Nutraceutical supplementation increases mobility in aged captive non-domesticated felids

BACKGROUND

Musculoskeletal diseases (MSDs) are an increasing issue as the lifespan of captive animals increases. Extracts of green-lipped mussels have been linked to alleviation of MSDs in domestic carnivores. Understanding their efficacy in non-domestic felids could provide another tool to improve the welfare of aged individuals in collections.

METHODS

A within-subject study design quantified steps per minute in each of 18 cats of 13 species before and after the addition of a nutraceutical containing green-lipped mussel extract (Antinol) to their diets. The age structure of four commonly kept subspecies of non-domestic cats was quantified to provide a demographic context to the need for managing aged individuals.

RESULTS

Each of the 18 cats exhibited a higher number of steps per minute after the addition of Antinol to their diet. At the group level, a paired t-test showed that the step rate was significantly increased after the addition of Antinol to the diet.

LIMITATIONS

While our results showed a strong significant increase in step rate following Antinol supplementation, further studies that incorporate a placebo, more individuals and more detailed metrics of mobility would provide a more detailed evidence base for practitioners.

CONCLUSION

Nutraceuticals may yield benefits to aged individual felids, including species kept widely in European collections. Their use warrants further, detailed research in collections.

Longevity of companion dog breeds: those at risk from early death

The companion dog is one of the most phenotypically diverse species. Variability between breeds extends not only to morphology and aspects of behaviour, but also to longevity. Despite this fact, little research has been devoted to assessing variation in life expectancy between breeds or evaluating the potential for phylogenetic characterisation of longevity. Using a dataset of 584,734 unique dogs located within the UK, including 284,734 deceased, we present variation in longevity estimates within the following: parental lineage (purebred = 1 breed, crossbred ≥ 2 breeds), breed (n = 155), body size (large, medium, small), sex (male, female) and cephalic index (brachycephalic, mesocephalic, dolichocephalic). Survival estimates were then partitioned amongst phylogenetic clades: providing evidence that canine evolutionary history (via domestication and associated artificial selection) is associated with breed lifespan. This information provides evidence to inform discussions regarding pedigree health, whilst helping current/prospective owners, breeders, policy makers, funding bodies and welfare organisations improve decision making regarding canine welfare.

Online classified adverts reflect the broader United Kingdom trade in turtles and tortoises rather than drive it

Online sales are increasingly a route by which exotic animals are sold in the global pet trade. There are numerous types of online platforms and transaction types, and dedicated classified advertisement sites are a popular means of buying and selling animals. Despite their large and increasing use, we have a relatively poor understanding of the number of, and taxonomic variation in, the animals sold online. This information may be key in efforts to optimise the welfare of the animals being sold, and the ethics and sustainability of the trade via that platform. To fill this knowledge gap, we monitored and analysed the advertisements of chelonians (turtles and tortoises) placed on one of the United Kingdom's largest dedicated classified ads sites, www.pets4homes.co.uk, over the course of a year, from July 2020 until June 2021. We analysed temporal, taxonomic, and advertiser related trends in the volumes of advertisements placed and compared the prices and the sentiment of language within adverts for different species. We found that the species advertised, the prices requested, and infrequent use of the site by most advertisers is consistent with most adverts being for animals being resold by casual users. Further, we found that turtles were consistently advertised for lower prices and in multiples than tortoises, and that the language with which they were advertised was less positive. We conclude that on this website the online trade reflects the broader trade, rather than drives the sales of chelonians in the UK, and that any interventions aiming to improve welfare and sustainability would be better placed earlier in the supply chain.

Drivers of Batrachochytrium dendrobatidis infection load, with evidence of infection tolerance in adult male toads (Bufo spinosus)

Chytridiomycosis is affecting hundreds of amphibian species worldwide, but while in tropical areas, adult individuals have been the focus of most investigations, the exact role played by infection intensity of breeding adults is not well understood in temperate areas. We conducted mark-recapture-capture surveys during spiny common toad breeding seasons from 2006 to 2018 at the site of the first recorded outbreak of chytridiomycosis in Europe, the Peñalara Massif (Sierra de Guadarrama National Park, central Spain), and collected infection samples and several variables related to the reproductive effort of male individuals. We used general linear mixed models to evaluate the contribution of study variables on the infection loads of adult male toads exhibited at their capturing date. We also analysed the differences on several male characteristics between the pond with the largest breeding population against the rest of the ponds. We found that the duration of time spent in the waterbody and the condition of the host predicted infection loads. Animals of good physical condition, that spent longer in water, have higher infection levels than individuals with the opposite set of traits. The pond supporting the largest breeding population housed smaller male toads and in poorer condition. Our results are consistent with a shift in reproductive strategy in response to infection and potentially a strategy of tolerance, rather than resistance to infection. These findings have applications for disease mitigation and theoretical implications related to the trade-offs made and the evolution of traits in response to the disease.

Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis

The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3-6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intensity, and potentially transmissibility and spread, and we attribute these differences to both host and pathogen biology.

Long-Term Monitoring of Amphibian Populations of a National Park in Northern Spain Reveals Negative Persisting Effects of Ranavirus, but Not Batrachochytrium dendrobatidis

Amphibians are the most highly threatened vertebrates, and emerging pathogens are a serious threat to their conservation. Amphibian chytrid fungi and the viruses of the Ranavirus genus are causing disease outbreaks worldwide, including in protected areas such as National Parks. However, we lack information about their effect over amphibian populations in the long-term, and sometimes these mortality episodes are considered as transient events without serious consequences over longer time-spans. Here, we relate the occurrence of both pathogens with the population trends of 24 amphibian populations at 15 sites across a national Park in northern Spain over a 14-year period. Just one out 24 populations presents a positive population trend being free of both pathogens, while seven populations exposed to one or two pathogens experienced strong declines during the study period. The rest of the study populations (16) remain stable, and these tend to be of species that are not susceptible to the pathogen present or are free of pathogens. Our study is consistent with infectious diseases playing an important role in dictating amphibian population trends and emphasizes the need to adopt measures to control these pathogens in nature. We highlight that sites housing species carrying Ranavirus seems to have experienced more severe population-level effects compared to those with the amphibian chytrid fungus, and that ranaviruses could be just as, or more important, other more high-profile amphibian emerging pathogens.

Host contribution to parasite persistence is consistent between parasites and over time, but varies spatially

Most parasites and pathogens infect multiple hosts, but a great deal of variation exists in the role of those hosts in persistence of infection. Understanding which hosts are most important in maintaining parasites can provide a clearer target for infection control. Recently developed empirical and theoretical approaches provide a way to quantify the relative contribution of hosts within a community and place them in a multi-host framework to better direct control efforts. Amphibians provide a framework for better understanding multi-host-multi-parasite dynamics. Two well-studied amphibian parasites, Batrachochytrium dendrobatidis (Bd) and Ranavirus, infect multiple host species and exhibit a great deal of heterogeneity in how they affect hosts. We used these two parasites and a community of five amphibian species to investigate the relative importance of hosts in parasite persistence, and how any patterns varied spatially and temporally. At two sites (Lake Ercina and Lake Lloroza in the Picos de Europa National Park, Spain) we collected data on the prevalence and shedding rate of parasite infection for both Bd and Ranavirus, and the abundance of each species' life stages. We used these data to parameterize a recently developed modeling framework, which was used to quantify the relative contribution of each host to the community reproductive number, R₀ . By comparing each host-category over time and between sites we were able to identify consistencies in which host was responsible for the maintenance of these two parasites. Within a site one species consistently contributed the most to the persistence of both parasites. This consistency did not transfer between sites, the maintenance host species being different for each. At one site (Ercina), life stages of the common midwife toad, Alytes obstetricans, acted as the maintenance host for both Bd and Ranavirus. In contrast, at the second site, Lloroza, the alpine newt, Ichthyosaura alpestris, fulfilled that role. A single host species was responsible for infection persistence of both parasites at each lake. Attempts to control the infection levels and impacts of multiple parasites can benefit from a community epidemiology approach, and provide clarity on which hosts are the foci of mitigation efforts. However, at a small spatial scale, the target host may vary according to the physical qualities of those sites and the demographics of the host community.

