Integrating species traits with extrinsic threats: closing the gap between predicting and preventing species declines

More losers than winners: investigating Anthropocene defaunation through the diversity of population trends

The global-scale decline of animal biodiversity ('defaunation') represents one of the most alarming consequences of human impacts on the planet. The quantification of this extinction crisis has traditionally relied on the use of IUCN Red List conservation categories assigned to each assessed species. This approach reveals that a quarter of the world's animal species are currently threatened with extinction, and ~1% have been declared extinct. However, extinctions are preceded by progressive population declines through time that leave demographic 'footprints' that can alert us about the trajectories of species towards extinction. Therefore, an exclusive focus on IUCN conservation categories, without consideration of dynamic population trends, may underestimate the true extent of the processes of ongoing extinctions across nature. In fact, emerging evidence (e.g. the Living Planet Report), reveals a widespread tendency for sustained demographic declines (an average 69% decline in population abundances) of species globally. Yet, animal species are not only declining. Many species worldwide exhibit stable populations, while others are even thriving. Here, using population trend data for >71,000 animal species spanning all five groups of vertebrates (mammals, birds, reptiles, amphibians and fishes) and insects, we provide a comprehensive global-scale assessment of the diversity of population trends across species undergoing not only declines, but also population stability and increases. We show a widespread global erosion of species, with 48% undergoing declines, while 49% and 3% of species currently remain stable or are increasing, respectively. Geographically, we reveal an intriguing pattern similar to that of threatened species, whereby declines tend to concentrate around tropical regions, whereas stability and increases show a tendency to expand towards temperate climates. Importantly, we find that for species currently classed by the IUCN Red List as 'non-threatened', 33% are declining. Critically, in contrast with previous mass extinction events, our assessment shows that the Anthropocene extinction crisis is undergoing a rapid biodiversity imbalance, with levels of declines (a symptom of extinction) greatly exceeding levels of increases (a symptom of ecological expansion and potentially of evolution) for all groups. Our study contributes a further signal indicating that global biodiversity is entering a mass extinction, with ecosystem heterogeneity and functioning, biodiversity persistence, and human well-being under increasing threat.

Primates facing climate crisis in a tropical forest hotspot will lose climatic suitable geographical range

Global climate changes affect biodiversity and cause species distribution shifts, contractions, and expansions. Climate change and disease are emerging threats to primates, and approximately one-quarter of primates' ranges have temperatures over historical ones. How will climate changes influence Atlantic Forest primate ranges? We used habitat suitability models and measured potential changes in area and distributions shifts. Climate change expected in 2100 may change the distribution area of Atlantic Forest primates. Fourteen species (74%) are predicted to lose more than 50% of their distribution, and nine species (47%) are predicted to lose more than 75% of their distribution. The balance was negative, indicating a potential future loss, and the strength of the reduction in the distribution is related to the severity of climate change (SSP scenarios). Directional shifts were detected to the south. The projected mean centroid latitudinal shift is ~ 51 km to the south for 2100 SSP5-8.5 scenario. The possibility of dispersal will depend on suitable routes and landscape configuration. Greenhouse gas emissions should be urgently reduced. Our results also emphasize that no more forest loss is acceptable in Atlantic Forest, and restoration, canopy bridges, friendly agroecosystems, and monitoring of infrastructure projects are urgent to enable dealing with climate change.

Geographic range size, water temperature, and extrinsic threats predict the extinction risk in global cetaceans

Despite the fact that cetaceans provide significant ecological contributions to the health and stability of aquatic ecosystems, many are highly endangered with nearly one-third of species assessed as threatened with extinction. Nevertheless, to date, few studies have explicitly examined the patterns and processes of extinction risk and threats for this taxon, and even less between the two subclades (Mysticeti and Odontoceti). To fill this gap, we compiled a dataset of six intrinsic traits (active region, geographic range size, body weight, diving depth, school size, and reproductive cycle), six environmental factors relating to sea surface temperature and chlorophyll concentration, and two human-related threat indices that are commonly recognized for cetaceans. We then employed phylogenetic generalized least squares models and model selection to identify the key predictors of extinction risk in all cetaceans, as well as in the two subclades. We found that geographic range size, sea surface temperature, and human threat index were the most important predictors of extinction risk in all cetaceans and in odontocetes. Interestingly, maximum body weight was positively associated with the extinction risk in mysticetes, but negatively related to that for odontocetes. By linking seven major threat types to extinction risk, we further revealed that fisheries bycatch was the most common threat, yet the impacts of certain threats could be overestimated when considering all species rather than just threatened ones. Overall, we suggest that conservation efforts should focus on small-ranged cetaceans and species living in warmer waters or under strong anthropogenic pressures. Moreover, further studies should consider the threatened status of species when superimposing risk maps and quantifying risk severity. Finally, we emphasize that mysticetes and odontocetes should be conserved with different strategies, because their extinction risk patterns and major threat types are considerably different. For instance, large-bodied mysticetes and small-ranged odontocetes require special conservation priority.

