Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human-wildlife interactions along gradients of human influence.

SNAPSHOT USA 2021: A third coordinated national camera trap survey of the United States

SNAPSHOT USA is a multicontributor, long-term camera trap survey designed to survey mammals across the United States. Participants are recruited through community networks and directly through a website application (https://www.snapshot-usa.org/). The growing Snapshot dataset is useful, for example, for tracking wildlife population responses to land use, land cover, and climate changes across spatial and temporal scales. Here we present the SNAPSHOT USA 2021 dataset, the third national camera trap survey across the US. Data were collected across 109 camera trap arrays and included 1711 camera sites. The total effort equaled 71,519 camera trap nights and resulted in 172,507 sequences of animal observations. Sampling effort varied among camera trap arrays, with a minimum of 126 camera trap nights, a maximum of 3355 nights, a median 546 nights, and a mean 656 ± 431 nights. This third dataset comprises 51 camera trap arrays that were surveyed during 2019, 2020, and 2021, along with 71 camera trap arrays that were surveyed in 2020 and 2021. All raw data and accompanying metadata are stored on Wildlife Insights (https://www.wildlifeinsights.org/), and are publicly available upon acceptance of the data papers. SNAPSHOT USA aims to sample multiple ecoregions in the United States with adequate representation of each ecoregion according to its relative size. Currently, the relative density of camera trap arrays varies by an order of magnitude for the various ecoregions (0.22-5.9 arrays per 100,000 km2), emphasizing the need to increase sampling effort by further recruiting and retaining contributors. There are no copyright restrictions on these data. We request that authors cite this paper when using these data, or a subset of these data, for publication. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.

Using global remote camera data of a solitary species complex to evaluate the drivers of group formation

The social system of animals involves a complex interplay between physiology, natural history, and the environment. Long relied upon discrete categorizations of "social" and "solitary" inhibit our capacity to understand species and their interactions with the world around them. Here, we use a globally distributed camera trapping dataset to test the drivers of aggregating into groups in a species complex (martens and relatives, family Mustelidae, Order Carnivora) assumed to be obligately solitary. We use a simple quantification, the probability of being detected in a group, that was applied across our globally derived camera trap dataset. Using a series of binomial generalized mixed-effects models applied to a dataset of 16,483 independent detections across 17 countries on four continents we test explicit hypotheses about potential drivers of group formation. We observe a wide range of probabilities of being detected in groups within the solitary model system, with the probability of aggregating in groups varying by more than an order of magnitude. We demonstrate that a species' context-dependent proclivity toward aggregating in groups is underpinned by a range of resource-related factors, primarily the distribution of resources, with increasing patchiness of resources facilitating group formation, as well as interactions between environmental conditions (resource constancy/winter severity) and physiology (energy storage capabilities). The wide variation in propensities to aggregate with conspecifics observed here highlights how continued failure to recognize complexities in the social behaviors of apparently solitary species limits our understanding not only of the individual species but also the causes and consequences of group formation.

Raccoon Roundworm (Baylisascaris procyonis) Undetected in Endangered Key Largo Woodrat (Neotoma floridana smalli) Endemic Range

Raccoon roundworm (Baylisascaris procyonis) negatively affects woodrat (Neotoma spp.) populations but is not known to occur in the endemic range of endangered Key Largo woodrats (Neotoma floridana smalli). Rectal swabs from 23 raccoons (Procyon lotor) in Key Largo were screened for raccoon roundworm by PCR. All tests were negative, suggesting continued absence.

Counting the Capital's cats: Estimating drivers of abundance of free-roaming cats with a novel hierarchical model