Increased tropospheric ozone levels enhance pathogen infection levels of amphibians

As a result of anthropogenic activities, changes to the chemistry of Earth's atmosphere pose a threat to ecosystem health and biodiversity. One such change is the increase in tropospheric ozone (O₃), which is particularly severe in the Mediterranean basin area, where the levels of this pollutant are chronically high during spring and summer time. Within this region, Mediterranean mountain ecosystems are hot spots for biodiversity which may be especially vulnerable to changes in O₃ levels. Declines in montane amphibian populations have been recorded worldwide, including the Mediterranean basin. A significant driver of these declines is the emerging infection disease, chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd). Chytridiomycosis has negatively affected populations of several amphibian species in the Spanish Central Range, including in the Sierra Guadarrama, and interactions with other biotic and abiotic factors are an important part of these declines. However, there is little evidence or knowledge of whether tropospheric O₃ levels may be another factor in the outbreaks of this disease. To test the hypothesis that O₃ levels are another interactive driver of Bd infection dynamics, two different approaches were followed: 1) an experimental study in open top chambers was used to quantify the aspects of how Bd infection progressed throughout the metamorphic process under four different O₃ levels; and 2) a field epidemiological study was used to analyse the relationship between the Bd infection load in the Sierra de Guadarrama and tropospheric O₃ levels during a 9 year period. Our results suggest that high O₃ levels significantly delayed the rate of development of tadpoles and increased Bd infection, providing empirical evidence of two new separate ways that may explain population declines of montane amphibians.

Complementarity, completeness and quality of long-term faunal archives in an Asian biodiversity hotspot

Long-term baselines on biodiversity change through time are crucial to inform conservation decision-making in biodiversity hotspots, but environmental archives remain unavailable for many regions. Extensive palaeontological, zooarchaeological and historical records and indigenous knowledge about past environmental conditions exist for China, a megadiverse country experiencing large-scale biodiversity loss, but their potential to understand past human-caused faunal turnover is not fully assessed. We investigate a series of complementary environmental archives to evaluate the quality of the Holocene-historical faunal record of Hainan Island, China's southernmost province, for establishing new baselines on postglacial mammalian diversity and extinction dynamics. Synthesis of multiple archives provides an integrated model of long-term biodiversity change, revealing that Hainan has experienced protracted and ongoing human-caused depletion of its mammal fauna from prehistory to the present, and that past baselines can inform practical conservation management. However, China's Holocene-historical archives exhibit substantial incompleteness and bias at regional and country-wide scales, with limited taxonomic representation especially for small-bodied species, and poor sampling of high-elevation landscapes facing current-day climate change risks. Establishing a clearer understanding of the quality of environmental archives in threatened ecoregions, and their ability to provide a meaningful understanding of the past, is needed to identify future conservation-relevant historical research priorities. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Eradication of introduced fish allows successful recovery of a stream-dwelling amphibian

Introduction of alien fish is a major problem for the conservation of amphibians inhabiting originally fishless mountain streams. While fish eradication programs in lakes and ponds have proven successful for the recovery of amphibian populations, there is no such information for stream-dwelling amphibians, possibly because fish removal from streams is difficult and costly. Here, we show the first case of successful recovery of a stream-dwelling amphibian (Rana iberica) in a mountain area of central Spain, following eradication of introduced brook trout (Salvelinus fontinalis) and native brown trout (Salmo trutta) translocated from downstream reaches by local anglers. Electrofishing for 12 consecutive years eradicated both fish species in the introduced area, and allowed the recovery of the R. iberica population as a result of natural recolonization from nearby streams and reintroduction of captive-reared individuals. Our results demonstrate how electrofishing can be a costly but effective method for the eradication of introduced fish and the conservation of stream-dwelling amphibians.

Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

Ecosystems have been modified by human activities for millennia, and insights about ecology and extinction risk based only on recent data are likely to be both incomplete and biased. We synthesize multiple long-term archives (over 250 archaeological and palaeontological sites dating from the early Holocene to the Ming Dynasty and over 4400 historical records) to reconstruct the spatio-temporal dynamics of Holocene–modern range change across China, a megadiverse country experiencing extensive current-day biodiversity loss, for 34 mammal species over three successive postglacial time intervals. Our combined zooarchaeological, palaeontological, historical and current-day datasets reveal that both phylogenetic and spatial patterns of extinction selectivity have varied through time in China, probably in response both to cumulative anthropogenic impacts (an ‘extinction filter’ associated with vulnerable species and accessible landscapes being affected earlier by human activities) and also to quantitative and qualitative changes in regional pressures. China has experienced few postglacial global species-level mammal extinctions, and most species retain over 50% of their maximum estimated Holocene range despite millennia of increasing regional human pressures, suggesting that the potential still exists for successful species conservation and ecosystem restoration. Data from long-term archives also demonstrate that herbivores have experienced more historical extinctions in China, and carnivores have until recently displayed greater resilience. Accurate assessment of patterns of biodiversity loss and the likely predictive power of current-day correlates of faunal vulnerability and resilience is dependent upon novel perspectives provided by long-term archives.

