Anthropogenic predictors of varying Holocene occurrence for Europe's large mammal fauna.

Understanding how species respond to different anthropogenic pressures is essential for conservation planning. The archaeological record has great potential to inform extinction risk assessment by providing evidence on past human-caused biodiversity loss, but identifying specific drivers of past declines from environmental archives has proved challenging. We used 17 684 Holocene zooarchaeological records for 15 European large mammal species together with data on past environmental conditions and anthropogenic activities across Europe, to assess the ability of environmental archives to determine the relative importance of different human pressures in shaping faunal distributions through time. Site occupancy probability showed differing significant relationships with environmental covariates for all species, and nine species also showed significant relationships with anthropogenic covariates (human population density, % cropland, % grazing land). Across-species differences in negative relationships with covariates provide ecological insights for understanding extinction dynamics: some mammals (red deer, aurochs, wolf, wildcat, lynx, pine marten and beech marten) were more vulnerable to past human-environmental interactions, and differing single and synergistic anthropogenic factors influenced likelihood of past occurrence across species. Our results provide new evidence for pre-industrial population fragmentation and depletion in European mammals, and demonstrate the usefulness of historical baselines for understanding species' varying long-term sensitivity to multiple threats.

The effect of habitat and human disturbance on the spatiotemporal activity of two urban carnivores: The results of an intensive camera trap study.

With rising urbanization, the presence of urban wildlife is becoming more common, increasing the need for wildlife-friendly spaces in urban planning. Despite this, understanding is limited to how wildlife exploits urban environments and interacts with human populations, and this is vital to our ability to manage and conserve wildlife in urban habitats. Here, we investigate how two urban mammal species, the red fox (Vulpes vulpes) and the European badger (Meles meles), exploit urban environments. Using intensive camera trap surveys, we assessed how habitat and human disturbance influenced the spatiotemporal activity of these species across south-west London. Firstly, we found elevated activity levels of both species at boundaries and within built-up areas, suggesting movement paths follow anthropogenic features. However, badgers were most active in woodland, indicating the importance of high cover habitats suitable for setts and foraging. Secondly, we found badger activity levels were negatively affected by human activity, whilst foxes were unaffected. Further investigation suggested foxes may adapt their activity patterns to avoid human disturbance, with badger activity patterns less plastic. Whilst the results of this study are useful for both the conservation and management of urban wildlife populations, these results also show potential factors which either facilitate or limit wildlife from fully exploiting urban environments.

Environmental factors influencing spotted hyena and lion population biomass across Africa.

The spotted hyena (Crocuta crocuta Erxleben) and the lion (Panthera leo Linnaeus) are two of the most abundant and charismatic large mammalian carnivores in Africa and yet both are experiencing declining populations and significant pressures from environmental change. However, with few exceptions, most studies have focused on influences upon spotted hyena and lion populations within individual sites, rather than synthesizing data from multiple locations. This has impeded the identification of over-arching trends behind the changing biomass of these large predators. Using partial least squares regression models, influences upon population biomass were therefore investigated, focusing upon prey biomass, temperature, precipitation, and vegetation cover. Additionally, as both species are in competition with one other for food, the influence of competition and evidence of environmental partitioning were assessed. Our results indicate that spotted hyena biomass is more strongly influenced by environmental conditions than lion, with larger hyena populations in areas with warmer winters, cooler summers, less drought, and more semi-open vegetation cover. Competition was found to have a negligible influence upon spotted hyena and lion populations, and environmental partitioning is suggested, with spotted hyena population biomass greater in areas with more semi-open vegetation cover. Moreover, spotted hyena is most heavily influenced by the availability of medium-sized prey biomass, whereas lion is influenced more by large size prey biomass. Given the influences identified upon spotted hyena populations in particular, the results of this study could be used to highlight populations potentially at greatest risk of decline, such as in areas with warming summers and increasingly arid conditions.

Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae).

We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies' MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).

Mammalian tolerance to humans is predicted by body mass: evidence from long-term archives.

Humans are implicated as a major driver of species extinctions from the Late Pleistocene to the present. However, our predictive understanding of human-caused extinction remains poor due to the restricted temporal and spatial scales at which this process is typically assessed, and the risks of bias due to "extinction filters" resulting from a poor understanding of past species declines. We develop a novel continent-wide data set containing country-level last-occurrence records for 31 European terrestrial mammals across the Holocene (c.11,500 yr BP to present), an epoch of relative climatic stability that captures major transitions in human demography. We analyze regional extirpations against a high-resolution database of human population density (HPD) estimates to identify species-specific tolerances to changing HPD through the Holocene. Mammalian thresholds to HPD scale strongly with body mass, with larger-bodied mammals experiencing regional population losses at lower HPDs than smaller-bodied mammals. Our analysis enables us to identify levels of tolerance to HPD for different species, and therefore has wide applicability for determining biotic vulnerability to human impacts. This ecological pattern is confirmed across wide spatiotemporal scales, providing insights into the dynamics of prehistoric extinctions and the modern biodiversity crisis, and emphasizing the role of long-term archives in understanding human-caused biodiversity loss.

Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests.

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids.

The limits to population density in birds and mammals.

We address two fundamental ecological questions: what are the limits to animal population density and what determines those limits? We develop simple alternative models to predict population limits in relation to body mass. A model assuming that within-species area use increases with the square of daily travel distance broadly predicts the scaling of empirical extremes of minimum density across birds and mammals. Consistent with model predictions, the estimated density range for a given mass, 'population scope', is greater for birds than for mammals. However, unlike mammals and carnivorous birds, expected broad relationships between body mass and density extremes are not supported by data on herbivorous and omnivorous birds. Our results suggest that simple constraints on mobility and energy use/supply are major determinants of the scaling of density limits, but further understanding of interactions between dietary constraints and density limits are needed to predict future wildlife population responses to anthropogenic threats.

Snake venom potency and yield are associated with prey-evolution, predator metabolism and habitat structure.

Snake venom is well known for its ability to incapacitate and kill prey. Yet, potency and the amount of venom available varies greatly across species, ranging from the seemingly harmless to those capable of killing vast numbers of potential prey. This variation is poorly understood, with comparative approaches confounded by the use of atypical prey species as models to measure venom potency. Here, we account for such confounding issues by incorporating the phylogenetic similarity between a snake's diet and the species used to measure its potency. In a comparative analysis of 102 species we show that snake venom potency is generally prey-specific. We also show that venom yields are lower in species occupying three dimensional environments and increases with body size corresponding to metabolic rate, but faster than predicted from increases in prey size. These results underline the importance of physiological and environmental factors in the evolution of predator traits.

Compatibility between agendas for improving human development and wildlife conservation outside protected areas: Insights from 20 years of data.

The UN Sustainable Development Goals (SDGs) include economic, social and environmental dimensions of human development and make explicit commitments to all of life on Earth. Evidence of continuing global biodiversity loss has, at the same time, led to a succession of internationally agreed conservation targets.With multiple targets (even within one policy realm, e.g. the CBD Aichi Targets for biodiversity), it is possible for different indicators to respond in the same direction, in opposite directions or to show no particular relationship. When considering the different sectors of the SDGs, there are many possible relationships among indicators that have been widely discussed, but rarely analysed in detail.Here, we present a comparative cross-national analysis exploring temporally integrated linkages between human development indicators and wildlife conservation trends.The results suggest that in lower income countries there are negative relationships between measures of human population growth and bird and mammal population abundance trends outside protected areas.The results also suggest a positive relationship between economic growth and wildlife population trends in lower income countries. We stress, however, the need for future research to further explore the relationships between economic growth and natural resource-based imports.Our results highlight a clear potential for compatibility of the conservation and development agendas and support the need for further integration among sustainable development strategies. A free Plain Language Summary can be found within the Supporting Information of this article.

Land-use change alters the mechanisms assembling rainforest mammal communities in Borneo.

The assembly of species communities at local scales is thought to be driven by environmental filtering, species interactions and spatial processes such as dispersal limitation. Little is known about how the relative balance of these drivers of community assembly changes along environmental gradients, especially man-made environmental gradients associated with land-use change. Using concurrent camera- and live-trapping, we investigated the local-scale assembly of mammal communities along a gradient of land-use intensity (old-growth forest, logged forest and oil palm plantations) in Borneo. We hypothesised that increasing land-use intensity would lead to an increasing dominance of environmental control over spatial processes in community assembly. Additionally, we hypothesised that competitive interactions among species might reduce in concert with declines in α-diversity (previously documented) along the land-use gradient. To test our first hypothesis, we partitioned community variance into the fractions explained by environmental and spatial variables. To test our second hypothesis, we used probabilistic models of expected species co-occurrence patterns, in particular focussing on the prevalence of spatial avoidance between species. Spatial avoidance might indicate competition, but might also be due to divergent habitat preferences. We found patterns that are consistent with a shift in the fundamental mechanics governing local community assembly. In support of our first hypothesis, the importance of spatial processes (dispersal limitation and fine-scale patterns of home-ranging) appeared to decrease from low to high intensity land-uses, whilst environmental control increased in importance (in particular due to fine-scale habitat structure). Support for our second hypothesis was weak: whilst we found that the prevalence of spatial avoidance decreased along the land-use gradient, in particular between congeneric species pairs most likely to be in competition, few instances of spatial avoidance were detected in any land-use, and most were likely due to divergent habitat preferences. The widespread changes in land-use occurring in the tropics might be altering not just the biodiversity found in landscapes, but also the fundamental mechanics governing the local assembly of communities. A better understanding of these mechanics, for a range of taxa, could underpin more effective conservation and management of threatened tropical landscapes.