Anthropogenic habitat modification alters calling phenology of frogs

Anthropogenic habitat modification significantly challenges biodiversity. With its intensification, understanding species' capacity to adapt is critical for conservation planning. However, little is known about whether and how different species are responding, particularly among frogs. We used a continental-scale citizen science dataset of >226,000 audio recordings of 42 Australian frog species to investigate how calling-a proxy for breeding-phenology varied along an anthropogenic modification gradient. Calling started earlier and breeding seasons lengthened with increasing modification intensity. Breeding seasons averaged 22.9 ± 8.25 days (standard error) longer in the most modified compared to the least modified regions, suggesting that frog breeding activity was sensitive to habitat modification. We also examined whether calls varied along a modification gradient by analysing the temporal and spectral properties of advertisement calls from a subset of 441 audio recordings of three broadly distributed frog species. There was no appreciable effect of anthropogenic habitat modification on any of the measured call variables, although there was high variability. With continued habitat modification, species may shift towards earlier and longer breeding seasons, with largely unknown ecological consequences in terms of proximate and ultimate fitness.

Survival of climate warming through niche shifts: Evidence from frogs on tropical islands

How will organisms cope when forced into warmer-than-preferred thermal environments? This is a key question facing our ability to monitor and manage biota as average annual temperatures increase, and is of particular concern for range-limited terrestrial species unable to track their preferred climatic envelope. Being ectothermic, desiccation prone, and often spatially restricted, island-inhabiting tropical amphibians exemplify this scenario. Pre-Anthropocene case studies of how insular amphibian populations responded to the enforced occupation of warmer-than-ancestral habitats may add a valuable, but currently lacking, perspective. We studied a population of frogs from the Seychelles endemic family Sooglossidae which, due to historic sea-level rise, have been forced to occupy a significantly warmer island (Praslin) than their ancestors and close living relatives. Evidence from thermal activity patterns, bioacoustics, body size distributions, and ancestral state estimations suggest that this population shifted its thermal niche in response to restricted opportunities for elevational dispersal. Relative to conspecifics, Praslin sooglossids also have divergent nuclear genotypes and call characters, a finding consistent with adaptation causing speciation in a novel thermal environment. Using an evolutionary perspective, our study reveals that some tropical amphibians have survived episodes of historic warming without the aid of dispersal and therefore may have the capacity to adapt to the currently warming climate. However, two otherwise co-distributed sooglossid species are absent from Praslin, and the deep evolutionary divergence between the frogs on Praslin and their closest extant relatives (~8 million years) may have allowed for gradual thermal adaptation and speciation. Thus, local extinction is still a likely outcome for tropical frogs experiencing warming climates in the absence of dispersal corridors to thermal refugia.

Assessing the Impact of Climate Change on Potential Distribution of Meconopsis punicea and Its Influence on Ecosystem Services Supply in the Southeastern Margin of Qinghai-Tibet Plateau

Meconopsis punicea is an iconic ornamental and medicinal plant whose natural habitat has degraded under global climate change, posing a serious threat to the future survival of the species. Therefore, it is critical to analyze the influence of climate change on possible distribution of M. punicea for conservation and sustainable utilization of this species. In this study, we used MaxEnt ecological niche modeling to predict the potential distribution of M. punicea under current and future climate scenarios in the southeastern margin region of Qinghai-Tibet Plateau. Model projections under current climate show that 16.8% of the study area is suitable habitat for Meconopsis. However, future projections indicate a sharp decline in potential habitat for 2050 and 2070 climate change scenarios. Soil type was the most important environmental variable in determining the habitat suitability of M. punicea, with 27.75% contribution to model output. Temperature seasonality (16.41%), precipitation of warmest quarter (14.01%), and precipitation of wettest month (13.02%), precipitation seasonality (9.41%) and annual temperature range (9.24%) also made significant contributions to model output. The mean elevation of suitable habitat for distribution of M. punicea is also likely to shift upward in most future climate change scenarios. This study provides vital information for the protection and sustainable use of medicinal species like M. punicea in the context of global environmental change. Our findings can aid in developing rational, broad-scale adaptation strategies for conservation and management for ecosystem services, in light of future climate changes.

Species' traits drive amphibian tolerance to anthropogenic habitat modification

Anthropogenic habitat modification is accelerating, threatening the world's biodiversity. Understanding species' responses to anthropogenic modification is vital for halting species' declines. However, this information is lacking for globally threatened amphibians, informed primarily by small community-level studies. We integrated >126,000 verified citizen science observations of frogs, with a global continuous measure of anthropogenic habitat modification for a continental scale analysis of the effects of habitat modification on frogs. We derived a modification tolerance index-accounting for anthropogenic stressors such as human habitation, agriculture, transport and energy production-for 87 species (36% of all Australian frog species). We used this index to quantify and rank each species' tolerance of anthropogenic habitat modification, then compiled traits of all the frog species and assessed how well these equipped species to tolerate modified habitats. Most of Australia's frog species examined were adversely affected by habitat modification. Habitat specialists and species with large geographic range sizes were the least tolerant of habitat modification. Call dominant frequency, body size, clutch type and calling position (i.e. from vegetation) were also related to tolerance of habitat modification. There is an urgent need for improved consideration of anthropogenic impacts and improved conservation measures to ensure the long-term persistence of frog populations, particularly focused on specialists and species identified as intolerant of modified habitats.

