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Most extinctions worldwide have occurred on islands, primarily due to interactions with exotic species, but rarely due to interactions among endemic species. This potential exists on two of the California Channel Islands, Santa Cruz and Santa Rosa, as endemic island spotted skunks (Spilogale gracilis amphiala) appear to have rapidly declined to rarity, possibly due to interference competition with endemic island foxes (Urocyon littoralis). Niche partitioning is expected in response to interference competition; hence, it is surprising that skunks and foxes show extensive overlap in macrohabitat use and circadian activity. However, the role of microhabitat associations and fine-scale temporal activity in facilitating coexistence of the two species has not been explored. We evaluated microhabitat associations of island spotted skunks and island foxes across both islands using data from live traps and wildlife cameras collected during 2015–2017, and we analyzed fine-scale temporal activity using camera data from 2016 and 2017. On both islands, skunks had a positive response to ground-level cover provided by rugged topography or woody vegetation such as shrubs or trees, whereas foxes had a weak or negative response, suggesting partitioning of these microhabitat characteristics. Additionally, on both islands the peak in timing of skunk activity offset the peak for foxes, which implies that skunks use fine-scale adjustments in activity to avoid foxes. Past grazing by exotic herbivores likely reduced habitat refuges for skunks; however, as vegetation on both islands recovers, regrowth of shrubs and trees may provide cover that will improve prospects for coexistence of island spotted skunks and island foxes.

Large high-severity fires are increasing in frequency in many parts of the world, including the coniferous forests of the Sierra Nevada mountains. These “megafires” alter vegetation and environmental conditions in forests, yet their impacts on native wildlife remain poorly understood. Bats play an important role in forest ecosystems, but their responses to megafires likewise are understudied. We investigated bat responses to the King Fire, a megafire that burned nearly 40,000 ha within the Eldorado National Forest in 2014, half of it at high severity. From June to September 2017, we used remote acoustic recorders to survey bats at 26 sites with varying fire severity (unburned, mixed, and high severity). We analyzed data with Royle–Nichols occupancy models to investigate how bat space use was influenced by megafires, and whether this response was driven by prey availability, fire severity, or fire-altered habitat conditions. We calculated prey species richness, biomass, and abundance, from moths sampled with blacklight surveys. Vegetation covariates included tree density, canopy cover, and shrub density, measured along vegetation transects. To capture general effects of fire, we also included fire severity and the percentage of dead trees as potential covariates on space use. Prey variables were highest in unburned forests, were the most common predictors of, and generally had positive effects on bat space use. Responses to tree density and canopy cover varied by species; the most common vegetation covariate, shrub density, had weak positive effects on bat space use. In spite of the varying prey and vegetation conditions across fire severity categories, most bats showed weak to no response in space use to fire severity and tree mortality. We attribute this to the highly mobile nature of bats, which reduces the impact of potentially negative local conditions.

Wildfires in many western North American forests are becoming more frequent, larger, and severe, with changed seasonal patterns. In response, coniferous forest ecosystems will transition toward dominance by fire-adapted hardwoods, shrubs, meadows, and grasslands, which may benefit some faunal communities, but not others. We describe factors that limit and promote faunal resilience to shifting wildfire regimes for terrestrial and aquatic ecosystems. We highlight the potential value of interspersed nonforest patches to terrestrial wildlife. Similarly, we review watershed thresholds and factors that control the resilience of aquatic ecosystems to wildfire, mediated by thermal changes and chemical, debris, and sediment loadings. We present a 2-dimensional life history framework to describe temporal and spatial life history traits that species use to resist wildfire effects or to recover after wildfire disturbance at a metapopulation scale. The role of fire refuge is explored for metapopulations of species. In aquatic systems, recovery of assemblages postfire may be faster for smaller fires where unburned tributary basins or instream structures provide refuge from debris and sediment flows. We envision that more-frequent, lower-severity fires will favor opportunistic species and that less-frequent high-severity fires will favor better competitors. Along the spatial dimension, we hypothesize that fire regimes that are predictable and generate burned patches in close proximity to refuge will favor species that move to refuges and later recolonize, whereas fire regimes that tend to generate less-severely burned patches may favor species that shelter in place. Looking beyond the trees to forest fauna, we consider mitigation options to enhance resilience and buy time for species facing a no-analog future., Ecology and Evolution, 11 (18), ISSN:2045-7758

Identifying mechanisms of population change is fundamental for conserving small and declining populations and determining effective management strategies. Few studies, however, have measured the demographic components of population change for small populations of mammals (, This research investigates population dynamics in two adjacent but genetically and geographically distinct, threatened brown bear (Ursus arctos) populations in southwestern British Columbia, Canada, following the caseation of hunting in that area. Differences in independent female and cub survival between the populations resulted in population increase in the larger, partially connected population, and population decrease in the smaller, isolated population. We suggest that when populations are small and isolated, population growth is rare and, even with intensive management, becomes prohibitive for population recovery.

Monitoring programs are key to determine bird population trends and to assess environmental policies, and therefore are central to conservation biology. The European approach commonly used to estimate bird population trends (TRends and Indices for Monitoring data, hereafter TRIM) has proved useful to fulfil this task, yet it fails to account for imperfect detection and assumes constant detectability across years. We tested the role of detectability for population trend estimation in an open Mediterranean farmland context, which is a dynamic landscape likely to undergo yearly changes in detectability, by using data of 30 bird species over a nine-year study period. We evaluated species-specific population trends under the TRIM approach and hierarchical distance sampling models (hereafter HDS) that estimate true abundance by accounting for imperfect detection. When comparing both methods, 13 species presented differences in population trend estimates between TRIM and HDS models. Moreover, detectability was not constant across the bird community: observer and year affected detection, and these effects varied among species. Our study highlights the importance of accounting for imperfect detection in bird monitoring programs to ensure reliable trend estimates, providing a first insight for an open farmland bird community. Aside from trend estimates, our HDS model may prove useful as a tool to obtain site-specific abundance estimates (for intance, within Special Protection Areas) and trend probabilities of bird populations.

AimUnsustainable hunting is leading to widespread defaunation across the tropics. To mitigate against this threat with limited conservation resources, stakeholders must make decisions on where to focus anti-poaching activities. Identifying priority areas in a robust way allows decision-makers to target areas of conservation importance, therefore maximizing the impact of conservation interventions.LocationAnnamite mountains, Vietnam and Laos.MethodsWe conducted systematic landscape-scale surveys across five study sites (four protected areas, one unprotected area) using camera-trapping and leech-derived environmental DNA. We analyzed detections within a Bayesian multi-species occupancy framework to evaluate species responses to environmental and anthropogenic influences. Species responses were then used to predict occurrence to unsampled regions. We used predicted species richness maps and occurrence of endemic species to identify areas of conservation importance for targeted conservation interventions.ResultsAnalyses showed that habitat-based covariates were uninformative. Our final model therefore incorporated three anthropogenic covariates as well as elevation, which reflects both ecological and anthropogenic factors. Conservation-priority species tended to found in areas that are more remote now or have been less accessible in the past, and at higher elevations. Predicted species richness was low and broadly similar across the sites, but slightly higher in the more remote site. Occupancy of the three endemic species showed a similar trend.Main conclusionIdentifying spatial patterns of biodiversity in heavily-defaunated landscapes may require novel methodological and analytical approaches. Our results indicate to build robust prediction maps it is beneficial to sample over large spatial scales, use multiple detection methods to increase detections for rare species, include anthropogenic covariates that capture different aspects of hunting pressure, and analyze data within a Bayesian multi-species framework. Our models further suggest that more remote areas should be prioritized for anti-poaching efforts to prevent the loss of rare and endemic species.