Climate forcing of an emerging pathogenic fungus across a montane multi-host community

Changes in the timings of seasonality as a result of anthropogenic climate change are predicted to occur over the coming decades. While this is expected to have widespread impacts on the dynamics of infectious disease through environmental forcing, empirical data are lacking. Here, we investigated whether seasonality, specifically the timing of spring ice-thaw, affected susceptibility to infection by the emerging pathogenic fungus Batrachochytrium dendrobatidis (Bd) across a montane community of amphibians that are suffering declines and extirpations as a consequence of this infection. We found a robust temporal association between the timing of the spring thaw and Bd infection in two host species, where we show that an early onset of spring forced high prevalences of infection. A third highly susceptible species (the midwife toad, Alytes obstetricans) maintained a high prevalence of infection independent of time of spring thaw. Our data show that perennially overwintering midwife toad larvae may act as a year-round reservoir of infection with variation in time of spring thaw determining the extent to which infection spills over into sympatric species. We used future temperature projections based on global climate models to demonstrate that the timing of spring thaw in this region will advance markedly by the 2050s, indicating that climate change will further force the severity of infection. Our findings on the effect of annual variability on multi-host infection dynamics show that the community-level impact of fungal infectious disease on biodiversity will need to be re-evaluated in the face of climate change.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Toward reassessing data-deficient species

One in 6 species (13,465 species) on the International Union for Conservation of Nature (IUCN) Red List is classified as data deficient due to lack of information on their taxonomy, population status, or impact of threats. Despite the chance that many are at high risk of extinction, data-deficient species are typically excluded from global and local conservation priorities, as well as funding schemes. The number of data-deficient species will greatly increase as the IUCN Red List becomes more inclusive of poorly known and speciose groups. A strategic approach is urgently needed to enhance the conservation value of data-deficient assessments. To develop this, we reviewed 2879 data-deficient assessments in 6 animal groups and identified 8 main justifications for assigning data-deficient status (type series, few records, old records, uncertain provenance, uncertain population status or distribution, uncertain threats, taxonomic uncertainty, and new species). Assigning a consistent set of justification tags (i.e., consistent assignment to assessment justifications) to species classified as data deficient is a simple way to achieve more strategic assessments. Such tags would clarify the causes of data deficiency; facilitate the prediction of extinction risk; facilitate comparisons of data deficiency among taxonomic groups; and help prioritize species for reassessment. With renewed efforts, it could be straightforward to prevent thousands of data-deficient species slipping unnoticed toward extinction.

Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus

The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male‐biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island‐restricted amphibians, especially in the context of disease and climate change.

Localised Badger Culling Increases Risk of Herd Breakdown on Nearby, Not Focal, Land

Bovine tuberculosis is an important disease affecting the UK livestock industry. Controlling bovine tuberculosis (TB) is made more complex by the presence of a wildlife host, the Eurasian badger, Meles meles. Repeated large-scale badger culls implemented in the Randomised Badger Culling Trial (RBCT) were associated with decreased cattle risks inside the culling area, but also with increased cattle risks up to the 2km outside the culling area. Intermediate reductions in badger density, as achieved by localised reactive culling in the RBCT, significantly increased cattle TB. Using a matched-pairs case-control study design (n = 221 pairs of cattle herds), we investigated the spatial scale over which localised badger culling had its biggest impact. We found that reactive badger culling had a significant positive association with the risk of cattle TB at distances of 1-3km and 3-5km, and that no such association existed over shorter distances (<1km). These findings indicate that localised badger culls had significant negative effects, not on the land on which culling took place, but, perhaps more importantly, on adjoining lands and farms.