Free-roaming cats are a conservation concern in many areas but identifying their impacts and developing mitigation strategies requires a robust understanding of their distribution and density patterns. Urban and residential areas may be especially relevant in this process because free-roaming cats are abundant in these anthropogenic landscapes. Here, we estimate the occupancy and density of free-roaming cats in Washington D.C. and relate these metrics to known landscape and social factors. We conducted an extended camera trap survey of public and private spaces across D.C. and analyzed data collected from 1483 camera deployments from 2018 to 2020. We estimated citywide cat distribution by fitting hierarchical occupancy models and further estimated cat abundance using a novel random thinning spatial capture-recapture model that allows for the use of photos that can and cannot be identified to individual. Within this model, we utilized individual covariates that provided identity exclusions between photos of unidentifiable cats with inconsistent coat patterns, thus increasing the precision of abundance estimates. This combined model also allowed for unbiased estimation of density when animals cannot be identified to individual at the same rate as for free-roaming cats whose identifiability depended on their coat characteristics. Cat occupancy and abundance declined with increasing distance from residential areas, an effect that was more pronounced in wealthier neighborhoods. There was noteworthy absence of cats detected in larger public spaces and forests. Realized densities ranged from 0.02 to 1.75 cats/ha in sampled areas, resulting in a district-wide estimate of ~7296 free-roaming cats. Ninety percent of cat detections lacked collars and nearly 35% of known individuals were ear-tipped, indicative of district Trap-Neuter-Return (TNR) programs. These results suggest that we mainly sampled and estimated the unowned cat subpopulation, such that indoor/outdoor housecats were not well represented. The precise estimation of cat population densities is difficult due to the varied behavior of subpopulations within free-roaming cat populations (housecats, stray and feral cats), but our methods provide a first step in establishing citywide baselines to inform data-driven management plans for free-roaming cats in urban environments.

Spatial and temporal overlap of domestic cats (Felis catus) and native urban wildlife

Free-roaming domestic cats (Felis catus) are known to pose threats to ecosystem health via transmission of zoonotic diseases and predation of native wildlife. Likewise, free-roaming cats are also susceptible to predation or disease transmission from native wildlife. Physical interactions are required for many of these risks to be manifested, necessitating spatial and temporal overlap between cats and wildlife species. Therefore, knowledge of the location and extent of shared habitat and activity periods would benefit management programs. We used data from a 3-year camera trap survey to model species-specific occupancy and identify landscape variables that contribute to the distribution of free-roaming domestic cats and eight native mammal species in Washington, DC. (USA). Our analysis includes five species that are common prey items of domestic cats, and three species that are potential disease vectors or are otherwise known to be a risk to cats. We then predicted the probability of occupancy and estimated the probability of spatial overlap between cats and each native wildlife species at multiple scales. We also used kernel density estimations to calculate temporal overlap between cats and each native wildlife species. Across spatial scales, occupancy for potential disease vector species was generally positively correlated with canopy cover and open water. Prey species were also generally positively correlated with canopy cover, but displayed negative associations with human population density and inconsistent associations with average per capita income. Domestic cat occupancy was negatively correlated with natural habitat characteristics and positively correlated with human population density. Predicted spatial overlap between domestic cats and native wildlife was greatest for potential disease vector species. Temporal overlap was high (>0.50) between cats and all but two native wildlife species, indicating that temporal overlap is probable wherever species overlap spatially. Our findings indicate that the risk to and from domestic cats varies across urban landscapes, but primarily arises from human activities. As such, humans are implicated in the negative outcomes that result from cats interacting with wildlife. Data-driven management to reduce such interactions can aid in cat population management, biodiversity conservation, and public health campaigns.

SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 pandemic

Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.

SNAPSHOT USA 2019: a coordinated national camera trap survey of the United States

With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August-24 November of 2019). We sampled wildlife at 1,509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the United States. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as will future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.

Activity patterns of tayra (Eira barbara) across their distribution

Species’ activity patterns are driven by the need to meet basic requirements of food, social interactions, movement, and rest, but often are influenced by a variety of biotic and abiotic factors. We used camera-trap data to describe and compare the activity patterns of the relatively poorly studied tayra (Eira barbara) across 10 populations distributed from the south of Mexico to the north of Argentina, and attempted to identify biotic or abiotic factors that may be associated with variation in level of diurnality. In a subset of sites we also aimed to document potential seasonal variation in activity. We used a kernel density estimator based on the time of independent photographic events to calculate the proportion of diurnal, crepuscular, and nocturnal activity of each population. Tayras were mostly active during diurnal periods (79.31%, 759 records), with a lower proportion of crepuscular activity (18.07%, 173 records) yet we documented some variation in patterns across the 10 study areas (activity overlap coefficient varied from Δ 4 = 0.64 to Δ 1 = 0.95). In northern localities, activity peaked twice during the day (bimodal) with most activity ocurring in the morning, whereas closer to the geographical equator, activity was constant (unimodal) throughout the day, peaking at midday: activity either was unimodal or bimodal in southern localities. Despite investigating multiple potential abiotic and biotic predictors, only latitude was associated with variation in the proportion of diurnal activity by tayras across its range, with increased diurnal activity closer to the equator. Seasonal comparisons in activity showed a tendency to reduce diurnality in dry versus rainy seasons, but the pattern was not consistently significant. This is the most comprehensive description of tayra activity patterns to date, and lends novel insight into the potential flexibility of the species to adapt to local conditions.