The frequency of large, high-severity "mega-fires" has increased in recent decades, with numerous consequences for forest ecosystems. In particular, small mammal communities are vulnerable to post-fire shifts in resource availability and play critical roles in forest ecosystems. Inconsistencies in previous observations of small mammal community responses to fire severity underscore the importance of examining mechanisms regulating the effects of fire severity on post-fire recovery of small mammal communities. We compared small mammal abundance, diversity, and community structure among habitats that burned at different severities, and used vegetation characteristics and small mammal functional traits to predict community responses to fire severity three years after one mega-fire in the Sierra Nevada, California. Using a model-based fourth-corner analysis, we examined how interactions between vegetation variables and small mammal traits associated with their resource use were associated with post-fire small mammal community structure among fire severity categories. Small mammal abundance was similar across fire severity categories, but diversity decreased and community structure shifted as fire severity increased. Differences in small mammal communities were large only between unburned and high-severity sites. Three highly correlated fire-dependent vegetation variables affected by fire and the volume of soft coarse woody debris were associated with small mammal community structures. Furthermore, we found that interactions between vegetation variables and three small mammal traits (feeding guild, primary foraging mode, and primary nesting habit) predicted community structure across fire severity categories. We concluded that resource use was important in regulating small mammal recovery after the fire because vegetation provided required resources to small mammals as determined by their functional traits. Given the mechanistic nature of our analyses, these results may be applicable to other fire-prone forest systems, although it will be important to conduct studies across large biogeographic regions and over long post-fire time periods to assess generality.

To offset the declining timber supply by shifting towards more sustainable forestry practices, industrial tree plantations are expanding in tropical production forests. The conversion of natural forests to tree plantation is generally associated with loss of biodiversity and shifts towards more generalist and disturbance tolerant communities, but effects of mixed‐landuse landscapes integrating natural and plantation forests remain little understood. Using camera traps, we surveyed the medium‐to‐large bodied terrestrial wildlife community across two mixed‐landuse forest management areas in Sarawak, Malaysia Borneo which include areas dedicated to logging of natural forests and adjacent planted Acacia forests. We analyzed data from a 25‐wildlife species community using a Bayesian community occupancy model to assess species richness and species‐specific occurrence responses to Acacia plantations at a broad scale, and to remote‐sensed local habitat conditions within the different forest landuse types. All species were estimated to occur in both landuse types, but species‐level percent area occupied and predicted average local species richness were slightly higher in the natural forest management areas compared to licensed planted forest management areas. Similarly, occupancy‐based species diversity profiles and defaunation indices for both a full community and only threatened and endemic species suggested the diversity and occurrence were slightly higher in the natural forest management areas. At the local scale, forest quality was the most prominent predictor of species occurrence. These associations with forest quality varied among species but were predominantly positive. Our results highlight the ability of a mixed‐landuse landscape with small‐scale Acacia plantations embedded in natural forests to retain terrestrial wildlife communities while providing an alternate source of timber. Nonetheless, there was a tendency towards reduced biodiversity in planted forests, which would likely be more pronounced in plantations that are larger or embedded in a less natural matrix.

The savannah enclaves (i.e. patches) in the southern Brazilian Amazonia are among the most threatened and poorly surveyed sites in Amazonia. As part of an extensive mammal survey, we set camera traps in three of these savannah enclaves. We obtained 23 independent records of pampas deer Ozotoceros bezoarticus, a medium sized Neotropical cervid that is strongly associated with open habitats and categorized as Vulnerable on the Brazilian Red List of threatened species. These savannah enclaves with confirmed populations of pampas deer lie outside the species’ previously presumed historical range and are at least 350 km from any known extant population. Together, these savannah enclaves add c. 4,000 km2 to the pampas deer's currently known range. The small pampas deer populations in these enclaves are probably isolated by a matrix of Amazon forest, raising questions about spatial genetic structure and meta-population dynamics, and making them vulnerable to local extinction. We highlight the need for further studies, particularly genetic, to assess the conservation status of these populations, the results of which could potentially inform management decisions in other areas of the heavily fragmented range of this species.

The study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.

We conducted DNA capture-recapture monitoring of grizzly bears (Ursus arctos) from 5 to 17 years after hunting was stopped in two adjacent but genetically distinct populations in southwestern British Columbia, Canada. We used spatial capture-recapture and non-spatial Pradel robust design modelling to estimate population density, trends, and the demographic components of population change for each population. The larger population had 21.5 bears/1000 km2 and was growing (λPradel = 1.02 ± 0.02 SE; λsecr = 1.01 ± 4.6 × 10−5 SE) following the cessation of hunting. The adjacent smaller population had 6.3 bears/1000 km2 and was likely declining (λPradel = 0.95 ± 0.03 SE; λsecr = 0.98 ± 0.02 SE). Estimates of apparent survival and apparent recruitment indicated that lower recruitment was the dominant factor limiting population growth in the smaller population. Factors limiting reproductive rates and population density could include poor habitat quality, particularly the abundance of high-energy foods, genetic Allee effects due to a long period of population isolation, or demographic effects affecting infanticide rates. The cessation of hunting was insufficient to promote population recovery for the low density, isolated population. Our research highlights the importance of considering mortality thresholds in addition to small population effects and habitat quality when recovering large carnivore populations.

The Annamite mountains of Viet Nam and the Lao People's Democratic Republic (Lao) are an area of exceptional mammalian endemism but intensive poaching has defaunated much of the region, creating an extinction crisis for the endemic species. To make efficient use of limited conservation resources, it is imperative that conservation stakeholders obtain basic information about poorly known and threatened endemics. We present the first comprehensive information on the ecology, distribution and status of the little-known endemic Annamite striped rabbit Nesolagus timminsi. We used a systematic camera-trapping design to study the species in five areas in Viet Nam and Lao. In 29,180 camera-trap-nights we recorded 152 independent events at 36 of 266 stations. We obtained an additional 143 independent detections across 12 stations from a supplementary non-systematic survey. We analysed activity patterns and social behaviour. We also used single-species occupancy models to assess factors that influence occupancy at the landscape scale. We used N-mixture models to obtain local abundance estimates in one target area. The Annamite striped rabbit was found to be nocturnal and primarily solitary. Species occupancy was best explained by a proxy for past hunting pressure, with no significant relationships to current anthropogenic or environmental factors. Local abundance was 0.57 individuals per camera-trap station for one of our sites, and estimated to be zero at the other site where hunting appears to have been more intense. Our results provide information on priority areas for targeted anti-poaching efforts and give the first conservation baseline for the species.