Infection and transmission heterogeneity of a multi-host pathogen (Batrachochytrium dendrobatidis) within an amphibian community

The majority of parasites infect multiple hosts. As the outcome of the infection is different in each of them, most studies of wildlife disease focus on the few species that suffer the most severe consequences. However, the role that each host plays in the persistence and transmission of infection can be crucial to understanding the spread of a parasite and the risk it poses to the community. Current theory predicts that certain host species can modulate the infection in other species by amplifying or diluting both infection prevalence and infection intensity, both of which have implications for disease risk within those communities. The fungus Batrachochytrium dendrobatidis (Bd), the causal agent of the disease chytridiomycosis, has caused global amphibian population declines and extinctions. However, not all infected species are affected equally, and thus Bd is a good example of a multi-host pathogen that must ultimately be studied with a community approach. To test whether the common midwife toad Alytes obstetricans is a reservoir and possible amplifier of infection of other species, we used experimental approaches in captive and wild populations to determine the effect of common midwife toad larvae on infection of other amphibian species found in the Peñalara Massif, Spain. We observed that the most widely and heavily infected species, the common midwife toad, may be amplifying the infection loads in other species, all of which have different degrees of susceptibility to Bd infection. Our results have important implications for performing mitigation actions focused on potential 'amplifier' hosts and for better understanding the mechanisms of Bd transmission.

Host species vary in infection probability, sub-lethal effects, and costs of immune response when exposed to an amphibian parasite

The amphibian parasite Batrachochytrium dendrobatidis (Bd) is regarded as an extreme generalist, infecting over 500 species, but amongst these hosts there exists a great deal of variation in the susceptibility to and the costs of parasite exposure. We use two infection experiments to determine whether inter-specific variation in the sublethal and lethal effects of parasite exposure exist in two host species. We then tested the relative roles of host density and diversity on infection probability of a focal susceptible host. Our results show significant heterogeneity in host species response to parasite exposure, and that both lethal and sub-lethal costs exist in individuals that are able to resist infection, indicating that successful immune response to infection comes at a cost. Further, we show that increasing host density significantly increased the likelihood of susceptible individuals becoming infected with Bd irrespective of host diversity and variation in host susceptibility. These results suggest that populations of resistant species are likely to suffer ill-effects of exposure to Bd regardless of their infection status, and that at the stage of initial infection there was no support for the dilution of transmission events, in contrast to other studies that focus on subsequent transmission of infection.

Predicting the conservation status of data-deficient species

There is little appreciation of the level of extinction risk faced by one-sixth of the over 65,000 species assessed by the International Union for Conservation of Nature. Determining the status of these data-deficient (DD) species is essential to developing an accurate picture of global biodiversity and identifying potentially threatened DD species. To address this knowledge gap, we used predictive models incorporating species' life history, geography, and threat information to predict the conservation status of DD terrestrial mammals. We constructed the models with 7 machine learning (ML) tools trained on species of known status. The resultant models showed very high species classification accuracy (up to 92%) and ability to correctly identify centers of threatened species richness. Applying the best model to DD species, we predicted 313 of 493 DD species (64%) to be at risk of extinction, which increases the estimated proportion of threatened terrestrial mammals from 22% to 27%. Regions predicted to contain large numbers of threatened DD species are already conservation priorities, but species in these areas show considerably higher levels of risk than previously recognized. We conclude that unless directly targeted for monitoring, species classified as DD are likely to go extinct without notice. Taking into account information on DD species may therefore help alleviate data gaps in biodiversity indicators and conserve poorly known biodiversity.

Geometric factors influencing the diet of vertebrate predators in marine and terrestrial environments

Predator–prey relationships are vital to ecosystem function and there is a need for greater predictive understanding of these interactions. We develop a geometric foraging model predicting minimum prey size scaling in marine and terrestrial vertebrate predators taking into account habitat dimensionality and biological traits. Our model predicts positive predator–prey size relationships on land but negative relationships in the sea. To test the model, we compiled data on diets of 794 predators (mammals, snakes, sharks and rays). Consistent with predictions, both terrestrial endotherm and ectotherm predators have significantly positive predator–prey size relationships. Marine predators, however, exhibit greater variation. Some of the largest predators specialise on small invertebrates while others are large vertebrate specialists. Prey–predator mass ratios were generally higher for ectothermic than endothermic predators, although dietary patterns were similar. Model-based simulations of predator–prey relationships were consistent with observed relationships, suggesting that our approach provides insights into both trends and diversity in predator–prey interactions.

Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis

Where wildlife disease requires management, culling is frequently considered but not always effective. In the British Isles, control of cattle tuberculosis (TB) is hindered by infection in wild badger (Meles meles) populations. Large-scale badger culling can reduce the incidence of confirmed cattle TB, but these benefits are undermined by culling-induced changes in badger behavior (termed perturbation), which can increase transmission among badgers and from badgers to cattle. Test-vaccinate/remove (TVR) is a novel approach that entails testing individual badgers for infection, vaccinating test-negative animals, and killing test-positive animals. Imperfect capture success, diagnostic sensitivity, and vaccine effectiveness mean that TVR would be expected to leave some infected and some susceptible badgers in the population. Existing simulation models predict that TVR could reduce cattle TB if such small-scale culling causes no perturbation, but could increase cattle TB if considerable perturbation occurs. Using data from a long-term study, we show that past small-scale culling was significantly associated with four metrics of perturbation in badgers: expanded ranging, more frequent immigration, lower genetic relatedness, and elevated prevalence of Mycobacterium bovis, the causative agent of TB. Though we could not reject the hypothesis that culling up to three badgers per social group might avoid perturbation, we also could not reject the hypothesis that killing a single badger prompted detectable perturbation. When considered alongside existing model predictions, our findings suggest that implementation of TVR, scheduled for 2014, risks exacerbating the TB problem rather than controlling it. Ongoing illegal badger culling is likewise expected to increase cattle TB risks.

Correlates of research effort in carnivores: body size, range size and diet matter

Given the budgetary restrictions on scientific research and the increasing need to better inform conservation actions, it is important to identify the patterns and causes of biases in research effort. We combine bibliometric information from a literature review of almost 16,500 peer-reviewed publications on a well-known group of 286 species, the Order Carnivora, with global datasets on species' life history and ecological traits to explore patterns in research effort. Our study explores how species' characteristics influenced the degree to which they were studied (measured as the number of publications). We identified a wide variation in intensity of research effort at both Family and Species levels, with some of the least studied being those which may need protection in future. Our findings hint at the complex role of human perspectives in setting research agendas. We found that better-studied species tended to be large-bodied and have a large geographic range whilst omnivory had a negative relationship with research effort. IUCN threat status did not exhibit a strong relationship with research effort which suggests that the conservation needs of individual species are not major drivers of research interest. This work is the first to use a combination of bibliometric analysis and biological data to quantify and interpret gaps in research knowledge across an entire Order. Our results could be combined with other resources, such as Biodiversity Action Plans, to prioritise and co-ordinate future research effort, whilst our methods can be applied across many scientific disciplines to describe knowledge gaps.

Assessing risk and guidance on monitoring of Batrachochytrium dendrobatidis in Europe through identification of taxonomic selectivity of infection

Amphibians are globally threatened, but not all species are affected equally by different threatening processes. This is true for the threat posed by the chytridiomycete fungus (Batrachochytrium dendrobatidis). We compiled a European data set for B. dendrobatidis to analyze the trends of infection in European amphibians. The risk of infection was not randomly distributed geographically or taxonomically across Europe. Within countries with different prevalence, infection was nonrandom in certain amphibian taxa. Brown frogs of the genus Rana were unlikely to be infected, whereas frogs in the families Alytidae and Bombinatoridae were significantly more likely to be infected than predicted by chance. Frogs in the 2 families susceptible to B. dendrobatidis should form the core of attempts to develop spatial surveillance studies of chytridiomycosis in Europe. Ideally, surveys for B. dendrobatidis should be augmented by sampling the widespread genus Pelophylax because this taxon exhibits geographically inconsistent overinfection with B. dendrobatidis and surveillance of it may facilitate recognition of factors causing spatial variability of infection intensity. Several European amphibian taxa were not represented in our data set; however, surveillance of unsampled species should also occur when warranted.

Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus

The rapid worldwide emergence of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) is having a profound negative impact on biodiversity. However, global research efforts are fragmented and an overarching synthesis of global infection data is lacking. Here, we provide results from a community tool for the compilation of worldwide Bd presence and report on the analyses of data collated over a four-year period. Using this online database, we analysed: 1) spatial and taxonomic patterns of infection, including amphibian families that appear over- and under-infected; 2) relationships between Bd occurrence and declining amphibian species, including associations among Bd occurrence, species richness, and enigmatic population declines; and 3) patterns of environmental correlates with Bd, including climate metrics for all species combined and three families (Hylidae, Bufonidae, Ranidae) separately, at both a global scale and regional (U.S.A.) scale. These associations provide new insights for downscaled hypothesis testing. The pathogen has been detected in 52 of 82 countries in which sampling was reported, and it has been detected in 516 of 1240 (42%) amphibian species. We show that detected Bd infections are related to amphibian biodiversity and locations experiencing rapid enigmatic declines, supporting the hypothesis that greater complexity of amphibian communities increases the likelihood of emergence of infection and transmission of Bd. Using a global model including all sampled species, the odds of Bd detection decreased with increasing temperature range at a site. Further consideration of temperature range, rather than maximum or minimum temperatures, may provide new insights into Bd-host ecology. Whereas caution is necessary when interpreting such a broad global dataset, the use of our pathogen database is helping to inform studies of the epidemiology of Bd, as well as enabling regional, national, and international prioritization of conservation efforts. We provide recommendations for adaptive management to enhance the database utility and relevance.

