and fenced farm dams (N = 31) within 17 livestock farms. Fenced farm dams recorded 32% less dissolved nitrogen, 39% less dissolved phosphorus, 22% more dissolved oxygen, and produced 56% less diffusive methane emissions than unfenced dams. We found no effect of farm dam management on diffusive carbon dioxide emissions and on the organic carbon in the soil. Dissolved oxygen was the most important variable explaining changes in carbon fluxes across dams, whereby doubling dissolved oxygen from 5 to 10 mg L -1 led to a 74% decrease in methane fluxes, a 124% decrease in carbon dioxide fluxes, and a 96% decrease in CO 2 -eq (CH 4  + CO 2 ) fluxes. Dams with very high dissolved oxygen (>10 mg L -1 ) showed a switch from positive to negative CO 2 -eq. (CO 2  + CH 4 ) fluxes (i.e., negative radiative balance), indicating a positive contribution to reduce atmospheric warming. Our results demonstrate that simple management actions can dramatically improve water quality and decrease methane emissions while contributing to more productive and sustainable farming., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Understanding the responses of rare species to altered fire disturbance regimes is an ongoing challenge for ecologists. We asked: are there associations between fire regimes and plant rarity across different vegetation communities? We combined 62 years of fire history records with vegetation surveys of 86 sites across three different dry sclerophyll vegetation communities in Booderee National Park, south-east Australia to: (1) compare associations between species richness and rare species richness with fire regimes, (2) test whether fire regimes influence the proportion of rare species present in an assemblage, and (3) examine whether rare species are associated with particular fire response traits and life history. We also sought to determine if different rarity categorisations influence the associations between fire regimes and plant rarity. We categorised plant rarity using three standard definitions; species' abundance, species' distribution, and Rabinowitz's measure of rarity, which considers a species' abundance, distribution and habitat specificity. We found that total species richness was negatively associated with short fire intervals but positively associated with time since fire and fire frequency in woodland communities. Total species richness was also positively associated with short fire intervals in forest communities. However, rare species richness was not associated with fire when categorised via abundance or distribution. Using Rabinowitz's measure of rarity, the proportion of rare species present was negatively associated with fire frequency in forest communities but positively associated with fire frequency in woodland communities. We found that rare species classified by all three measures of rarity exhibited no difference in fire response traits and serotiny compared to species not classified as rare. Rare species based on abundance differed to species not classified as rare across each life history category, while species rare by distribution differed in preferences for seed storage location. Our findings suggest that species categorised as rare by Rabinowitz's definition of rarity are the most sensitive to the effects of fire regimes. Nevertheless, the paucity of responses observed between rare species with fire regimes in a fire-prone ecosystem suggests that other biotic drivers may play a greater role in influencing the rarity of a species in this system., (© 2022. Crown.)

In many farming landscapes, aquatic features, such as wetlands, creeks, and dams, provide water for stock and irrigation, while also acting as habitat for a range of plants and animals. Indeed, some species threatened by land-use change may otherwise be considerably rarer-or even suffer extinction-in the absence of these habitats. Therefore, a critical issue for the maintenance of biodiversity in agricultural landscapes is the extent to which the management of aquatic systems can promote the integration of agricultural production and biodiversity conservation. We completed a cross-sectional study in southern New South Wales (southeastern Australia) to quantify the efficacy of two concurrently implemented management practices-partial revegetation and control of livestock grazing-aimed at enhancing the vegetation structure, biodiversity value, and water quality of farm dams. We found that excluding livestock for even short periods resulted in increased vegetation cover. Relative to unenhanced dams (such as those that remained unfenced), those that had been enhanced for several years were characterized by reduced levels of turbidity, nutrients, and fecal contamination. Enhanced dams also supported increased richness and abundance of macroinvertebrates. In contrast, unenhanced control dams tended to have high abundance of a few macroinvertebrate taxa. Notably, differences remained between the macroinvertebrate assemblages of enhanced dams and nearby "natural" waterbodies that we monitored as reference sites. While the biodiversity value of semilotic, natural waterbodies in the region cannot be replicated by artificial lentic systems, we consider the extensive system of farm dams in the region to represent a novel ecosystem that may nonetheless support some native macroinvertebrates. Our results show that management interventions such as fencing and grazing control can improve water quality in farm dams, improve vegetation structure around farm dams, and support greater abundance and diversity of aquatic macroinvertebrates., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Determining the drivers of plant rarity is a major challenge in ecology. Analysing spatial associations between different plant species can provide an exploratory avenue for understanding the ecological drivers of plant rarity. Here, we examined the different types of spatial associations between rare and common plants to determine if they influence the occurrence patterns of rare species. We completed vegetation surveys at 86 sites in woodland, forest, and heath communities in south-east Australia. We also examined two different rarity measures to quantify how categorisation criteria affected our results. Rare species were more likely to have positive associations with both rare and common species across all three vegetation communities. However, common species had positive or negative associations with rare and other common species, depending on the vegetation community in which they occurred. Rare species were positively associated with species diversity in forest communities. In woodland communities, rare species were associated negatively with species diversity but positively associated with species evenness. Rare species with high habitat specificity were more clustered spatially than expected by chance. Efforts to understand the drivers of plant rarity should use rarity definitions that consider habitat specificity. Our findings suggest that examining spatial associations between plants can help understand the drivers of plant rarity., Competing Interests: The authors have declared that no competing interests exist.