Commercial timber extraction and agricultural expansion lead to substantial degradation and loss of tropical rainforests, posing a severe threat to biodiversity in South-east Asia. Although the impacts of these disturbances are well understood for some species, they remain largely unknown for most species, impeding any directed conservation efforts. One of these little known, presumably forest-dwelling species is the moonrat Echinosorex gymnura, an insectivorous mammal ranging from southern Myanmar and southern Thailand to Sumatra and Borneo. While the moonrat is currently listed as Least Concern on The IUCN Red List of Threatened Species, large parts of its range have been severely degraded due to unsustainable logging practices and the conversion of forest to oil palm plantations. We conducted a systematic large-scale camera trap survey in three forest reserves under different forest management strategies in Sabah, Malaysian Borneo. We recorded a total of 67 independent moonrat detections at 22 of 180 camera trap stations over 12,281 camera trap days. We analysed moonrat habitat associations using occupancy modelling and a set of 9 different environmental covariates. Canopy closure and forest quality were positively associated with moonrat occurrence and were the most important determinants of the species’ occurrence in our study area. Proximity to plantations (oil palm and industrial timber) and elevation negatively affected moonrat occurrence. Our results thus indicate that the moonrat strongly depends on high-quality lowland forest and is unlikely to occur close to plantations. Moonrat occupancy was highest in the sustainably managed forest reserve, suggesting that this species responds much better to reduced-impact logging compared to conventional logging practices. Our first ecological survey indicates that the moonrat may be more threatened by the continued conversion, degradation, and fragmentation of tropical lowland rainforests than previously assumed.

Measuring the multidimensional diversity properties of a community is of great importance for ecologists, conservationists and stakeholders. Diversity profiles, a plotted series of Hill numbers, simultaneously capture the common diversity indices. However, diversity metrics require information on species abundance, often relying on raw count data without accounting for imperfect and varying detection. Hierarchical occupancy models account for variation in detectability, and Hill numbers have been expanded to allow estimation based on occupancy probability. But the ability of occupancy-based diversity profiles to reproduce patterns in abundance-based diversity has not been investigated. Here, we fit community occupancy models to simulated animal communities to explore how well occupancy-based diversity profiles reflect patterns in true abundance-based diversity. Because we expect occupancy-based diversity to be overestimated, we further tested a occupancy thresholding approach to reduce potential biases in the estimated diversity profiles. Finally, we use empirical bird community data to present how the framework can be extended to consider species similarity. The simulation study showed that occupancy-based diversity profiles produced among-community patterns in diversity similar to true abundance diversity profiles, although within-community diversity was generally overestimated. Applying an occupancy threshold reduced positive bias, but resulted in negative bias in richness estimates and slightly reduced the ability to reproduce true differences among the simulated communities; thus, we do not recommend application of this threshold. Application of our approach to a large bird dataset indicated differential species diversity patterns in communities of different habitat types. Accounting for phylogenetic and ecological similarities between species reduced variability in diversity among habitats. Our framework allows investigating the complexity of diversity from species detection data, while accounting for imperfect and varying detection probabilities, as well as species similarities. Visualizing results in the form of diversity profiles facilitates comparison of diversity between sites or across time. The approach offers opportunities for further development, for example by using local abundances estimated using the Royle-Nichols or N-mixture models and further exploration of thresholding methods. In spite of some challenges, occupancy-based diversity profiles are useful for studying and monitoring patterns in biodiversity.

Reintroductions are an important recovery tool for endangered species but have had varying success. We used demographic data to evaluate the use of reintroductions for the recovery of the federally endangered Sierra Nevada Yellow-legged Frog (Rana sierrae) in stream populations in its northern range where the species is particularly at risk. We conducted a capture–mark–recapture study from 2016–2018 in four diverse streams. One of the streams contained a high abundance of frogs that allowed us to investigate demography in a relatively healthy population. In another of the streams, we tested a reintroduction using captive-reared frogs. We used robust design Huggins and Pradel models to estimate abundance, apparent overwinter survival, recruitment, longevity, and sex ratios. Annual abundance estimates were small, with ≤52 wild adult frogs at three streams and few tadpoles or subadults seen in any of the streams. The oldest frog in our streams was at least 13 yr. Estimates of apparent survival rates of wild adults ranged from 0.55 ± 0.05 standard error (SE) to 0.90 ± 0.05 SE, and estimates of annual recruitment ranged from 0.02 ± 0.11 SE to 0.26 ± 0.03 SE per site. High survival rates leading to long-lived adults may facilitate persistence of these stream populations, whereas low recruitment may limit population growth and recovery. The two largest populations were in intermittent streams, which may reflect their roles as a refuge from fishes. At least 52% of captive-reared frogs survived their first summer after release and at least 36% survived their first winter. Apparent overwinter survival of captive-reared frogs was lower than for wild frogs, ranging from 0.29 ± 0.13 SE to 0.56 ± 0.14 SE. Because of the apparent low survival of wild eggs, tadpoles, and subadults, releasing adults as was done in this study, rather than younger life stages, may be more successful. Our results offer promise for the use of reintroductions to augment depleted populations and suggest that further research on factors affecting recruitment and survival of younger life stages is needed.

With continued global changes, such as climate change, biodiversity loss, and habitat fragmentation, the need for assessment of long‐term population dynamics and population monitoring of threatened species is growing. One powerful way to estimate population size and dynamics is through capture–recapture methods. Spatial capture (SCR) models for open populations make efficient use of capture–recapture data, while being robust to design changes. Relatively few studies have implemented open SCR models, and to date, very few have explored potential issues in defining these models. We develop a series of simulation studies to examine the effects of the state‐space definition and between‐primary‐period movement models on demographic parameter estimation. We demonstrate the implications on a 10‐year camera‐trap study of tigers in India. The results of our simulation study show that movement biases survival estimates in open SCR models when little is known about between‐primary‐period movements of animals. The size of the state‐space delineation can also bias the estimates of survival in certain cases.We found that both the state‐space definition and the between‐primary‐period movement specification affected survival estimates in the analysis of the tiger dataset (posterior mean estimates of survival ranged from 0.71 to 0.89). In general, we suggest that open SCR models can provide an efficient and flexible framework for long‐term monitoring of populations; however, in many cases, realistic modeling of between‐primary‐period movements is crucial for unbiased estimates of survival and density.

The Sunda stink-badger Mydaus javanensis is one of the most frequently recorded carnivore species in portions of Sabah, Malaysian Borneo. However, its current distribution on Borneo is patchy, with recent records lacking from areas where the species was previously considered common. We assessed the hypothesis that occurrence of Sunda stink-badgers is restricted to areas of high earthworm density. We also assessed the influence of forest disturbance on occurrence, as the species is thought to be disturbance-tolerant. We compiled camera-trap data from three commercial forest reserves in central Sabah collected during 2008–2010 and 2014–2015. We used single season occupancy modeling to estimate probability of occupancy and detection. We obtained 323 detections of Sunda stink-badger over 19,875 trap-nights. We found no fine-scale association between occurrence and earthworm abundance, suggesting that Sunda stink-badgers have broader diets than currently assumed, or that earthworm density potentially influences their occurrence at larger scales. The influence of forest disturbance on occurrence was mixed; although our results suggested that Sunda stink-badgers might have a higher probability of occupancy in more disturbed forests, it is possible that a disturbance threshold exists where extreme forest conversion (e.g., oil palm plantations, human settlements) results in lower occupancy. We did not find strong associations with proximity to water, oil palm plantation, bare earth, or shrub landcovers, suggesting that Sunda stink-badgers are not affected by edge effects or the proximity of disturbed areas. Despite our large dataset across three forest reserves, this study is only a first step in understanding the current irregular distribution of Sunda stink-badgers on Borneo. Further studies across a larger gradient of habitat disturbance are needed to determine potential habitat disturbance thresholds, which will aid in management of this species as the landscape on Borneo continues to undergo anthropogenic change.