Biological and extrinsic correlates of extinction risk in Chinese lizards

China is a country with one of the most species-rich reptile faunas in the world. However, nearly a quarter of Chinese lizard species assessed by the China Biodiversity Red List are threatened. Nevertheless, to date, no study has explicitly examined the pattern and processes of extinction and threat in Chinese lizards. In this study, we conducted the first comparative phylogenetic analysis of extinction risk in Chinese lizards. We addressed the following 3 questions: (1) What is the pattern of extinction and threat in Chinese lizards? (2) Which species traits and extrinsic factors are related to their extinction risk? (3) How can we protect Chinese lizards based on our results? We collected data on 10 species traits (body size [BS], clutch size, geographic range size, activity time, reproductive mode, habitat specialization [HS], habitat use, leg development, maximum elevation, and elevation range) and 7 extrinsic factors (mean annual precipitation (MAP), mean annual temperature, mean annual solar insolation, normalized difference vegetation index (NDVI), human footprint, human population density, and human exploitation). After phylogenetic correction, these variables were used separately and in combination to assess their associations with extinction risk. We found that Chinese lizards with a small geographic range, large BS, high HS, and living in high MAP areas were vulnerable to extinction. Conservation priority should thus be given to species with the above extinction-prone traits so as to effectively protect Chinese lizards. Preventing future habitat destruction should also be a primary focus of management efforts because species with small range size and high HS are particularly vulnerable to habitat loss.

Targeting Conservation Actions at Species Threat Response Thresholds

Given the failure of the world's governments to improve the status of biodiversity by 2020, a new strategic plan for 2030 is being developed. In order to be successful, a step-change is needed to not just simply halt biodiversity loss, but to bend the curve of biodiversity loss to stable or increasing species' populations. Here, we propose a framework that quantifies species' responses across gradients of threat intensity to implement more efficient and better targeted conservation actions. Our framework acknowledges the variation in threat intensities as well as the differences among species in their capacity to respond, and is implemented at a relevant scale for national and international policy-making.

Invasion syndromes: a systematic approach for predicting biological invasions and facilitating effective management

Our ability to predict invasions has been hindered by the seemingly idiosyncratic context-dependency of individual invasions. However, we argue that robust and useful generalisations in invasion science can be made by considering “invasion syndromes” which we define as “a combination of pathways, alien species traits, and characteristics of the recipient ecosystem which collectively result in predictable dynamics and impacts, and that can be managed effectively using specific policy and management actions”. We describe this approach and outline examples that highlight its utility, including: cacti with clonal fragmentation in arid ecosystems; small aquatic organisms introduced through ballast water in harbours; large ranid frogs with frequent secondary transfers; piscivorous freshwater fishes in connected aquatic ecosystems; plant invasions in high-elevation areas; tall-statured grasses; and tree-feeding insects in forests with suitable hosts. We propose a systematic method for identifying and delimiting invasion syndromes. We argue that invasion syndromes can account for the context-dependency of biological invasions while incorporating insights from comparative studies. Adopting this approach will help to structure thinking, identify transferrable risk assessment and management lessons, and highlight similarities among events that were previously considered disparate invasion phenomena.

Phylogenetic investigation of skin sloughing rates in frogs: relationships with skin characteristics and disease-driven declines

Amphibian skin is highly variable in structure and function across anurans, and plays an important role in physiological homeostasis and immune defence. For example, skin sloughing has been shown to reduce pathogen loads on the skin, such as the lethal fungus Batrachochytrium dendrobatidis ( Bd), but interspecific variation in sloughing frequency is largely unknown. Using phylogenetic linear mixed models, we assessed the relationship between skin turnover rate, skin morphology, ecological traits and overall evidence of Bd-driven declines. We examined skin sloughing rates in 21 frog species from three continents, as well as structural skin characteristics measured from preserved specimens. We found that sloughing rate varies significantly with phylogenetic group, but was not associated with evidence of Bd-driven declines, or other skin characteristics examined. This is the first comparison of sloughing rate across a wide range of amphibian species, and creates the first database of amphibian sloughing behaviour. Given the strong phylogenetic signal observed in sloughing rate, approximate sloughing rates of related species may be predicted based on phylogenetic position. While not related to available evidence of declines, understanding variation in sloughing rate may help explain differences in the severity of infection in genera with relatively slow skin turnover rates (e.g. Atelopus).

Forest-type specialization strongly predicts avian responses to tropical agriculture

Species' traits influence how populations respond to land-use change. However, even in well-characterized groups such as birds, widely studied traits explain only a modest proportion of the variance in response across species. Here, we show that associations with particular forest types strongly predict the sensitivity of forest-dwelling Amazonian birds to agriculture. Incorporating these fine-scale habitat associations into models of population response dramatically improves predictive performance and markedly outperforms the functional traits that commonly appear in similar analyses. Moreover, by identifying habitat features that support assemblages of unusually sensitive habitat-specialist species, our model furnishes straightforward conservation recommendations. In Amazonia, species that specialize on forests along a soil-nutrient gradient (i.e. both rich-soil specialists and poor-soil specialists) are exceptionally sensitive to agriculture, whereas species that specialize on floodplain forests are unusually insensitive. Thus, habitat specialization per se does not predict disturbance sensitivity, but particular habitat associations do. A focus on conserving specific habitats that harbour highly sensitive avifaunas (e.g. poor-soil forest) would protect a critically threatened component of regional biodiversity. We present a conceptual model to explain the divergent responses of habitat specialists in the different habitats, and we suggest that similar patterns and conservation opportunities probably exist for other taxa and regions.