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

Batrachochytrium dendrobatidis (Bd) is a globally ubiquitous fungal infection that has emerged to become a primary driver of amphibian biodiversity loss. Despite widespread effort to understand the emergence of this panzootic, the origins of the infection, its patterns of global spread, and principle mode of evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages of Bd associated with amphibians. Two of these lineages were found in multiple continents and are associated with known introductions by the amphibian trade. We found that isolates belonging to one clade, the global panzootic lineage (BdGPL) have emerged across at least five continents during the 20th century and are associated with the onset of epizootics in North America, Central America, the Caribbean, Australia, and Europe. The two newly identified divergent lineages, Cape lineage (BdCAPE) and Swiss lineage (BdCH), were found to differ in morphological traits when compared against one another and BdGPL, and we show that BdGPL is hypervirulent. BdGPL uniquely bears the hallmarks of genomic recombination, manifested as extensive intergenomic phylogenetic conflict and patchily distributed heterozygosity. We postulate that contact between previously genetically isolated allopatric populations of Bd may have allowed recombination to occur, resulting in the generation, spread, and invasion of the hypervirulent BdGPL leading to contemporary disease-driven losses in amphibian biodiversity.

Intra-guild competition and its implications for one of the biggest terrestrial predators, Tyrannosaurus rex

Identifying tradeoffs between hunting and scavenging in an ecological context is important for understanding predatory guilds. In the past century, the feeding strategy of one of the largest and best-known terrestrial carnivores, Tyrannosaurus rex, has been the subject of much debate: was it an active predator or an obligate scavenger? Here we look at the feasibility of an adult T. rex being an obligate scavenger in the environmental conditions of Late Cretaceous North America, given the size distributions of sympatric herbivorous dinosaurs and likely competition with more abundant small-bodied theropods. We predict that nearly 50 per cent of herbivores would have been within a 55–85 kg range, and calculate based on expected encounter rates that carcasses from these individuals would have been quickly consumed by smaller theropods. Larger carcasses would have been very rare and heavily competed for, making them an unreliable food source. The potential carcass search rates of smaller theropods are predicted to be 14–60 times that of an adult T. rex. Our results suggest that T. rex and other extremely large carnivorous dinosaurs would have been unable to compete as obligate scavengers and would have primarily hunted large vertebrate prey, similar to many large mammalian carnivores in modern-day ecosystems.

The link between rapid enigmatic amphibian decline and the globally emerging chytrid fungus

Amphibians are globally declining and approximately one-third of all species are threatened with extinction. Some of the most severe declines have occurred suddenly and for unknown reasons in apparently pristine habitats. It has been hypothesized that these "rapid enigmatic declines" are the result of a panzootic of the disease chytridiomycosis caused by globally emerging amphibian chytrid fungus. In a Species Distribution Model, we identified the potential distribution of this pathogen. Areas and species from which rapid enigmatic decline are known significantly overlap with those of highest environmental suitability to the chytrid fungus. We confirm the plausibility of a link between rapid enigmatic decline in worldwide amphibian species and epizootic chytridiomycosis.

Fatal chytridiomycosis in the tyrrhenian painted frog

Batrachochytrium dendrobatidis (Bd), the causative agent of the amphibian disease chytridiomycosis, is an important factor in the global decline of amphibians. Within Europe, animals that exhibit clinical signs of the disease have only been reported in Spain despite the pathogen's wide, but patchy, distribution on the continent. Recently, another occurrence of chytridiomycosis was reported in Euproctus platycephalus, the Sardinian brook newt, on the Mediterranean island of Sardinia, but without any evidence of fatal disease. We report further evidence of the emergence of Bd on Sardinia and the first evidence of lethal chytridiomycosis outside of Spain. Unusual mortalities of the Tyrrhenian painted frog (Discoglossus sardus) were found at three sites in the Limbara mountains of northern Sardinia. Molecular and histological screens of corpses, frogs, and tadpoles from these sites revealed infection with Bd. Infection and mortality occurred at locations that are unusual in terms of the published habitat requirements of the pathogen. Given the endemicity, the IUCN Red List status of the amphibian species on Sardinia, and the occurrence of infection and mortality caused by chytridiomycosis, there is serious reason for concern for the impact that disease emergence may have on the conservation of the amphibians of the island.