Activity patterns reflect adaptations to local biological and physical conditions. We estimated the activity patterns of 3 mesocarnivore species in a semiarid environment in northeastern Brazil: the ocelot (Leopardus pardalis), crab-eating fox (Cerdocyon thous), and oncilla (Leopardus tigrinus). We compared the overlap of daily activity among these species and to apex predators. We also estimated nighttime activity of these mesocarnivores during 2 years and compared activity peaks with those of apex predators and potential prey. All 3 mesocarnivores were nocturnal, with ocelots having only 1 record during daytime. Coefficients of overlap with larger predators were high (Δ1 > 0.7) for all pairwise comparisons, since all species were very nocturnal. Nighttime-only activity comparisons (Kolmogorov–Smirnov tests) showed that activity of oncillas differed from that of both larger mesocarnivores and jaguar activity, suggesting temporal segregation. Contrary to our expectations, rodent activity was dissimilar from that of ocelots and crab-eating foxes, but activity of rodents and oncillas was relatively synchronous. Activity of both cat species seems limited to the cooler nighttime, and nocturnal behavior of oncillas more likely reflects activity of potential prey rather than regulation by intraguild predators. Future studies in arid regions should consider climatic factors when estimating activity patterns.

Carnivores face conflicts with humans, which has reduced their numbers and distribution. Carnivores compete in intraguild predation systems, Subordinate predators usually avoid top predators through spatial or temporal separation. Coexistence requires a complex combination of resources and environmental conditions. In this study, we assessed the occupancy and temporal activity during night time of the jaguar ( Panthera onca ) and puma ( Puma concolor ) in the Serra da Capivara National Park (SCNP), located in the semi-arid Caatinga biome of Brazil. Felines face biological limitations in hot environments. We used camera-traps, occupancy models and temporal analysis to evaluate their patterns of habitat use, activity and interactions in SCNP between 2009 and 2011. We considered jaguar as dominant predator and puma as subordinate, and expected to find spatial and temporal avoidance between them. We found evidence of spatial and temporal coexistence. This coexistence could be a result of a restriction of niche separation between both species, influenced by the harsh conditions in the Caatinga, represented by a combination of extreme temperatures, scarcity of refuges to thermoregulate, an environment around SCNP with a high level of human disturbance and an apparent increase in prey due conservation policies.

Coarse-scale patterns of distribution and abundance of species are the outcome of processes occurring at finer spatial scales, hence the conservation of species depends on understanding their fine-scale ecology. For Bornean carnivores, little is known about fine-scale predictors of species occurrence and it is assumed that the two main threats to wildlife on Borneo, habitat disturbance and hunting, also impact their occurrence. To increase our understanding of the Borneo carnivore community, we deployed 60 cameras in a logging concession in northern Sarawak, Malaysian Borneo, where different landscape covariates, both natural and anthropogenic, were present. We built single-species occupancy models to investigate fine-scale carnivore occupancy. Overall, forest disturbance had a negative effect on Hose’s civet (Diplogale hosei), banded civet (Hemigalus derbyanus) and yellow-throated marten (Martes flavigula). Further, banded civet had greater occupancy probabilities in more remote areas. Logging roads had the most diverse effect on carnivore occupancy, with Hose’s civet and masked palm civet (Paguma larvata) negatively affected by roads, whereas Malay civet (Viverra tangalunga), short-tailed mongoose (Herpestes brachyurus) and leopard cat (Prionailurus bengalensis) showed higher occupancy closer to roads. Canopy height, canopy closure, number of trees with holes (cavities) and distance to nearest village also affected occupancy, though the directions of these effects varied among species. Our results highlight the need to collect often overlooked habitat variables: moss cover and ‘kerangas’ (tropical heath forest) were the most important variables predicting occurrence of Hose’s civet. The preservation of such forest conditions may be crucial for the long-term conservation of this little-known species. Our results confirm that logged forests, when left to regenerate, can host diverse carnivore communities on Borneo, provided less disturbed habitat is available nearby, though human access needs to be controlled. We recommend easy-to-implement forest management strategies including maintaining forest next to logging roads; preserving fruiting trees and trees with cavities, both standing and fallen; and blocks of remote, less disturbed, mid- to high-elevation forest with understorey vegetation.

This study investigated the presence of Hepatozoon spp. in jaguars ( Panthera onca ) and domestic animals in the Cerrado, Amazon, and Pantanal biomes of Brazil. Between February 2000 and January 2010, blood samples were collected from 30 jaguars, 129 domestic dogs ( Canis lupus familiaris), and 22 domestic cats ( Felis catus ) for molecular tests. All of the jaguars from the Pantanal (n = 22) and Cerrado (n = 4) and 3 of 4 jaguars from the Amazon were positive for Hepatozoon spp. Domestic dogs (62.8%) and cats (31.8%) were also positive for the agent. Hepatozoon nucleotide sequences from jaguars and domestic cats grouped with other Hepatozoon felis, whereas Hepatozoon from domestic dogs showed high similarity to Hepatozoon canis. Different species of Amblyomma were identified as parasitizing the jaguars and may act as vectors for Hepatozoon spp. Jaguars from the 3 sites were healthy and did not seem to be threatened by the hemoparasite within its population or environments. Most likely, jaguars play an important role in the maintenance of Hepatozoon spp. in nature.

Aim Financial incentives to manage forests sustainably, such as certification or carbon storage payments, are assumed to have co-benefits for biodiversity conservation. This claim remains little studied for rain forest mammals, which are particularly threatened, but challenging to survey. Location Sabah, Malaysia, Borneo. Methods We used photographic data from three commercial forest reserves to show how community occupancy modelling can be used to quantify mammalian diversity conservation co-benefits of forest certification. These reserves had different management histories, and one was certified by the Forest Stewardship Council. Results Many threatened species occupied larger areas in the certified reserve. Species richness, estimated per 200 × 200-m grid cell throughout all reserves, was higher in the certified site, particularly for threatened species. The certified reserve held the highest aboveground biomass. Within reserves, aboveground biomass was not strongly correlated with patterns of mammal richness (Spearman's rho from 0.03 to 0.32); discrepancies were strongest along reserve borders. Main conclusions Our approach provides a flexible and standardized tool to assess biodiversity and identify winners of sustainable forestry. Inferring patterns of species richness from camera-trapping carries potential for the objective designation of high conservation value forest. Correlating species richness with aboveground biomass further allows evaluating the biodiversity co-benefits of carbon protection. These advantages make the present approach an ideal tool to overcome the difficulties to rigorously quantify biodiversity co-benefits of forest certification and carbon storage payments.