Differential Responses to Climate and Land-Use Changes in Threatened Chinese Taxus Species

Rapid climate and land-use changes have been considered as the foremost threat to global biodiversity. China contains more than 3500 threatened higher plants, whereas the relative influence of climate and land-use changes on these endangered plants have not been explored simultaneously under topographical constraints. Here, using Taxus plants as the case study genus, we simulated the distribution range of threatened species under three scenarios of current and future climate and land-use conditions under topographical constraints. We also measured the associated difference in the responses of Taxus species to climate and land-use changes. Our results demonstrated the substantial influence of climate and land-use changes on the distributions of Taxus species. However, we observed different responses of Taxus species to these environmental changes. The distribution range of T. cuspidate Siebold & Zuccarini and T. mairei Lemee & H. Léveillé would substantially shrink, whereas the habitat range of T. fuana Nan Li & R. R. Mill would sharply expand under RCP 8.5(Representative Concentration Pathway scenarios) scenario. Meanwhile, T. wallichiana Zuccarini and T. chinensis (Pilger) Florin would experience apparent range shifts. Furthermore, topographical factors played non-negligible roles in shaping species distributions, and modifying the influence of climate and land-use changes. Together, these results provide robust evidence that even threatened species will have multiple responses to climate and land-use changes (e.g., shrinking, expanding, shifting). Our findings highlight that taking species ecological traits, habitat characteristics, and topographical constraints into account might provide valuable insights into threatened species conservation in the face of global environmental changes.

Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

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.

Climate and land use changes will degrade the distribution of Rhododendrons in China

Biodiversity loss and variation in species responses to climate and land use change have been found across broad taxonomic groups. However, whether species from the same taxonomic group with distinct geographical ranges will respond differently is poorly understood. The aim of this study is to predict the potential impacts of future climate and land use change on the distribution of narrow- and wide-ranging Rhododendron species, and estimate their relative contribution in China. We applied the presence-only ecological niche model MaxEnt to predict the distribution of 10 narrow-ranging and 10 wide-ranging Rhododendron species for the year 2070, using three general circulation models and three scenarios of climate and land use change. We measured the predicted distribution change of each species using change ratio, distance and direction of core range shifts, and niche overlap using Schoener's D. We found that the distribution areas of six narrow-ranging species would decrease, of which one species would go extinct. The remaining four narrow-ranging species would experience range expansion. Distribution of all the wide-ranging Rhododendron species would decrease. All Rhododendrons will shift to the northwest. We conclude that Rhododendron species generally will be negatively affected by the climatic and land use change expected in 2070 from the three scenarios evaluated in this study, but some narrow-ranging species may be positively influenced. Narrow-ranging Rhododendron species are more vulnerable compared to wide-ranging Rhododendron species. This study demonstrated that the effects of climate and land use change on alpine and subalpine plant species is species-specific, thereby strengthening our understanding of the impacts of climate and land use change on plant distribution.

Assessing Fish Species Tolerance in the Huntai River Basin, China: Biological Traits versus Weighted Averaging Approaches

Fish species tolerance used as a component of fish-index of biological integrity (F-IBI) can be problematic as it is usually classified using the historical data, data from literature or expert judgments. In this study, fish assemblages, water quality parameters and physical habitat factors from 206 sampling sites in the Huntai River Basin were analyzed to develop tolerance indicator values (TIVs) of fish based on a (Fb-TIVs) and the weighted averaging (WA) method (FW-TIVs). The two quantitative methods for fish tolerance were then compared. The FW-TIVs and Fb-TIVs of fish species were calculated separately using a WA inference model based on ten water quality parameters (WT, pH, DO, SC, TDS, NH3, NO2−, NO3−, TP, Cl−, and SO42−), and six biological traits (lithophilic spawning, benthic invertivores, cold water species, equilibrium or periodic life history strategies, families of Cottidae, and species distribution range). Fish species were then classified into biological traits approach three categories (tolerant species, moderately tolerant species, and sensitive species). The results indicated that only 30.3% fish species have the same classification based on FW-TIVs and Fb-TIVs. However, the proportion of tolerant species based on two methods had a similar response to environmental stress, and these tolerant species were correlated with PCA axes 1 site scores obtained by (FW-TIVs, p < 0.05, R2 = 0.434; Fb-TIVs, p < 0.05, R2 = 0.334) and not correlated with PCA axis 2 site scores (FW-TIVs, p > 0.05, R2 = 0.001; Fb-TIVs, p > 0.05, R2 = 0.012) and PCA axis 3 site scores (FW-TIVs, p > 0.05, R2 = 0.000; Fb-TIVs, p > 0.05, R2 = 0.013). The results of linear regression analyses indicated that Fb-TIVs can be used for the study of fish tolerance. Fish tolerance assessments based on FW-TIVs requires long-term monitoring of fish assemblages and water quality parameters to provide sufficient data for quantitative studies. The Fb-TIV method relies on the accurate identification of fish traits by an ichthyologist. The two methods used in this study can provide methodological references for quantitative studies of fish tolerance in other regions, and are of great significance for the development of biological assessment tools.