The recent introduction of the chytrid fungus Batrachochytrium salamandrivorans into northeastern Spain threatens salamander diversity on the Iberian Peninsula. We assessed the current epidemiological situation with extensive field sampling of urodele populations. We then sought to delineate priority regions and identify conservation units for the Iberian Peninsula by estimating the susceptibility of Iberian urodeles using laboratory experiments, evidence from mortality events in nature and captivity and inference from phylogeny. None of the 1395 field samples, collected between 2015 and 2021 were positive for Bsal and no Bsal -associated mortality events were recorded, in contrast to the confirmed occurrence of Bsal outbreak previously described in 2018. We classified five of eleven Iberian urodele species as highly susceptible, predicting elevated mortality and population declines following potential Bsal emergence in the wild, five species as intermediately susceptible with variable disease outcomes and one species as resistant to disease and mortality. We identified the six conservation units (i.e., species or lineages within species) at highest risk and propose priority areas for active disease surveillance and field biosecurity measures. The magnitude of the disease threat identified here emphasizes the need for region-tailored disease abatement plans that couple active disease surveillance to rapid and drastic actions.

Australia's 2019-2020 mega-fires were exacerbated by drought, anthropogenic climate change and existing land-use management. Here, using a combination of remotely sensed data and species distribution models, we found these fires burnt ~97,000 km 2 of vegetation across southern and eastern Australia, which is considered habitat for 832 species of native vertebrate fauna. Seventy taxa had a substantial proportion (>30%) of habitat impacted; 21 of these were already listed as threatened with extinction. To avoid further species declines, Australia must urgently reassess the extinction vulnerability of fire-impacted species and assist the recovery of populations in both burnt and unburnt areas. Population recovery requires multipronged strategies aimed at ameliorating current and fire-induced threats, including proactively protecting unburnt habitats.

Lambert et al question our retrospective and holistic epidemiological assessment of the role of chytridiomycosis in amphibian declines. Their alternative assessment is narrow and provides an incomplete evaluation of evidence. Adopting this approach limits understanding of infectious disease impacts and hampers conservation efforts. We reaffirm that our study provides unambiguous evidence that chytridiomycosis has affected at least 501 amphibian species., (Copyright © 2020, American Association for the Advancement of Science.)

Achieving coexistence between large carnivores and humans in human-dominated landscapes (HDLs) is a key challenge for societies globally. This challenge cannot be adequately met with the current sectoral approaches to HDL governance and an academic community largely dominated by disciplinary sectors. Academia (universities and other research institutions and organizations) should take a more active role in embracing societal challenges around conservation of large carnivores in HDLs by facilitating cross-sectoral cooperation to mainstream coexistence of humans and large carnivores. Drawing on lessons from populated regions of Europe, Asia, and South America with substantial densities of large carnivores, we suggest academia should better embrace the principles and methods of sustainability sciences and create institutional spaces for the implementation of transdisciplinary curricula and projects; reflect on research approaches (i.e., disciplinary, interdisciplinary, or transdisciplinary) they apply and how their outcomes could aid leveraging institutional transformations for mainstreaming; and engage with various institutions and stakeholder groups to create novel institutional structures that can respond to multiple challenges of HDL management and human-large carnivore coexistence. Success in mainstreaming this coexistence in HDL will rest on the ability to think and act cooperatively. Such a conservation achievement, if realized, stands to have far-reaching benefits for people and biodiversity., (© 2019 Society for Conservation Biology.)