Measuring links among genotype, phenotype, and survival in the wild has long been a focus of studies of adaptation. We conducted a four-year capture-recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched colouration in S. cowlesi from the heart of the dunes is associated with mutations in the melanocortin-1 receptor gene (Mc1r), ecotonal S. cowlesi showed minimal association between colour phenotype and Mc1r genotype. Second, the frequency of the derived Mc1r allele in ecotonal S. cowlesi appeared to decrease over time. Third, our capture-recapture data revealed a lower survival rate for S. cowlesi individuals with the derived Mc1r allele. Thus, our results suggest that selection at the ecotone may have favoured the wildtype allele in recent years. Even in a system where a genotype-phenotype association appeared to be black and white, our study suggests that additional factors - including phenotypic plasticity, epistasis, pleiotropy, and gene flow - may play important roles at the White Sands ecotone. Our study highlights the importance of linking molecular, genomic, and organismal approaches for understanding adaptation in the wild. Furthermore, our findings indicate that dynamics of natural selection can be particularly complex in transitional habitats like ecotones, and emphasize the need for future research that examines the patterns of ongoing selection in other ecological “grey” zones. This article is protected by copyright. All rights reserved.

Human-induced environmental changes, particularly climate change, pose a threat to many tropical montane species, making the identification of optimal future habitat a conservation priority. Here we used maximum entropy (Maxent) and boosted regression trees to predict suitable habitat of the threatened Bornean highland endemic Hose's civet (Diplogale hosei), that is currently available, and for future time periods (2050s and 2080s), considering future land cover and climate change predictions. Next, we identified areas that were consistently suitable under current and future model predictions as forest refuges. Our analysis predicted that Hose's civet is restricted mainly to the highlands of Borneo to an area less than 20,000 km2 (about 2% of the entire island of Borneo). Changes in land cover have little impact on predicted suitable area for the species. However, we predicted habitat loss due to climate change to approximate 86% by 2080, except under a “green economy scenario” which showed stable or increasing suitable habitat. Refuges were small, about 11% of 2010 habitat, and mostly restricted to lower montane forest. About 28–35% of refuges lie within the current protected area network though much is designated as commercial forests within the proposed Heart of Borneo (HoB). For the conservation of Hose's civet and likely other Bornean highland endemics, we recommend increased wildlife and forest law enforcement in identified protected refuges and sustainable timber harvesting practices in surrounding commercial forests, both within the HoB and the extensions we identified. Results of our green model showed that efforts to reduce greenhouse gas emissions will likely contribute immensely to the long-term conservation of highland species such as Hose's civet. Keywords: Biomod2, Climate change, Conservation planning, IPCC, Species distribution modelling, Southeast Asia

Even with intensive sampling effort, data often remain sparse when estimating population density of elusive species such as the Sunda clouded leopard Neofelis diardi. An inadequate number of recaptures can make it difficult to account for heterogeneity in detection parameters. We used data from large-scale camera-trapping surveys in three forest reserves in Sabah, Malaysian Borneo, to (1) examine whether a high-density camera-trap network increases the number of recaptures for females, which tend to be more difficult to detect, thus improving the accuracy of density estimates; (2) compare density estimates from models incorporating individual heterogeneity in detection parameters with estimates from the null model to evaluate its potential bias; and (3) investigate how the size of the camera-trap grid affects density and movement estimates. We found that individual heterogeneity could not be incorporated in the single-site data analysis and only conservative null model estimates could be generated. However, aggregating data across study sites enabled us to account for individual heterogeneity and we estimated densities of 1.27–2.82 individuals/100 km2, 2–3 times higher than estimates from null models. In light of these findings, it is possible that earlier studies underestimated population density. Similar densities found in well-managed forest and recently selectively logged forest suggest that Sunda clouded leopards are relatively resilient to forest disturbances. Our analysis also revealed that camera-trapping grids for Sunda clouded leopard density estimations should cover large areas (c. 250 km2), although smaller grids could be appropriate if density or detectability are higher.

Assessing spatiotemporal interactions between species is of fundamental interest to behavioural and community ecology. Observer‐independent methods such as camera trapping facilitate the study of interactions, but analyses are hampered by the lack of comparative assessment of available approaches. We present a flexible and expandable framework to simulate and explore spatiotemporal interactions between species from camera trapping data with well‐defined properties, and compare methods to detect such interactions in a two‐species system with two types of (spatio)temporal interactions: spatiotemporal avoidance (of a site by a species after the presence of another species) and temporal segregation (shifts in daily activity patterns between species), across a range of daily activity patterns and interaction strengths. For spatiotemporal avoidance, we analysed time intervals between species records using linear models, the Mann–Whitney U‐test, a permutation test and a test based on randomly generated records. For temporal segregation, we applied a permutation test. Statistical power (the ability to detect an existing effect) for detecting spatiotemporal avoidance between species was strongly affected by interaction strength, highest for linear models and reliable above 50 records per species. Reliably detecting strong temporal segregation required fewer records (10–20 records) but depended heavily on the underlying activity pattern. All tests were valid (uniform distribution of P‐values under the null hypothesis) even at low sample sizes above a minimum of 10 records per species. Linear models were the most suitable approach to analyse spatiotemporal avoidance and can easily correct for other sources of variation in interactions. The framework presented here can help to improve survey design in camera trapping and be extended to more complex settings (e.g. with imperfect detection). In addition, it allows researchers to validate the methods used for inference of spatiotemporal interactions from camera trapping data in their specific circumstances.

Summary Camera trapping is a widely applied method to study mammalian biodiversity and is still gaining popularity. It can quickly generate large amounts of data which need to be managed in an efficient and transparent way that links data acquisition with analytical tools. We describe the free and open-source R package camtrapR, a new toolbox for flexible and efficient management of data generated in camera trap-based wildlife studies. The package implements a complete workflow for processing camera trapping data. It assists in image organization, species and individual identification, data extraction from images, tabulation and visualization of results and export of data for subsequent analyses. There is no limitation to the number of images stored in this data management system; the system is portable and compatible across operating systems. The functions provide extensive automation to minimize data entry mistakes and, apart from species and individual identification, require minimal manual user input. Species and individual identification are performed outside the R environment, either via tags assigned in dedicated image management software or by moving images into species directories. Input for occupancy and (spatial) capture–recapture analyses for density and abundance estimation, for example in the R packages unmarked or secr, is computed in a flexible and reproducible manner. In addition, survey summary reports can be generated, spatial distributions of records can be plotted and exported to gis software, and single- and two-species activity patterns can be visualized. camtrapR allows for streamlined and flexible camera trap data management and should be most useful to researchers and practitioners who regularly handle large amounts of camera trapping data.

Summary Distance sampling is a common survey method in wildlife studies, because it allows accounting for imperfect detection. The framework has been extended to hierarchical distance sampling (HDS), which accommodates the modelling of abundance as a function of covariates, but rare and elusive species may not yield enough observations to fit such a model. We integrate HDS into a community modelling framework that accommodates multi-species spatially replicated distance sampling data. The model allows species-specific parameters, but these come from a common underlying distribution. This form of information sharing enables estimation of parameters for species with sparse data sets that would otherwise be discarded from analysis. We evaluate the performance of the model under varying community sizes with different species-specific abundances through a simulation study. We further fit the model to a seabird data set obtained from shipboard distance sampling surveys off the East Coast of the USA. Comparing communities comprised of 5, 15 or 30 species, bias of all community-level parameters and some species-level parameters decreased with increasing community size, while precision increased. Most species-level parameters were less biased for more abundant species. For larger communities, the community model increased precision in abundance estimates of rarely observed species when compared to single-species models. For the seabird application, we found a strong negative association of community and species abundance with distance to shore. Water temperature and prey density had weak effects on seabird abundance. Patterns in overall abundance were consistent with known seabird ecology. The community distance sampling model can be expanded to account for imperfect availability, imperfect species identification or other missing individual covariates. The model allowed us to make inference about ecology of species communities, including rarely observed species, which is particularly important in conservation and management. The approach holds great potential to improve inference on species communities that can be surveyed with distance sampling.