Edge effects in fire-prone landscapes: Ecological importance and implications for fauna

Edges are ecologically important environmental features and have been well researched in agricultural and urban landscapes. However, little work has been conducted in flammable ecosystems where spatially and temporally dynamic fire edges are expected to influence important processes such as recolonization of burnt areas and landscape connectivity. We review the literature on fire, fauna, and edge effects to summarize current knowledge of faunal responses to fire edges and identify knowledge gaps. We then develop a conceptual model to predict faunal responses to fire edges and present an agenda for future research. Faunal abundance at fire edges changes over time, but patterns depend on species traits and resource availability. Responses are also influenced by edge architecture (e.g., size and shape), site and landscape context, and spatial scale. However, data are limited and the influence of fire edges on both local abundance and regional distributions of fauna is largely unknown. In our conceptual model, biophysical properties interact with the fire regime (e.g., patchiness, frequency) to influence edge architecture. Edge architecture and species traits influence edge permeability, which is linked to important processes such as movement, resource selection, and species interactions. Predicting the effect of fire edges on fauna is challenging, but important for biodiversity conservation in flammable landscapes. Our conceptual model combines several drivers of faunal fire responses (biophysical properties, regime attributes, species traits) and will therefore lead to improved predictions. Future research is needed to understand fire as an agent of edge creation; the spatio-temporal flux of fire edges across landscapes; and the effect of fire edges on faunal movement, resource selection, and biotic interactions. To aid the incorporation of new data into our predictive framework, our model has been designed as a Bayesian Network, a statistical tool capable of analyzing complex environmental relationships, dealing with data gaps, and generating testable hypotheses.

Batrachochytrium salamandrivorans and the Risk of a Second Amphibian Pandemic

Amphibians are experiencing devastating population declines globally. A major driver is chytridiomycosis, an emerging infectious disease caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Bd was described in 1999 and has been linked with declines since the 1970s, while Bsal is a more recently discovered pathogen that was described in 2013. It is hypothesized that Bsal originated in Asia and spread via international trade to Europe, where it has been linked to salamander die-offs. Trade in live amphibians thus represents a significant threat to global biodiversity in amphibians. We review the current state of knowledge regarding Bsal and describe the risk of Bsal spread. We discuss regional responses to Bsal and barriers that impede a rapid, coordinated global effort. The discovery of a second deadly emerging chytrid fungal pathogen in amphibians poses an opportunity for scientists, conservationists, and governments to improve global biosecurity and further protect humans and wildlife from a growing number of emerging infectious diseases.

What makes a successful species? Traits facilitating survival in altered tropical forests

Background

Ongoing conversion, disturbance and fragmentation of tropical forests stress this ecosystem and cause the decline or disappearance of many species. Particular traits have been identified which indicate an increasing extinction risk of a species, but traits facilitating survival in altered habitats have mostly been neglected. Here we search for traits that make a species tolerant to disturbances, thus independent of pristine forests. We identify the fauna that have an increasing effect on the ecosystem and its functioning in our human-dominated landscapes.

Methods

We use a unique set of published data on the occurrences of 243 frog species in pristine and altered forests throughout the tropics. We established a forest dependency index with four levels, based on these occurrence data and applied Random Forest classification and binomial Generalized Linear Models to test whether species life history traits, ecological traits or range size influence the likelihood of a species to persist in disturbed habitats.

Results

Our results revealed that indirect developing species exhibiting a large range size and wide elevational distribution, being independent of streams, and inhabiting the leaf litter, cope best with modifications of their natural habitats.

Conclusion

The traits identified in our study will likely persist in altered tropical forest systems and are comparable to those generally recognized for a low species extinction risk. Hence our findings will help to predict future frog communities in our human-dominated world.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-017-0135-y) contains supplementary material, which is available to authorized users.

Scientific and technical assistance concerning the survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU

A new fungus, Batrachochytrium salamandrivorans (Bsal), was identified in wild populations of salamanders in the Netherlands and Belgium, and in kept salamander populations in Germany and the United Kingdom. EFSA assessed the potential of Bsal to affect the health of wild and kept salamanders in the EU, the effectiveness and feasibility of a movement ban of traded salamanders, the validity, reliability and robustness of available diagnostic methods for Bsal detection, and possible alternative methods and feasible risk mitigation measures to ensure safe international and EU trade of salamanders and their products. Bsal was isolated and characterised in 2013 from a declining fire salamander (Salamandra salamandra) population in the Netherlands. Based on the available evidence, it is likely that Bsal is a sufficient cause for the death of S. salamandra both in the laboratory and in the wild. Despite small sample sizes, the available experimental evidence indicates that Bsal is associated with disease and death in individuals of 12 European and 3 Asian salamander species, and with high mortality rate outbreaks in kept salamanders. Bsal experimental infection was detected in individuals of at least one species pertaining to the families Salamandridae, Plethodontidae, Hynobiidae and Sirenidae. Movement bans constitute key risk mitigation measures to prevent pathogen spread into naïve areas and populations. The effectiveness of a movement ban is mainly dependent on the import volumes, possibility of Bsal to remain viable outside susceptible/tolerant species, and the capacity to limit illegal movements. Duplex real-time PCR can be used to detect Bsal DNA, but has not been fully validated. Quarantining salamanders, enacting legislation that requires testing of animals to demonstrate freedom from Bsal, before movement can take place, restricting salamander movements, tracking all traded species, hygienic procedures/biosecurity measures before and during movements, and increasing public awareness are relevant measures for ensuring safe intra-EU and international trade of salamanders.