Forests globally are subject to disturbances such as logging and fire that create complex temporal variation in spatial patterns of forest cover and stand age. However, investigations that quantify temporal changes in biodiversity in response to multiple forms of disturbance in space and time are relatively uncommon. Over a 10-yr period, we investigated the response of bird species to spatiotemporal changes in forest cover associated with logging and wildfire in the mountain ash (Eucalyptus regnans) forests of southeastern Australia. Specifically, we examined how bird occurrence changed with shifts in the proportion of area burned or logged in a 4.5 km radius surrounding our 88 long-term field survey sites, each measuring 1 ha in size. Overall species richness was greatest in older forest patches, but declined as the amount of fire around each site increased. At the individual species level, 31 of the 37 bird species we modeled exhibited a negative response to the amount of fire in the surrounding landscape, while one species responded positively to fire. Only nine species exhibited signs of recovery in the 6 yr of surveys following the fire. Five species were more likely to be detected as the proportion of logged forest surrounding a site increased, suggesting a possible "concentration effect" with displaced birds moving into unlogged areas following harvesting of adjacent areas. We also identified relationships between the coefficients of life history attributes and spatiotemporal changes in forest cover and stand age. Large-bodied birds and migratory species were associated with landscapes subject to large amounts of fire in 2009. There were associations between old growth stands and small-bodied bird species and species that were not insectivores. Our study shows that birds in mountain ash forests are strongly associated with old growth stands and exhibit complex, time-dependent, and species-specific responses to landscape disturbance. Despite logging and fire both being high-severity perturbations, no bird species exhibited similar responses to fire and logging in the landscape surrounding our sites. Thus, species responses to one kind of landscape-scale disturbance are not readily predictable based on an understanding of the responses to another kind of (albeit superficially similar) disturbance., (© 2019 by the Ecological Society of America.)

Few taxa exhibit the variability of sex-determining modes as amphibians. However, due to the presence of homomorphic sex chromosomes in many species, this phenomenon has been difficult to study. The Australian frog, Litoria aurea, has been relatively well studied over the past 20 years due to widespread declines largely attributable to chytrid fungus. However, it has been subject to few molecular studies and its mode of sex determination remained unknown. We applied DArTseq™ to develop sex-linked single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 44 phenotypically sexed L. aurea individuals from the Molonglo River in NSW, Australia. We conclusively identified a male heterogametic (XX-XY) sex determination mode in this species, identifying 11 perfectly sex-linked SNP and six strongly sex-linked PA markers. We identified a further 47 moderately sex-linked SNP loci, likely serving as evidence indicative of XY recombination. Furthermore, within these 47 loci, a group of nine males were found to have a feminised Y chromosome that significantly differed to all other males. We postulate ancestral sex-reversal as a means for the evolution of this now pseudoautosomal region on the Y chromosome. Our findings present new evidence for the 'fountain of youth' hypothesis for the retention of homomorphic sex chromosomes in amphibians and describe a novel approach for the study of sex chromosome evolution in amphibia.

Anthropogenic trade and development have broken down dispersal barriers, facilitating the spread of diseases that threaten Earth's biodiversity. We present a global, quantitative assessment of the amphibian chytridiomycosis panzootic, one of the most impactful examples of disease spread, and demonstrate its role in the decline of at least 501 amphibian species over the past half-century, including 90 presumed extinctions. The effects of chytridiomycosis have been greatest in large-bodied, range-restricted anurans in wet climates in the Americas and Australia. Declines peaked in the 1980s, and only 12% of declined species show signs of recovery, whereas 39% are experiencing ongoing decline. There is risk of further chytridiomycosis outbreaks in new areas. The chytridiomycosis panzootic represents the greatest recorded loss of biodiversity attributable to a disease., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Species occurrence is influenced by a range of factors including habitat attributes, climate, weather, and human landscape modification. These drivers are likely to interact, but their effects are frequently quantified independently. Here, we report the results of a 13-year study of temperate woodland birds in south-eastern Australia to quantify how different-sized birds respond to the interacting effects of: (a) short-term weather (rainfall and temperature in the 12 months preceding our surveys), (b) long-term climate (average rainfall and maximum and minimum temperatures over the period 1970-2014), and (c) broad structural forms of vegetation (old-growth woodland, regrowth woodland, and restoration plantings). We uncovered significant interactions between bird body size, vegetation type, climate, and weather. High short-term rainfall was associated with decreased occurrence of large birds in old-growth and regrowth woodland, but not in restoration plantings. Conversely, small bird occurrence peaked in wet years, but this effect was most pronounced in locations with a history of high rainfall, and was actually reversed (peak occurrence in dry years) in restoration plantings in dry climates. The occurrence of small birds was depressed-and large birds elevated-in hot years, except in restoration plantings which supported few large birds under these circumstances. Our investigation suggests that different mechanisms may underpin contrasting responses of small and large birds to the interacting effects of climate, weather, and vegetation type. A diversity of vegetation cover is needed across a landscape to promote the occurrence of different-sized bird species in agriculture-dominated landscapes, particularly under variable weather conditions. Climate change is predicted to lead to widespread drying of our study region, and restoration plantings-especially currently climatically wet areas-may become critically important for conserving bird species, particularly small-bodied taxa., (© 2018 John Wiley & Sons Ltd.)