The predictability of extinction: biological and external correlates of decline in mammals

Extinction risk varies among species, and comparative analyses can help clarify the causes of this variation. Here we present a phylogenetic comparative analysis of species-level extinction risk across nearly the whole of the class Mammalia. Our aims were to examine systematically the degree to which general predictors of extinction risk can be identified, and to investigate the relative importance of different types of predictors (life history, ecological, human impact and environmental) in determining extinction risk. A single global model explained 27.3% of variation in mammal extinction risk, but explanatory power was lower for region-specific models (median R2=0.248) and usually higher for taxon-specific models (median R2=0.383). Geographical range size, human population density and latitude were the most consistently significant predictors of extinction risk, but otherwise there was little evidence for general, prescriptive indicators of high extinction risk across mammals. Our results therefore support the view that comparative models of relatively narrow taxonomic scope are likely to be the most precise.

Colloquium paper: phylogenetic trees and the future of mammalian biodiversity

Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerable to increased human pressure. We outline how the approach might be extended to consider future trends in anthropogenic drivers, to identify likely future battlegrounds of mammalian conservation, and the likely casualties. This framework could help to highlight consequences of choosing among different future climatic and socioeconomic scenarios. We end by discussing priority-setting, showing how alternative currencies for diversity can suggest very different priorities. We argue that aiming to maximize long-term evolutionary responses is inappropriate, that conservation planning needs to consider costs as well as benefits, and that proactive conservation of largely intact systems should be part of a balanced strategy.

The fast-slow continuum in mammalian life history: an empirical reevaluation

Many life-history traits co-vary across species, even when body size differences are controlled for. This phenomenon has led to the concept of a "fast-slow continuum," which has been influential in both empirical and theoretical studies of life-history evolution. We present a comparative analysis of mammalian life histories showing that, for mammals at least, there is not a single fast-slow continuum. Rather, both across and within mammalian clades, the speed of life varies along at least two largely independent axes when body size effects are removed. One axis reflects how species balance offspring size against offspring number, while the other describes the timing of reproductive bouts.

Pinpointing and preventing imminent extinctions

Slowing rates of global biodiversity loss requires preventing species extinctions. Here we pinpoint centers of imminent extinction, where highly threatened species are confined to single sites. Within five globally assessed taxa (i.e., mammals, birds, selected reptiles, amphibians, and conifers), we find 794 such species, three times the number recorded as having gone extinct since 1500. These species occur in 595 sites, concentrated in tropical forests, on islands, and in mountainous areas. Their taxonomic and geographical distribution differs significantly from that of historical extinctions, indicating an expansion of the current extinction episode beyond sensitive species and places toward the planet's most biodiverse mainland regions. Only one-third of the sites are legally protected, and most are surrounded by intense human development. These sites represent clear opportunities for urgent conservation action to prevent species loss.

Multiple Causes of High Extinction Risk in Large Mammal Species

Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.

Human population density and extinction risk in the world's carnivores

Understanding why some species are at high risk of extinction, while others remain relatively safe, is central to the development of a predictive conservation science. Recent studies have shown that a species' extinction risk may be determined by two types of factors: intrinsic biological traits and exposure to external anthropogenic threats. However, little is known about the relative and interacting effects of intrinsic and external variables on extinction risk. Using phylogenetic comparative methods, we show that extinction risk in the mammal order Carnivora is predicted more strongly by biology than exposure to high-density human populations. However, biology interacts with human population density to determine extinction risk: biological traits explain 80% of variation in risk for carnivore species with high levels of exposure to human populations, compared to 45% for carnivores generally. The results suggest that biology will become a more critical determinant of risk as human populations expand. We demonstrate how a model predicting extinction risk from biology can be combined with projected human population density to identify species likely to move most rapidly towards extinction by the year 2030. African viverrid species are particularly likely to become threatened, even though most are currently considered relatively safe. We suggest that a preemptive approach to species conservation is needed to identify and protect species that may not be threatened at present but may become so in the near future.