Linking Ecology and Epidemiology to Understand Predictors of Multi-Host Responses to an Emerging Pathogen, the Amphibian Chytrid Fungus

Variation in host responses to pathogens can have cascading effects on populations and communities when some individuals or groups of individuals display disproportionate vulnerability to infection or differ in their competence to transmit infection. The fungal pathogen, Batrachochytrium dendrobatidis (Bd) has been detected in almost 700 different amphibian species and is implicated in numerous global amphibian population declines. Identifying key hosts in the amphibian-Bd system–those who are at greatest risk or who pose the greatest risk for others–is challenging due in part to many extrinsic environmental factors driving spatiotemporal Bd distribution and context-dependent host responses to Bd in the wild. One way to improve predictive risk models and generate testable mechanistic hypotheses about vulnerability is to complement what we know about the spatial epidemiology of Bd with data collected through comparative experimental studies. We used standardized pathogen challenges to quantify amphibian survival and infection trajectories across 20 post-metamorphic North American species raised from eggs. We then incorporated trait-based models to investigate the predictive power of phylogenetic history, habitat use, and ecological and life history traits in explaining responses to Bd. True frogs (Ranidae) displayed the lowest infection intensities, whereas toads (Bufonidae) generally displayed the greatest levels of mortality after Bd exposure. Affiliation with ephemeral aquatic habitat and breadth of habitat use were strong predictors of vulnerability to and intensity of infection and several other traits including body size, lifespan, age at sexual maturity, and geographic range also appeared in top models explaining host responses to Bd. Several of the species examined are highly understudied with respect to Bd such that this study represents the first experimental susceptibility data. Combining insights gained from experimental studies with observations of landscape-level disease prevalence may help explain current and predict future pathogen dynamics in the Bd system.

Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations

Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd. We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis.

Historical drivers of extinction risk: using past evidence to direct future monitoring

Global commitments to halt biodiversity decline mean that it is essential to monitor species' extinction risk. However, the work required to assess extinction risk is intensive. We demonstrate an alternative approach to monitoring extinction risk, based on the response of species to external conditions. Using retrospective International Union for Conservation of Nature Red List assessments, we classify transitions in the extinction risk of 497 mammalian carnivores and ungulates between 1975 and 2013. Species that moved to lower Red List categories, or remained Least Concern, were classified as 'lower risk'; species that stayed in a threatened category, or moved to a higher category of risk, were classified as 'higher risk'. Twenty-four predictor variables were used to predict transitions, including intrinsic traits (species biology) and external conditions (human pressure, distribution state and conservation interventions). The model correctly classified up to 90% of all transitions and revealed complex interactions between variables, such as protected areas (PAs) versus human impact. The most important predictors were: past extinction risk, PA extent, geographical range size, body size, taxonomic family and human impact. Our results suggest that monitoring a targeted set of metrics would efficiently identify species facing a higher risk, and could guide the allocation of resources between monitoring species' extinction risk and monitoring external conditions.

Dramatic Declines of Montane Frogs in a Central African Biodiversity Hotspot

Amphibian populations are vanishing worldwide. Declines and extinctions of many populations have been attributed to chytridiomycosis, a disease induced by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). In Africa, however, changes in amphibian assemblages were typically attributed to habitat change. We conducted a retrospective study utilizing field surveys from 2004–2012 of the anuran faunas on two mountains in western Cameroon, a hotspot of African amphibian diversity. The number of species detected was negatively influenced by year, habitat degradation, and elevation, and we detected a decline of certain species. Because another study in this region revealed an emergence of Bd in 2008, we screened additional recent field-collected samples and also pre-decline preserved museum specimens for the presence of Bd supporting emergence before 2008. When comparing the years before and after Bd detection, we found significantly diminished frog species richness and abundance on both mountains after Bd emergence. Our analyses suggest that this may be the first disease-driven community-level decline in anuran biodiversity in Central Africa. The disappearance of several species known to tolerate habitat degradation, and a trend of stronger declines at higher elevations, are consistent with Bd-induced declines in other regions. Not all species decreased; populations of some species remained constant, and others increased after the emergence of Bd. This variation might be explained by species-specific differences in infection probability. Increased habitat protection and Bd-mitigation strategies are needed for sustaining diverse amphibian communities such as those on Mt. Manengouba, which contains nearly half of Cameroon’s frog diversity.

Priorities for management of chytridiomycosis in Australia: saving frogs from extinction

To protect Australian amphibian biodiversity, we have identified and prioritised frog species at an imminent risk of extinction from chytridiomycosis, and devised national management and research priorities for disease mitigation. Six Australian frogs have not been observed in the wild since the initial emergence of chytridiomycosis and may be extinct. Seven extant frog species were assessed as needing urgent conservation interventions because of (1) their small populations and/or ongoing declines throughout their ranges (southern corroboree frog (Pseudophryne corroboree, New South Wales), northern corroboree frog (Pseudophryne pengilleyi, Australian Capital Territory, New South Wales), Baw Baw frog (Philoria frosti, Victoria), Litoria spenceri (spotted tree frog, Victoria, New South Wales), Kroombit tinkerfrog (Taudactylus pleione, Queensland), armoured mist frog (Litoria lorica, Queensland)) or (2) predicted severe decline associated with the spread of chytridiomycosis in the case of Tasmanian tree frog (Litoria burrowsae, Tasmania). For these species, the risk of extinction is high, but can be mitigated. They require increased survey effort to define their distributional limits and to monitor and detect further population changes, as well as well-resourced management strategies that include captive assurance populations. A further 22 frog species were considered at a moderate to lower risk of extinction from chytridiomycosis. Management actions that identify and create or maintain habitat refugia from chytridiomycosis and target other threatening processes such as habitat loss and degradation may be effective in promoting their recovery. Our assessments for some of these species remain uncertain and further taxonomical clarification is needed to determine their conservation importance. Management actions are currently being developed and trialled to mitigate the threat posed by chytridiomycosis. However, proven solutions to facilitate population recovery in the wild are lacking; hence, we prioritise research topics to achieve this aim. Importantly, the effectiveness of novel management solutions will likely differ among species due to variation in disease ecology, highlighting the need for species-specific research. We call for an independent management and research fund of AU$15 million over 5 years to be allocated to recovery actions as determined by a National Chytridiomycosis Working Group of amphibian managers and scientists. Procrastination on this issue will likely result in additional extinction of Australia’s amphibians in the near future.