Infectious diseases can alter the demography of their host populations, reducing their viability even in the absence of mass mortality. Amphibians are the most threatened group of vertebrates globally, and emerging infectious diseases play a large role in their continued population declines. Viruses belonging to the genus Ranavirus are responsible for one of the deadliest and most widespread of these diseases. To date, no work has used individual level data to investigate how ranaviruses affect population demographic structure. We used skeletochronology and morphology to evaluate the impact of ranaviruses on the age structure of populations of the European common frog ( Rana temporaria ) in the UK. We compared ecologically similar populations that differed most notably in their historical presence or absence of ranavirosis (the acute syndrome caused by ranavirus infection). Our results suggest that ranavirosis may truncate the age structure of R. temporaria populations. One potential explanation for such a shift might be increased adult mortality and subsequent shifts in the life history of younger age classes that increase reproductive output earlier in life. Additionally, we constructed population projection models which indicated that such increased adult mortality could heighten the vulnerability of frog populations to stochastic environmental challenges., Competing Interests: Xavier A Harrison serves as an Academic Editor for PeerJ. Amber G F Griffiths is a director of FoAM Kernow (FoAM Kernow is an affiliated studio of FoAM, which is a multinational, not for profit, network of transdisciplinary labs at the intersection of art, science, nature and everyday life).

The fungal skin disease, chytridiomycosis (caused by Batrachochytrium dendrobatidis and B. salamandrivorans ), has caused amphibian declines and extinctions globally since its emergence. Characterizing the host immune response to chytridiomycosis has been a focus of study with the aim of disease mitigation. However, many aspects of the innate and adaptive arms of this response are still poorly understood, likely due to the wide range of species' responses to infection. In this paper we provide an overview of expected immunological responses (with inference based on amphibian and mammalian immunology), together with a synthesis of current knowledge about these responses for the amphibian-chytridiomycosis system. We structure our review around four key immune stages: (1) the naïve immunocompetent state, (2) immune defenses that are always present (constitutive defenses), (3) mechanisms for recognition of a pathogen threat and innate immune defenses, and (4) adaptive immune responses. We also evaluate the current hot topics of immunosuppression and immunopathology in chytridiomycosis, and discuss their respective roles in pathogenesis. Our synthesis reveals that susceptibility to chytridiomycosis is likely to be multifactorial. Susceptible amphibians appear to have ineffective constitutive and innate defenses, and a late-stage response characterized by immunopathology and Bd-induced suppression of lymphocyte responses. Overall, we identify substantial gaps in current knowledge, particularly concerning the entire innate immune response (mechanisms of initial pathogen detection and possible immunoevasion by Bd, degree of activation and efficacy of the innate immune response, the unexpected absence of innate leukocyte infiltration, and the cause and role of late-stage immunopathology in pathogenesis). There are also gaps concerning most of the adaptive immune system (the relative importance of B and T cell responses for pathogen clearance, the capacity and extent of immunological memory, and specific mechanisms of pathogen-induced immunosuppression). Improving our capacity for amphibian immunological research will require selection of an appropriate Bd-susceptible model species, the development of taxon-specific affinity reagents and cell lines for functional assays, and the application of a suite of conventional and emerging immunological methods. Despite current knowledge gaps, immunological research remains a promising avenue for amphibian conservation management.