Thinking outside the park: recommendations for camera trapping mammal communities in the urban matrix

Urbanization is increasing globally, fragmenting habitats and prompting human–wildlife conflict. Urban wildlife research is concurrently expanding, but sampling methods are often biased towards large and intact habitats in public green spaces, neglecting the far more abundant, but degraded, habitats in the urban matrix. Here, we introduce the Five P’s of Urban Ecology—Partnerships, Planning, Placements, Public participation and Processing—as a path to overcoming the logistical barriers often associated with camera-trapping in the urban matrix. Though the Five P’s can be applied to a variety of urban sampling methods, we showcase the camera-trapping efforts of the DC Cat Count project in Washington, DC, as a case study. We compared occupancy models for eight urban mammal species using broad categorizations of land cover and local land use to determine drivers of mammal occurrence within the urban matrix as compared with urban habitat patches. Many native species maintained a strong association with large, semi-natural green spaces, but occupancy was not limited to these locations, and in some cases, the use of private yards and the built environment were not notably different. Furthermore, some species exhibited higher occupancy probabilities in developed areas over green spaces. Though seemingly intuitive, we offer advice on how to greatly reduce habitat-biased sampling methods in urban wildlife research and illustrate the importance of doing so to ensure accurate results that support the formation of effective urban planning and policy.

Assessing the role of habitat and species interactions in the population decline and detection bias of Neotropical leaf litter frogs in and around La Selva Biological Station, Costa Rica

Worldwide, amphibian populations have been declining rapidly. This decline can be attributed to many factors including climate change, pesticide exposure, and emerging infectious diseases, among other important factors, but few studies have examined the influence of species interactions. In this study, we examined how habitat factors and co-occurring avian and mammalian species, as well as humans, exert direct and indirect effects on Neotropical amphibian population dynamics. We further examined how these habitat and species interactions could affect our ability to reliably detect amphibian presence to robustly estimate population trends. We conducted amphibian visual encounter surveys at 26 randomly selected sites in the La Selva Biological Station, in northeastern Costa Rica, as well as 26 sites across five additional forest fragments in the region. Furthermore, we used camera traps to collect data on avian and mammalian communities and human visitation at those amphibian survey plots. From these data, we were able to estimate species occupancy probabilities for leaf litter frogs across sites and their relationships to habitat and interspecific species interaction covariates. We also conducted an experiment with plastic model frogs to estimate detection probabilities when a population is known to occur at a site with certainty. Our results suggested that strawberry poison dart frog (Oophagapumilio) occupancy was positively related to secondary forest and their detection was negatively related to increasing air temperatures at the times of the surveys. Leaf litter frog occupancy was negatively related to core La Selva sites and human detections at sites, yet their detection was positively related to human trail presence, which might be related to reduced leaf litter cover due to heavy trampling. Our experimental surveys suggested that Neotropical leaf litter frog communities are difficult to detect when present and future studies should explicitly account for this detection bias to effectively monitor population trends.

Land management strategies can increase oil palm plantation use by some terrestrial mammals in Colombia

While the conservation role of remaining natural habitats in anthropogenic landscapes is clear, the degree to which agricultural matrices impose limitations to animal use is not well understood, but vital to assess species’ resilience to land use change. Using an occupancy framework, we evaluated how oil palm plantations affect the occurrence and habitat use of terrestrial mammals in the Colombian Llanos. Further, we evaluated the effect of undergrowth vegetation and proximity to forest on habitat use within plantations. Most species exhibited restricted distributions across the study area, especially in oil palm plantations. Habitat type strongly influenced habitat use of four of the 12 more widely distributed species with oil palm negatively affecting species such as capybara and naked-tailed armadillo. The remaining species showed no apparent effect of habitat type, but oil palm and forest use probabilities varied among species. Overall, generalist mesocarnivores, white-tailed deer, and giant anteater were more likely to use oil palm while the remaining species, including ocelot and lesser anteater, showed preferences for forest. Distance to nearest forest had mixed effects on species habitat use, while understory vegetation facilitated the presence of species using oil palm. Our findings suggest that allowing undergrowth vegetation inside plantations and maintaining nearby riparian corridors would increase the likelihood of terrestrial mammals’ occurrence within oil palm landscapes.