Correlates of Recent Declines of Rodents in Northern and Southern Australia: Habitat Structure Is Critical

Australia has experienced dramatic declines and extinctions of its native rodent species over the last 200 years, particularly in southern Australia. In the tropical savanna of northern Australia significant declines have occurred only in recent decades. The later onset of these declines suggests that the causes may differ from earlier declines in the south. We examine potential regional effects (northern versus southern Australia) on biological and ecological correlates of range decline in Australian rodents. We demonstrate that rodent declines have been greater in the south than in the tropical north, are strongly influenced by phylogeny, and are consistently greater for species inhabiting relatively open or sparsely vegetated habitat. Unlike in marsupials, where some species have much larger body size than rodents, body mass was not an important predictor of decline in rodents. All Australian rodent species are within the prey-size range of cats (throughout the continent) and red foxes (in the south). Contrary to the hypothesis that mammal declines are related directly to ecosystem productivity (annual rainfall), our results are consistent with the hypothesis that disturbances such as fire and grazing, which occur in non-rainforest habitats and remove cover used by rodents for shelter, nesting and foraging, increase predation risk. We agree with calls to introduce conservation management that limits the size and intensity of fires, increases fire patchiness and reduces grazing impacts at ecological scales appropriate for rodents. Controlling feral predators, even creating predator-free reserves in relatively sparsely-vegetated habitats, is urgently required to ensure the survival of rodent species, particularly in northern Australia where declines are not yet as severe as those in the south.

Rapid Response to Evaluate the Presence of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) and Ranavirus in Wild Amphibian Populations in Madagascar

We performed a rapid response investigation to evaluate the presence and distribution of amphibian pathogens in Madagascar following our identification of amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) and ranavirus in commercially exported amphibians. This targeted risk-based field surveillance program was conducted from February to April 2014 encompassing 12 regions and 47 survey sites. We simultaneously collected amphibian and environmental samples to increase survey sensitivity and performed sampling both in wilderness areas and commercial amphibian trade facilities. Bd was not detected in any of 508 amphibian skin swabs or 68 water filter samples, suggesting pathogen prevalence was below 0.8%, with 95% confidence during our visit. Ranavirus was detected in 5 of 97 amphibians, including one adult Mantidactylus cowanii and three unidentified larvae from Ranomafana National Park, and one adult Mantidactylus mocquardi from Ankaratra. Ranavirus was also detected in water samples collected from two commercial amphibian export facilities. We also provide the first report of an amphibian mass-mortality event observed in wild amphibians in Madagascar. Although neither Bd nor ranavirus appeared widespread in Madagascar during this investigation, additional health surveys are required to disentangle potential seasonal variations in pathogen abundance and detectability from actual changes in pathogen distribution and rates of spread. Accordingly, our results should be conservatively interpreted until a comparable survey effort during winter months has been performed. It is imperative that biosecurity practices be immediately adopted to limit the unintentional increased spread of disease through the movement of contaminated equipment or direct disposal of contaminated material from wildlife trade facilities. The presence of potentially introduced strains of ranaviruses suggests that Madagascar's reptile species might also be threatened by disease. Standardized population monitoring of key amphibian and reptile species should be established with urgency to enable early detection of potential impacts of disease emergence in this global biodiversity hotspot.

Predicting and setting conservation priorities for Bolivian mammals based on biological correlates of the risk of decline

The recognition that growing proportions of species worldwide are endangered has led to the development of comparative analyses to elucidate why some species are more prone to extinction than others. Understanding factors and patterns of species vulnerability might provide an opportunity to develop proactive conservation strategies. Such comparative analyses are of special concern at national scales because this is the scale at which most conservation initiatives take place. We applied powerful ensemble learning models to test for biological correlates of the risk of decline among the Bolivian mammals to understand species vulnerability at a national scale and to predict the population trend for poorly known species. Risk of decline was nonrandomly distributed: higher proportions of large-sized taxa were under decline, whereas small-sized taxa were less vulnerable. Body mass, mode of life (i.e., aquatic, terrestrial, volant), geographic range size, litter size, home range, niche specialization, and reproductive potential were strongly associated with species vulnerability. Moreover, we found interacting and nonlinear effects of key traits on the risk of decline of mammals at a national scale. Our model predicted 35 data-deficient species in decline on the basis of their biological vulnerability, which should receive more attention in order to prevent their decline. Our results highlight the relevance of comparative analysis at relatively narrow geographical scales, reveal previously unknown factors related to species vulnerability, and offer species-by-species outcomes that can be used to identify targets for conservation, especially for insufficiently known species.