Targeted threatened species management is a central component of efforts to prevent species extinction. Despite the development of a range of management frameworks to improve conservation outcomes over the past decade, threatened species management is still commonly characterised as ad hoc. Although there are notable successes, many management programs are ineffective, with relatively few species experiencing improvements in their conservation status. We identify underlying factors that commonly lead to ineffective and inefficient management. Drawing attention to some of the key challenges, and suggesting ways forward, may lead to improved management effectiveness and better conservation outcomes. We highlight six key areas where improvements are needed: 1) stakeholder engagement and communication; 2) fostering strong leadership and the development of achievable long-term goals; 3) knowledge of target species' biology and threats, particularly focusing on filling knowledge gaps that impede management, while noting that in many cases there will be a need for conservation management to proceed initially despite knowledge gaps; 4) setting objectives with measurable outcomes; 5) strategic monitoring to evaluate management effectiveness; and 6) greater accountability for species declines and failure to recover species to ensure timely action and guard against complacency. We demonstrate the importance of these six key areas by providing examples of innovative approaches leading to successful species management. We also discuss overarching factors outside the realm of management influence that can help or impede conservation success. Clear recognition of factors that make species' management more straightforward - or more challenging - is important for setting realistic management objectives, outlining strategic action, and prioritising resources. We also highlight the need to more clearly demonstrate the benefit of current investment, and communicate that the risk of under-investment is species extinctions. Together, improvements in conservation practice, along with increased resource allocation and re-evaluation of the prioritisation of competing interests that threaten species, will help enhance conservation outcomes for threatened species., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) from multiple populations (one evolutionarily naïve to chytridiomycosis) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments. We investigated (A) survival outcomes and clinical pathogen burdens between populations and clutches, and (B) individual host tissue responses to chytridiomycosis. Here we present multiple interrelated datasets associated with these exposure experiments, including animal signalment, survival and pathogen burden of 355 animals from Experiment A, and the following datasets related to 61 animals from Experiment B: animal signalment and pathogen burden; raw RNA-Seq reads from skin, liver and spleen tissues; de novo assembled transcriptomes for each tissue type; raw gene expression data; annotation data for each gene; and raw metabolite expression data from skin and liver tissues. These data provide an extensive baseline for future analyses.

Potentiating the evolution of immunity is a promising strategy for addressing biodiversity diseases. Assisted selection for infection resistance may enable the recovery and persistence of amphibians threatened by chytridiomycosis, a devastating fungal skin disease threatening hundreds of species globally. However, knowledge of the mechanisms involved in the natural evolution of immunity to chytridiomycosis is limited. Understanding the mechanisms of such resistance may help speed-assisted selection. Using a transcriptomics approach, we examined gene expression responses of endangered alpine tree frogs (Litoria verreauxii alpina) to subclinical infection, comparing two long-exposed populations with a naïve population. We performed a blinded, randomized and controlled exposure experiment, collecting skin, liver and spleen tissues at 4, 8 and 14 days postexposure from 51 wild-caught captively reared infection-naïve adult frogs for transcriptome assembly and differential gene expression analyses. We analysed our results in conjunction with infection intensity data, and the results of a large clinical survival experiment run concurrently with individuals from the same clutches. Here, we show that frogs from an evolutionarily long-exposed and phenotypically more resistant population of the highly susceptible alpine tree frog demonstrate a more robust innate and adaptive immune response at the critical early subclinical stage of infection when compared with two more susceptible populations. These results are consistent with the occurrence of evolution of resistance against chytridiomycosis, help to explain underlying resistance mechanisms, and provide genes of potential interest and sequence data for future research. We recommend further investigation of cell-mediated immunity pathways, the role of interferons and mechanisms of lymphocyte suppression., (© 2018 John Wiley & Sons Ltd.)

Emerging pathogens can drive evolutionary shifts in host life-history traits, yet this process remains poorly documented in vertebrate hosts. Amphibian chytridiomycosis, caused by infection with the fungal pathogen Batrachochytrium dendrobatidis (Bd), is the worst recorded wildlife disease and has caused the extinction of over 100 species across multiple continents. A similar number of additional species have experienced mass declines and Bd remains a major source of mortality in many populations of declined species now persisting with the pathogen. Life-history theory predicts that increased extrinsic mortality in Bd-infected populations may alter amphibian life-history traits, but this has not been examined. Here, we investigate whether population Bd status is associated with age and size at maturity by comparing long-exposed Bd-infected populations, Bd-free populations, and museum specimens collected prior to Bd emergence for the endangered Australian frog Litoria verreauxii alpina. We show that Bd-infected populations have a higher proportion of males that mature at 1 year of age, and females that mature at 2 years of age, compared to Bd-free populations. Earlier maturation was associated with reduced size at maturity in males. Consistent with life-history theory, our findings may represent an adaptive evolutionary shift towards earlier maturation in response to high Bd-induced mortality. To our knowledge, this study provides the first evidence for a post-metamorphic Bd-associated shift in an amphibian life-history trait. Given high mortality in other Bd-challenged species, we suggest that chytridiomycosis may be a substantial new selection pressure shaping life-history traits in impacted amphibian species across multiple continents.