Small mammals comprise an important component of forest vertebrate communities. Our understanding of how small mammals use forested habitat has relied heavily on studies in forest systems not naturally prone to frequent disturbances. Small mammal populations that evolved in frequent-fire forests, however, may be less restricted to specific habitat conditions due to the instability of these resources in time and space. We investigate how canopy cover and the volume of coarse woody debris (CWD), covariates that are considered important for small mammals, impact abundance and body mass of eight small mammal species. Based on live-trapping data collected across 23 sites over three years in a frequent fire forest in the Sierra Nevada we apply capture-recapture models for stratified populations, a statistically rigorous, rarely used framework that allows joint modeling of detection, abundance and its response to covariates. Canopy cover had a strong negative association with the abundance of yellow-pine chipmunks and California ground squirrels, and a strong positive association with deer mice. CWD had a strong negative association with the abundance of golden-mantled ground squirrels, yellow-pine and long-eared chipmunks, and a strong positive association with deer mice. Whereas canopy cover influenced abundance and body mass similarly, CWD had a positive association with body mass and a negative association with abundance in some species. These patterns could arise if suitable habitat is monopolized by socially dominant individuals. Despite these habitat associations, the small mammal community in our study was dynamic and diverse, with spatial and temporal variation in dominant species suggesting that species were flexible in their use of habitat. This study suggests that it is important to understand the disturbance regimes when investigating habitat requirements, coexistence and evolutionary ecology of small mammal species.

Human activities affect large carnivores worldwide by increasing mortality due to destruction and fragmentation of habitats, decrease of prey availability, and hunting pressure. The jaguar (Panthera onca) is a large carnivore strongly influenced by these threats, with poaching of predators being primarily a retaliatory response that is motivated by depredation of domestic animals. We investigate the distribution of jaguars and cattle depredation in 21 sampling units located in Central Brazil. We consider native and domestic prey availability as well as landscape configuration and composition as possible contributory factors. We removed correlated variables and conducted a set of logistic regressions in a step-wise approach. We used the difference between χ2 of the newest and the previous model to evaluate if the addition of a variable increased the explanatory power of the newest model. Jaguar occurrence was influenced by prey richness, which is correlated with habitat aggregation in the landscape, revealing the attributes that can act as proxies for environmental quality for jaguar. The relationship between jaguar and prey richness also suggests that jaguar can act as a surrogate for the presence of other species. Jaguar occurrence is also related to the availability of non-native prey such as cattle, but not cattle depredation, suggesting that cattle depredation could be an opportunistic event. Patterns of cattle depredation warrant further study because human-wildlife conflict is one of the greatest threats to jaguar conservation.

In 2014, Wiley and the Zoological Society of London launched Remote Sensing in Ecology and Conservation, an open-access journal that aims to support communication and collaboration among experts in remote sensing, ecology and conservation science. Remote sensing was from the start understood as the acquisition of information about an object or phenomenon through a device that is not in physical contact with the object, thus including camera traps, field spectrometry, terrestrial and aquatic acoustic sensors, aerial and satellite monitoring as well as ship-borne automatic identification systems. The primary goals of this new journal were, and still are, to maximize the understanding and uptake of remote sensing-based techniques and products by the ecological and conservation communities, prioritizing findings that advance the scientific basis of, and applied outcomes from, ecology and conservation science; and to identify ecological challenges that might direct development of future remote sensors and data products. In October 2015, the first issue of the journal was published, with four other issues produced in 2016 and four to be published in 2017. As Remote Sensing in Ecology and Conservation is about to complete its second full year of publication and is working towards a first impact factor score in early 2019, the time has come to reflect on how the journal has done to date, what impact it has had, which niches it has successfully filled and where the journal is yet to meet its full potential. By sharing our successes and experiences so far with our contributors and readers, we hope to demonstrate how Remote Sensing in Ecology and Conservation has swiftly gained significant visibility and status among scientists and practitioners interested in natural resource management. Fil: Pettorelli, Nathalie. The Zoological Society Of London; Reino Unido Fil: Nagendra, Harini. Azim Premji University; India Fil: Rocchini, Duccio. Università Degli Studi Di Trento; Italia Fil: Rowcliffe, Marcus. The Zoological Society Of London; Reino Unido Fil: Williams, Rob. Oceans Initiative; Estados Unidos Fil: Ahumada, Jorge. Conservation International; Estados Unidos Fil: de Angelo, Carlos Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina Fil: Atzberger, Clement. Universitat Fur Bodenkultur Wien; Austria Fil: Boyd, Doreen. Science and Technology Facilities Council of Nottingham. Rutherford Appleton Laboratory; Reino Unido. University of Nottingham; Estados Unidos Fil: Buchanan, Graeme. Royal Society For The Protection Of Birds; Reino Unido Fil: Chauvenet, Alienor. University of Queensland; Australia Fil: Disney, Mathias. Colegio Universitario de Londres; Reino Unido Fil: Duncan, Clare. Deakin University; Australia Fil: Fatoyinbo, Temilola. NASA Goddard Space Flight Center; Estados Unidos Fil: Fernandez, Nestor. Consejo Superior de Investigaciones Científicas. Estación Biológica de Doñana; España Fil: Haklay, Muki. Colegio Universitario de Londres; Reino Unido Fil: He, Kate. Murray State University Murray; Estados Unidos Fil: Horning, Ned. American Museum of Natural History; Estados Unidos Fil: Kelly, Natalie. Australian Antarctic Division; Australia Fil: de Klerk, Helen. Stellenbosch University; Sudáfrica Fil: Liu, Xuehua. Tsinghua University; China Fil: Merchant, Nathan. Centre for Environment, Fisheries and Aquaculture Science; Reino Unido Fil: Paruelo, José. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Roy, Helen. NERC Centre for Ecology & Hydrology; Reino Unido Fil: Roy, Shovonlal. University of Reading; Reino Unido Fil: Ryan, Sadie. University of Florida; Estados Unidos Fil: Sollmann, Rahel. University of California at Davis; Estados Unidos Fil: Swenson, Jennifer. University of Duke; Estados Unidos Fil: Wegmann, Martin. Universität Würzburg; Alemania

Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services., This Perspective is a product of the EO-BESS Working Group, organized by H.B., D.R. and B.C. and funded by the UK Natural Environment Research Council.

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult‐to‐capture species, genetic surveys from noninvasive collection of hair or scat has proved cost‐efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single‐session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost‐effective sampling protocols.