Foraging constraints reverse the scaling of activity time in carnivores.

The proportion of time an animal spends actively foraging in a day determines its long-term fitness. Here, we derive a general mathematical model for the scaling of this activity time with body size in consumers. We show that this scaling can change from positive (increasing with size) to negative (decreasing with size) if the detectability and availability of preferred prey sizes is a limiting factor. These predictions are supported by a global dataset on 73 terrestrial carnivore species from 8 families spanning >3 orders of magnitude in size. Carnivores weighing ∼5 kg experience high foraging costs because their diets include significant proportions of relatively small (invertebrate) prey. As a result, they show an increase in activity time with size. This shifts to a negative scaling in larger carnivores as they shift to foraging on less costly vertebrate prey. Our model can be generalized to other classes of terrestrial and aquatic consumers and offers a general framework for mechanistically linking body size to population fitness and vulnerability in consumers.

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that ß-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected ß-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and ß-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as ß-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); ß-diversity was quantified by comparing observed ß-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the ß-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant ß-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The ß-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to ß-diversity at a range of spatial grains.

Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene.

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18,700 mammalian zooarchaeological records for the last 11,700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of 'static' past baselines to inform current-day environmental management and restoration.

Applying a random encounter model to estimate lion density from camera traps in Serengeti National Park, Tanzania.

The random encounter model (REM) is a novel method for estimating animal density from camera trap data without the need for individual recognition. It has never been used to estimate the density of large carnivore species, despite these being the focus of most camera trap studies worldwide. In this context, we applied the REM to estimate the density of female lions (Panthera leo) from camera traps implemented in Serengeti National Park, Tanzania, comparing estimates to reference values derived from pride census data. More specifically, we attempted to account for bias resulting from non-random camera placement at lion resting sites under isolated trees by comparing estimates derived from night versus day photographs, between dry and wet seasons, and between habitats that differ in their amount of tree cover. Overall, we recorded 169 and 163 independent photographic events of female lions from 7,608 and 12,137 camera trap days carried out in the dry season of 2010 and the wet season of 2011, respectively. Although all REM models considered over-estimated female lion density, models that considered only night-time events resulted in estimates that were much less biased relative to those based on all photographic events. We conclude that restricting REM estimation to periods and habitats in which animal movement is more likely to be random with respect to cameras can help reduce bias in estimates of density for female Serengeti lions. We highlight that accurate REM estimates will nonetheless be dependent on reliable measures of average speed of animal movement and camera detection zone dimensions. © 2015 The Authors. Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.

Is the scaling of swim speed in sharks driven by metabolism?

The movement rates of sharks are intrinsically linked to foraging ecology, predator-prey dynamics and wider ecosystem functioning in marine systems. During ram ventilation, however, shark movement rates are linked not only to ecological parameters, but also to physiology, as minimum speeds are required to provide sufficient water flow across the gills to maintain metabolism. We develop a geometric model predicting a positive scaling relationship between swim speeds in relation to body size and ultimately shark metabolism, taking into account estimates for the scaling of gill dimensions. Empirical data from 64 studies (26 species) were compiled to test our model while controlling for the influence of phylogenetic similarity between related species. Our model predictions were found to closely resemble the observed relationships from tracked sharks, providing a means to infer mobility in particularly intractable species.

Mass enhances speed but diminishes turn capacity in terrestrial pursuit predators.

The dynamics of predator-prey pursuit appears complex, making the development of a framework explaining predator and prey strategies problematic. We develop a model for terrestrial, cursorial predators to examine how animal mass modulates predator and prey trajectories and affects best strategies for both parties. We incorporated the maximum speed-mass relationship with an explanation of why larger animals should have greater turn radii; the forces needed to turn scale linearly with mass whereas the maximum forces an animal can exert scale to a 2/3 power law. This clarifies why in a meta-analysis, we found a preponderance of predator/prey mass ratios that minimized the turn radii of predators compared to their prey. It also explained why acceleration data from wild cheetahs pursuing different prey showed different cornering behaviour with prey type. The outcome of predator prey pursuits thus depends critically on mass effects and the ability of animals to time turns precisely.