Emerging wildlife pathogens are an increasing threat to biodiversity. One of the most serious wildlife diseases is chytridiomycosis, caused by the fungal pathogen, Batrachochytrium dendrobatidis (Bd), which has been documented in over 500 amphibian species. Amphibians vary greatly in their susceptibility to Bd; some species tolerate infection, whereas others experience rapid mortality. Reservoir hosts-species that carry infection while maintaining high abundance but are rarely killed by disease-can increase extinction risk in highly susceptible, sympatric species. However, whether reservoir hosts amplify Bd in declining amphibian species has not been examined. We investigated the role of reservoir hosts in the decline of the threatened northern corroboree frog (Pseudophryne pengilleyi) in an amphibian community in southeastern Australia. In the laboratory, we characterized the response of a potential reservoir host, the (nondeclining) common eastern froglet (Crinia signifera), to Bd infection. In the field, we conducted frog abundance surveys and Bd sampling for both P. pengilleyi and C. signifera. We built multinomial logistic regression models to test whether Crinia signifera and environmental factors were associated with P. pengilleyi decline. C. signifera was a reservoir host for Bd. In the laboratory, many individuals maintained intense infections (>1000 zoospore equivalents) over 12 weeks without mortality, and 79% of individuals sampled in the wild also carried infections. The presence of C. signifera at a site was strongly associated with increased Bd prevalence in sympatric P. pengilleyi. Consistent with disease amplification by a reservoir host, P. pengilleyi declined at sites with high C. signifera abundance. Our results suggest that when reservoir hosts are present, population declines of susceptible species may continue long after the initial emergence of Bd, highlighting an urgent need to assess extinction risk in remnant populations of other declined amphibian species., (© 2016 Society for Conservation Biology.)

A fundamental aim of conservation biology is to understand how species respond to threatening processes, with much research effort focused on identifying threats and quantifying spatial and temporal patterns of species decline. Here, we argue that threats often reduce the realized niche breadth of declining species because environmental, biotic, and evolutionary processes reduce or amplify threats, or because a species' capacity to tolerate threats varies across niche space. Our 'niche reduction hypothesis' provides a new lens for understanding why species decline in some locations and not others. This perspective can improve management of declining species by identifying where to focus resources and which interventions are most likely to be effective in a given environment., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Pathogen emergence can drive major changes in host population demography, with implications for population dynamics and sensitivity to environmental fluctuations. The amphibian disease chytridiomycosis, caused by infection with the fungal pathogen Batrachochytrium dendrobatidis (Bd), is implicated in the severe decline of over 200 amphibian species. In species that have declined but not become extinct, Bd persists and can cause substantial ongoing mortality. High rates of mortality associated with Bd may drive major changes in host demography, but this process is poorly understood. Here, we compared population age structure of Bd-infected populations, Bd-free populations and museum specimens collected prior to Bd emergence for the endangered Australian frog, Litoria verreauxii alpina (alpine tree frog). We then used population simulations to investigate how pathogen-associated demographic shifts affect the ability of populations to persist in stochastic environments. We found that Bd-infected populations have a severely truncated age structure associated with very high rates of annual adult mortality. Near-complete annual adult turnover in Bd-infected populations means that individuals breed once, compared with Bd-free populations where adults may breed across multiple years. Our simulations showed that truncated age structure erodes the capacity of populations to withstand periodic recruitment failure; a common challenge for species reproducing in uncertain environments. We document previously undescribed demographic shifts associated with a globally emerging pathogen and demonstrate how these shifts alter host ecology. Truncation of age structure associated with Bd effectively reduces host niche width and can help explain the contraction of L. v. alpina to perennial waterbodies where the risk of drought-induced recruitment failure is low. Reduced capacity to tolerate other sources of mortality may explain variation in decline severity among other chytridiomycosis-challenged species and highlights the potential to mitigate disease impacts through minimizing other sources of mortality., (© 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.)