Maximizing detection probability is a common goal for occupancy studies using camera traps for data collection. Placing additional cameras at a survey station may improve precision of occupancy and detection estimates. However, these benefits are situational and potentially influenced by species' physical characteristics and behavior. We estimated null occupancy and detection probabilities for 20 mammalian species with >10 detections at multiple sites from one- and two-camera data sets from 63 stations set in a commercial forest reserve in Sabah, Malaysian Borneo during October–December 2015. We used a cross-validated absolute shrinkage and selection operator approach to model the effects of species’ body mass, social behavior, dietary niche, and foot posture on detection probability using one- and two-camera designs. The number of species detections, sites where species were detected, detection probability estimates, and precision of model parameter estimates for all species improved using two cameras. Our results showed that unguligrade species were associated with both high detection probability estimates with one camera and also the greatest improvements using the two-camera design in detection probability compared to all other species. Greater improvements in precision of model parameter estimates from two-camera designs were observed in species detected less frequently. Our data suggests that camera designs need to be adapted based on the focal species and we suggest that future occupancy studies collect preliminary information to maximize effectiveness of camera effort and ensure that data collection is efficient and meets project needs. Keywords: Camera trapping, Occupancy modelling, LASSO regression

Diet of the jaguar Panthera onca in the Cerrado, central Brazil, was investigated based on a sample of genetically identified jaguar scats. At least nine prey species were observed in 35 scat samples. Giant anteaters Myrmecophaga tridactyla contributed more than 75 % of biomass to the observed diet. Tapirs Tapirus terrestris and peccaries Tayassu pecari and Pecari tajacu contributed approximately 6 % to jaguar diet each, and small mammals contributed least to the jaguar diet. At 0.121, dietary niche breadth was narrower than reported in most other studies. Due to their physical characteristics and abundance, giant anteaters are likely the most profitable prey for jaguars in Emas National Park, and as an important prey, they should be included in jaguar conservation efforts. © 2013 Springer-Verlag Berlin Heidelberg.

Camera-traps are a widely applied to monitor wildlife populations. For individually marked species, cap- ture–recapture models provide robust population estimates, but for unmarked species, inference is often based on relative abundance indices (RAI, number of records per trap effort), although these do not account for imperfect and variable detection. We use a simulation study and empirical camera-trapping data to illustrate how ecological and sampling-related factors can bias RAIs. Our simulations showed that (1) differences in detection between species led to bias in RAI ratios toward the more detectable species, especially at low detection levels, (2) species with larger home ranges were photographed more often, inflating RAIs, (3) species specific responses to different types of trap setup biased RAI ratios, and (4) changes in detection over time blurred true population trends inferred from RAIs. Empirical data for leop- ard cats Prionailurus bengalensis and common palm civets Paradoxurus hermaphroditus showed that traps set up along roads led to higher RAIs than off-road traps, but targeting roads increased detection more for leopard cats than for common palm civets. Comparing RAIs of Sunda clouded leopards Neofelis diardi and leopard cats with spatial capture–recapture based density estimates across sites, RAIs did not reflect dif- ferences in density. Analytical options for estimating density from camera-trapping data of unmarked populations are limited. Consequently, we fear that RAIs will continue to be applied. This is alarming, since these measures often form the basis for conservation and management decisions. We suggest con- sidering alternative analytical and survey methods, especially when dealing with threatened species.

White-lipped peccaries (Tayassu pecari) are important seed predators and dispersers throughout the Neotropics. Because they occur in groups as large as 300 individuals, they need large areas to persist. We investigated homerange size and overlap of 13 groups using radiotelemetry data from 3 years of monitoring in the Emas National Park and surrounding farmland in central Brazil. Average home-range sizes were 1,710.64 ha for 50% of the locations and 8,659.99 ha for 95% based on minimum convex polygons and 790.38 ha for 50% of the locations and 7,986.92 ha for 95% based on the fixed kernel estimator. Home-range size did not correlate with group size, the monitoring period, or the number of locations obtained. Home ranges were larger during the wet season than the dry season. Average home-range overlap among groups was 31%; there were no significant differences in overlap between seasons. Home ranges varied seasonally, most likely in response to the dynamic landscape of crop plantations surrounding the park. Although the peccaries fared well in the heterogeneous agricultural landscape surrounding the park, conflict with farmers due to crop damage and landscape changes due to expansion of sugarcane plantations need to be addressed by conservation strategies.

The small (2- to 7-kg) leopard cat (Prionailurus bengalensis) is the most common cat species in Asia. Although it occurs in a wide range of habitats and seems to adapt well to anthropogenic habitat changes, surprisingly little is known about this species in the wild. All studies have focused on protected areas, although a large proportion of Southeast Asian forests are timber concessions. During this study, we used large camera-trapping data sets (783 records of 124 individuals) from 3 commercially used forests to investigate consequences of different logging regimes on density and habitat associations of the leopard cat. We applied spatial capture–recapture models accounting for the location of camera-traps (on or off road) to obtain estimates of leopard cat density. Density was higher in the 2 more disturbed forest reserves (X = 12.4 individuals/100 km2 ± 1.6 SE and 16.5 ± 2 individuals/100 km2) than in the sustainably managed forest (9.6 ± 1.7 individuals/100 km2). Encounter rates with off-ro...

American black bears are closely associated with forest habitat. They were nearly extirpated from the Central Interior Highlands, United States, in the early twentieth century, but have recolonized this part of the range since the 1960s. Due to lower population densities (as a result of recent recolonization), we hypothesized that bears in this region would show strong associations with forest habitat at both the home range and landscape scale. To test this, we analyzed hair snare and GPS telemetry data from five sampling grids with a combined spatial capture–recapture and resource selection function model to investigate individual space use within home ranges and landscape scale variation in density of black bears in the southern Missouri part of the Interior Highlands. We performed a linear discriminant analysis to identify habitat correlates of black bear density. We found that at the home range level, bears selected for more forested habitat and steeper slopes. Black bear density varied among sampling grids from 0.842 to 10.248 individuals/100 km2 which is at the low end of the spectrum of reported black bear densities. There were no clear habitat correlates for among-grid variation in density, but in the three higher-density grids, density declined with increasing forest cover and increasing distance from human settlements. This suggests that the bear populations benefited from more heterogeneous habitat and that rural settlements may represent food resources. Exploiting these anthropogenic resources could be facilitated by the fact that bears in our study were not hunted and were viewed as a novelty rather than a nuisance, which may lead to low perceived risk from anthropogenic sources. Our results highlight the need to interpret habitat associations of American black bears not only at local scales but also in the landscape context.

The planning of protected areas take into consideration the current distributions of target species, disregarding possible future range shifts under climate change. This study tested potential shifts in the distribution of three xenarthran species (the giant anteater, Myrmecophaga tridactyla ; the giant armadillo, Priodontes maximus ; and the three-banded armadillo, Tolypeutes tricinctus ) due to the effects of climate change under different dispersal scenarios. In addition, we tested the adequacy of the current Brazilian protected areas in preserving these species under future climate changes (future distribution for the year 2050), under full and null dispersal scenarios. The final occurrence maps were then confronted with two Brazilian reserve systems for the year 2010: one consisting of reserves for integral protection only (IPCU), and one that included also reserves for sustainable use and indigenous reserves (SUCU). In the IPCU system, none of the species have or will have ⩾10% of their distributions protected, under neither dispersal scenario. Including SUCU, however, M. tridactyla and P. maximus already are, and will still be, adequately protected in the future. T. tricinctus , which is endemic to the Brazilian semi-arid, will not reach the 10% goal under neither dispersal scenario, even under the SUCU system. We stress the need for management actions in the northeastern and central parts of Brazil. Opportunities for the creation of more reserves are highlighted, considering the potential range shifts and the natural habitats still present in these regions.