Mapping the Drivers of Climate Change Vulnerability for Australia's Threatened Species

Effective conservation management for climate adaptation rests on understanding the factors driving species' vulnerability in a spatially explicit manner so as to direct on-ground action. However, there have been only few attempts to map the spatial distribution of the factors driving vulnerability to climate change. Here we conduct a species-level assessment of climate change vulnerability for a sample of Australia's threatened species and map the distribution of species affected by each factor driving climate change vulnerability across the continent. Almost half of the threatened species assessed were considered vulnerable to the impacts of climate change: amphibians being the most vulnerable group, followed by plants, reptiles, mammals and birds. Species with more restricted distributions were more likely to show high climate change vulnerability than widespread species. The main factors driving climate change vulnerability were low genetic variation, dependence on a particular disturbance regime and reliance on a particular moisture regime or habitat. The geographic distribution of the species impacted by each driver varies markedly across the continent, for example species impacted by low genetic variation are prevalent across the human-dominated south-east of the country, while reliance on particular moisture regimes is prevalent across northern Australia. Our results show that actions to address climate adaptation will need to be spatially appropriate, and that in some regions a complex suite of factors driving climate change vulnerability will need to be addressed. Taxonomic and geographic variation in the factors driving climate change vulnerability highlights an urgent need for a spatial prioritisation of climate adaptation actions for threatened species.

Shifting ranges and conservation challenges for lemurs in the face of climate change

Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth's biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding future impacts on threatened biota. Here, we employ predictive modeling under a conservative estimate of future climate change to examine impacts on the future abundance and geographic distributions of Malagasy lemurs. Using distribution data from the primary literature, we employed ensemble species distribution models and geospatial analyses to predict future changes in species distributions. Current species distribution models (SDMs) were created within the BIOMOD2 framework that capitalizes on ten widely used modeling techniques. Future and current SDMs were then subtracted from each other, and areas of contraction, expansion, and stability were calculated. Model overprediction is a common issue associated Malagasy taxa. Accordingly, we introduce novel methods for incorporating biological data on dispersal potential to better inform the selection of pseudo-absence points. This study predicts that 60% of the 57 species examined will experience a considerable range of reductions in the next seventy years entirely due to future climate change. Of these species, range sizes are predicted to decrease by an average of 59.6%. Nine lemur species (16%) are predicted to expand their ranges, and 13 species (22.8%) distribution sizes were predicted to be stable through time. Species ranges will experience severe shifts, typically contractions, and for the majority of lemur species, geographic distributions will be considerably altered. We identify three areas in dire need of protection, concluding that strategically managed forest corridors must be a key component of lemur and other biodiversity conservation strategies. This recommendation is all the more urgent given that the results presented here do not take into account patterns of ongoing habitat destruction relating to human activities.

Using site-occupancy models to prepare for the spread of chytridiomyosis and identify factors affecting detectability of a cryptic susceptible species, the Tasmanian tree frog

Context The global reduction of amphibian biodiversity as a result of the disease chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis; Bd) has highlighted the need to accurately detect local population declines in association with Bd presence. Although Bd has spread globally, some remote regions such as the Tasmanian Wilderness World Heritage Area (1.40 million ha; TWWHA) in Australia, remain largely, but not entirely, disease free. The Tasmanian tree frog (Litoria burrowsae) resides primarily within TWWHA boundaries, and is believed to be susceptible to chytridiomycosis. Aims In the absence of historical abundance data, we used a single-season multi-state site-occupancy model to investigate the impact of Bd on L. burrowsae populations, on factors affecting species detection and to inform ongoing surveillance and conservation. Methods We recorded frog detection and ranked call intensity (estimation of population size) from repeated independent surveys within a season to estimate the role of covariates, such as presence of Bd and environmental variables, on species occupancy and detection probability. Key results Modelling revealed large frog populations are more likely to be present at naturally formed than human-formed ponds, strong winds negatively affect detection of populations, and time after sunset affects detection of large populations. Large frog populations were more likely to be Bd-negative; however, models including Bd presence were not well supported, in part a result of the small number of Bd-positive sites recorded. Conclusions and Implications The utility of site-occupancy modelling in understanding the impact of disease on populations is little known, but has the potential to improve the accuracy and efficiency of many conservation programs.

A statistical assessment of population trends for data deficient Mexican amphibians

Background. Mexico has the world’s fifth largest population of amphibians and the second country with the highest quantity of threatened amphibian species. About 10% of Mexican amphibians lack enough data to be assigned to a risk category by the IUCN, so in this paper we want to test a statistical tool that, in the absence of specific demographic data, can assess a species’ risk of extinction, population trend, and to better understand which variables increase their vulnerability. Recent studies have demonstrated that the risk of species decline depends on extrinsic and intrinsic traits, thus including both of them for assessing extinction might render more accurate assessment of threats.

Methods. We harvested data from the Encyclopedia of Life (EOL) and the published literature for Mexican amphibians, and used these data to assess the population trend of some of the Mexican species that have been assigned to the Data Deficient category of the IUCN using Random Forests, a Machine Learning method that gives a prediction of complex processes and identifies the most important variables that account for the predictions.

Results. Our results show that most of the data deficient Mexican amphibians that we used have decreasing population trends. We found that Random Forests is a solid way to identify species with decreasing population trends when no demographic data is available. Moreover, we point to the most important variables that make species more vulnerable for extinction. This exercise is a very valuable first step in assigning conservation priorities for poorly known species.