Co-occurrence dynamics of endangered Lower Keys marsh rabbits and free-ranging domestic cats: Prey responses to an exotic predator removal program

The Lower Keys marsh rabbit (Sylvilagus palustris hefneri) is one of many endangered endemic species of the Florida Keys. The main threats are habitat loss and fragmentation from sea-level rise, development, and habitat succession. Exotic predators such as free-ranging domestic cats (Felis catus) pose an additional threat to these endangered small mammals. Management strategies have focused on habitat restoration and exotic predator control. However, the effectiveness of predator removal and the effects of anthropogenic habitat modifications and restoration have not been evaluated. Between 2013 and 2015, we used camera traps to survey marsh rabbits and free-ranging cats at 84 sites in the National Key Deer Refuge, Big Pine Key, Florida, USA. We used dynamic occupancy models to determine factors associated with marsh rabbit occurrence, colonization, extinction, and the co-occurrence of marsh rabbits and cats during a period of predator removal. Rabbit occurrence was positively related to freshwater habitat and patch size, but was negatively related to the number of individual cats detected at each site. Furthermore, marsh rabbit colonization was negatively associated with relative increases in the number of individual cats at each site between survey years. Cat occurrence was negatively associated with increasing distance from human developments. The probability of cat site extinction was positively related to a 2-year trapping effort, indicating that predator removal reduced the cat population. Dynamic co-occurrence models suggested that cats and marsh rabbits co-occur less frequently than expected under random conditions, whereas co-detections were site and survey-specific. Rabbit site extinction and colonization were not strongly conditional on cat presence, but corresponded with a negative association. Our results suggest that while rabbits can colonize and persist at sites where cats occur, it is the number of individual cats at a site that more strongly influences rabbit occupancy and colonization. These findings indicate that continued predator management would likely benefit endangered small mammals as they recolonize restored habitats.

Do coyotes Canis latrans influence occupancy of prey in suburban forest fragments?

With the extirpation of apex predators from many North American systems, coyotes Canis latrans have become the de facto top predator and are ubiquitous members of most ecosystems. Keystone predators aid in maintaining ecosystem function by regulating the mammal community through direct predation and instilling the landscape of fear, yet the value of coyotes regulating systems to this capacity is understudied and likely variable across environments. Since coyotes are common in the Midwestern United States, we utilized camera traps and occupancy analyses to assess their role in regulating the distribution of mammalian herbivores in a fragmented suburban ecosystem. Forest cover was a strong positive predictor of white-tailed deer Odocoileus virginianus detection, while coyote occurrence had a negative effect. Coyotes exerted a negative effect on squirrel (Sciurus spp.) and eastern cottontail rabbit Sylvilagus floridanus occurrence, while urban cover was a positive predictor for the prey species’ occurrence. These results suggest all 3 species behaviorally avoid coyotes whereby deer seek denser forest cover and squirrels and cottontails mitigate risk by increasing use of urban areas. Although previous studies reveal limited influence of coyote on the rest of the carnivore guild in suburban systems, we suggest coyotes play an important role in regulating the herbivorous mammals and hence may provide similar ecological benefits in urban/suburban forest fragments through trophic cascades. Furthermore, since hunting may not be allowed in urban and suburban habitats, coyotes might also serve as the primary regulator of nuisance species occurring at high abundance such as white-tailed deer and squirrels.

The role of fragmentation and landscape changes in the ecological release of common nest predators in the Neotropics

Loss of large mammalian carnivores may allow smaller mesopredators to become abundant and threaten other community members. There is considerable debate about mesopredator release and the role that other potential factors such as landscape variables and human alterations to land cover lead to increased mesopredator abundance. We used camera traps to detect four mesopredators (tayra, Eira barbara; white-nosed coati, Nasua narica; northern raccoon, Procyon lotor; and common opossum, Didelphis opossum) in a biological corridor in Costa Rica to estimate habitat covariates that influenced the species' detection and occurrence. We selected these mesopredators because as semi-arboreal species they might be common nest predators, posing a serious threat to resident and migratory songbirds. Pineapple production had a pronounced positive effect on the detectability of tayras, while forest cover had a negative effect on the detection of coatis. This suggests that abundance might be elevated due to the availability of agricultural food resources and foraging activities are concentrated in forest fragments and pineapple edge habitats. Raccoon and opossum models exhibited little influence on detection from habitat covariates. Occurrence models did not suggest any significant factors influencing site use by nest predators, revealing that all four species are habitat generalists adapted to co-existing in human altered landscapes. Furthermore, fragmentation and land cover changes may predispose nesting birds, herpetofauna, and small mammals to heightened predation risk by mesopredators in the Neotropics.