Aim The four Mentawai islands, south-west of Sumatra, have long been isolated from the remainder of Sundaland, resulting in a high level of endemism. We examined the distribution of 151 species of the Mentawai Islands in Sundaland and assessed various processes that may have resulted in the various biogeographical patterns. Location Southeast Asia, particularly the Mentawai Islands and nearby large landmasses (Sumatra, Java, Borneo and Peninsular Malaysia). Methods We compared the faunal composition of the Mentawai Islands for selected taxa (43 mammals, 92 reptiles and 16 amphibians) with that of the four nearby large landmasses of Sundaland using morphological comparisons and the most recent molecular phylogenetic analyses available in the literature. These comparisons yielded sister taxa, which were used to simulate species absence data for the four Sundaland landmasses under several scenarios to investigate how patterns of species absence could have arisen. Results In contrast to our expectations, several Mentawai species did not have their closest relatives on neighbouring Sumatra, but rather on the more distant Borneo, Java or Peninsular Malaysia. For mammals, the similarity between species from Mentawai and Borneo was greater than that observed between species from Mentawai and Sumatra. We conclude that the relationships represent traces of species historically distributed throughout Sundaland that became extinct in Sumatra during the Pleistocene. For reptiles and amphibians the observed pattern of species absences generally resembled the simulated pattern expected under the scenario of absence rates increasing with landmass isolation, whereas for mammals we observed more species than expected missing from Java and Sumatra, and fewer than expected from Borneo. Main conclusions The potential extinctions on Sumatra probably had two causes: changes of climate and vegetation during the Pleistocene and environmental impacts from the Toba supervolcanic eruption.

Recently the Sunda clouded leopard Neofelis diardi was recognized as a separate species distinct from the clouded leopard Neofelis nebulosa of mainland Asia. Both species are categorized as Vulnerable on the IUCN Red List. Little is known about the newly identified species and, in particular, information from forests outside protected areas is scarce. Here we present one of the first density estimates calculated with spatial capture–recapture models using camera-trap data. In two commercial forest reserves in Sabah (both certified for their sustainable management practices) the density of the Sunda clouded leopard was estimated to be c. 1 per 100 km2 (0.84±SE 0.42 and 1.04±SE 0.58). The presence of the Sunda clouded leopard in such forests is encouraging for its conservation but additional studies from other areas, including protected forests, are needed to compare and evaluate these densities.

Camera trapping has become a popular technique to monitor carnivore populations due to its usefulness in estimating abundance. Nevertheless, there are a number of problems associated with study design which are motivating researchers to search for a compromise that ensures improvement of precision while being cost-effective. We have used data from a capture–recapture study in a forested area in central Brazil to evaluate the effectiveness of using one versus two cameras per trapping station for determining jaguar (Panthera onca) density and capture rates of several other mammals. The capture rate for the jaguar and other species recorded with only one camera was lower than that with two cameras. The number of jaguars identified using photos from one camera ranged between six and seven animals, but reached ten individuals when two-camera sets were used where pictures of both flanks could be positively individualized. These differences, combined with different estimates of effective sampled area size, resulted in jaguar densities estimates ranging from 2.18 to 5.40 and 3.99 individuals/100 km2 when one and two cameras were used per station, respectively (using the half-MMDM and Heterogeneity model). Based on our results, we recommend the use of two cameras per station for jaguar density monitoring to ensure reasonable levels of reliability and accuracy of estimates despite a small sample size.

Coexistence of sympatric species is mediated by resource partitioning. Pumas occur sympatrically with jaguars throughout most of the jaguar's range but few studies have investigated space partitioning between both species. Here, camera trapping and occupancy models accounting for imperfect detection were employed in a Bayesian framework to investigate space partitioning between the jaguar and puma in Emas National Park (ENP), central Brazil. Jaguars were estimated to occupy 54.1% and pumas 39.3% of the sample sites. Jaguar occupancy was negatively correlated with distance to water and positively correlated with the amount of dense habitat surrounding the camera trap. Puma occupancy only showed a weak negative correlation with distance to water and with jaguar presence. Both species were less often present at the same site than expected under independent distributions. Jaguars had a significantly higher detection probability at cameras on roads than at off-road locations. For pumas, detection was similar on and off-road. Results indicate that both differences in habitat use and active avoidance shape space partitioning between jaguars and pumas in ENP. Considering its size, the jaguar is likely the competitively dominant of the two species. Owing to its habitat preferences, suitable jaguar habitat outside the park is probably sparse. Consequently, the jaguar population is likely largely confined to the park, while the puma population is known to extend into ENP's surroundings.

Owing to habitat conversion and conflict with humans, many carnivores are of conservation concern. Because of their elusive nature, camera trapping is a standard tool for studying carnivores. In many vertebrates, sex-specific differences in movements – and therefore detection by cameras – are likely. We used camera trapping data and spatially explicit sex-specific capture–recapture models to estimate jaguar density in Emas National Park in the central Brazilian Cerrado grassland, an ecological hotspot of international importance. Our spatially explicit model considered differences in movements and trap encounter rate between genders and the location of camera traps (on/off road). We compared results with estimates from a sex-specific non-spatial capture–recapture model. The spatial model estimated a density of 0.29 jaguars 100 km−2 and showed that males moved larger distances and had higher trap encounter rates than females. Encounter rates with off-road traps were one tenth of those for on-road traps. In the non-spatial model, males had a higher capture probability than females; density was estimated at 0.62 individuals 100 km−2. The non-spatial model likely overestimated density because it did not adequately account for animal movements. The spatial model probably underestimated density because it assumed a uniform distribution of jaguars within and outside the reserve. Overall, the spatial model is preferable because it explicitly considers animal movements and allows incorporating site-specific and individual covariates. With both methods, jaguar density was lower than reported from most other study sites. For rare species such as grassland jaguars, spatially explicit capture–recapture models present an important advance for informed conservation planning.

Although many carnivores are of conservation concern, most are poorly studied. The maned wolf Chrysocyon brachyurus Illiger, 1811 is the largest South American canid with a broad distribution; however, the largest portion of its range is in the Brazilian Cerrado savannah, where due to intensive agricultural expansion, it is threatened by habitat loss. Maned wolf population trends are virtually unknown. We analyzed radio telemetry data from a 13-year study in Emas National Park, central Brazil, with Burnham's live recapture/dead recovery models in the program MARK to obtain the first analytically sound estimate of the apparent maned wolf survival rate. We constructed 16 candidate models including variation in survival rate and resighting probability associated with an individual's sex or age and year of study. Apparent adult survival rate throughout the study ranged from 0.28 (se=0.08) to 0.97 (se=0.06). There was no evidence for sex specificity but strong support for time variation. Model weights supported an age effect and the subadult survival rate was 0.63 (se=0.15). Results indicate similar life patterns for male and female maned wolves and similar mortality risks for adults and subadults in the study area. The observed temporal fluctuations of adult survival rate are important for population dynamics as they decrease average population growth rates. Population dynamics are central for conservation planning and our results are an important step towards a better understanding of the maned wolf's ecology.

The maned wolf (Chrysocyon brachyurus) inhabits the savannah-like Cerrado of Brazil. Although 80% of this biome has already been affected by human activity, little is known about maned wolf abundance. Using mark–recapture models, we obtained the first density estimate from central Brazil, the core of maned wolf distribution. With 5.19 individuals/100 km2, even large reserves support only small maned wolf populations. Therefore, long-term conservation of the maned wolf depends on land management outside of reserves.