Environmental Gradients Shape Mammal and Galliform Bird Communities in a Mountain Reserve Through Species Turnover and Niche Differentiation

Tourist activity in natural areas may impact species' behavior and ecology as well as predator-prey dynamics. Although previous research has demonstrated effects of human disturbance on wildlife communities, only a limited number of studies have focused on small mammals and coyote predator-prey systems. To generate an overview of human impacts on these wildlife communities, we analyzed camera trap data from a human-disturbed site at Lake Tahoe, California. To compare species' activity patterns in relation to distances from human-disturbed areas, we used single-species occupancy models, estimations of species' temporal activity overlaps, and the time between detections of different species at camera sites. We found that in general black bears (Ursus americanus) avoided areas of high human disturbance, whereas coyotes (Canis latrans), rodents, and lagomorphs favored them. However, rodents and lagomorphs also avoided areas with high coyote detections, indicating that rodents and lagomorphs mostly used human-disturbed areas that were not highly frequented by coyotes. Additionally, all aforementioned species avoided humans temporally and this avoidance increased in closer proximity to human-disturbed areas. These findings indicate that while some species frequented human-disturbed areas more than others, all species studied exhibited greater temporal avoidance of humans when closer to areas of higher human activity. Our results also indicate that rodents' and lagomorphs' activity patterns overlapped more with coyotes' activity patterns closer to human-disturbed areas and rodents and lagomorphs avoided coyotes less in these areas. The greater overlap of the species' activity patterns suggests that there is likely more interaction between coyotes and their prey closer to areas of high human activity. The changes in the behavior and ecology of wildlife communities closer to human-disturbed areas reported here emphasize how proximity to human-disturbed areas may influence both predator and prey demographics.

Further notes on the analysis of mammal inventory data collected with camera traps

Intensive resource extraction activity in the oil sands of Canada alters the quantity, structure and distribution of native ecosystems, which in turn creates substantive challenges for conservation, land management and habitat reclamation. Progressive reclamation occurs on active mine sites in the Athabasca oil sands region (AOSR) of Canada, along with concurrent assessments of reclamation effectiveness. Yet, little is known about the ability of reclaimed habitats to mitigate for the short‐ and long‐term impacts associated with open‐pit mines and provide functional habitat for wildlife. We used a robust quasi‐experiment that combined camera trap data from an observational study with an innovative occupancy model to assess the effectiveness of upland reclamation to provide habitat for wildlife in the AOSR. The dynamic occupancy models were applied to 15 years of camera trap data to assess wildlife usage patterns of nine species of wildlife over seven types of habitats. The habitats sampled ranged from mining‐disturbed habitats reclaimed to upland forest ecosites common in the region, habitats disturbed by natural (fire) and human disturbances (clear‐cut logging), with comparisons to mostly intact mature forests. Our results indicate that the nine species of wildlife assessed used habitats in a manner consistent with expectations: some preferred disturbance‐dominated habitats while others used mature forest to a higher degree. We demonstrate that the application of dynamic occupancy models to camera trap data reliably discerned these trends, providing the means to predict wildlife usage patterns in an ever‐changing landscape, including one containing bitumen extraction as a contributor to landscape‐level modifications. Practical implication : Our work illustrates how continued monitoring of wildlife using camera traps contributes to assessments of reclamation effectiveness with respect to wildlife occurrence, distribution and usage patterns in anthropogenically and naturally disturbed landscapes. Evaluating the effectiveness of reclamation is especially important given the expected increase in habitat reclamation on active oil sands mines over the next several decades, coupled with the need to ensure that disturbed habitats regain ecological function able to sustain wildlife in the future.

SummaryOver the last two decades, a large number of camera trap surveys have been carried out around the world and camera traps have been proposed as an ideal tool for inventorying and monitoring medium to large‐sized terrestrial vertebrates. However, few studies have analysed camera trap data at the community level.We developed a multi‐session multi‐species occupancy model that allows us to obtain estimates for species richness and occupancy combining data from multiple camera trap surveys (sessions). By estimating species presence at the session‐level and modelling detection probability and occupancy for each species and sessions as nested random effects, we could improve parameter estimates for each session, especially for species with sparse data. We developed two variants of our model: one was a binary latent states model while the other used a Royle–Nichols formulation for the relationship between detection probability and abundance.We applied both models to data from eight camera trap surveys from south‐eastern Peru including six study sites, 263 camera stations and 17 423 camera days. Sites covered protected areas, a logging concession and Brazil nut concessions. We included habitat (terra firmevs. floodplain) as a covariate for occupancy and trail vs. off‐trail as a covariate for detection.Among‐camera heterogeneity was a serious problem for our data and the Royle–Nichols variant of our model had a much better fit than the binary‐state variant. Both models resulted in similar species richness estimates showing that most of the sites contained intact large mammal communities. Detection probabilities and occupancy values were more variable across species than across sessions within species. Three species showed a habitat preference and four species showed preference or avoidance of trails.Synthesis and applications. Our multi‐session multi‐species occupancy model provides improved estimates for species richness and occupancy for a large data set. Our model is ideally suited for integrating large numbers of camera trap data sets to investigate regional and/or temporal patterns in the distribution and composition of mammal communities in relation to natural or anthropogenic factors or to monitor mammal communities over time.

Simple SummaryTropical forests are one of the most impacted habitats in the world due mostly to anthropogenic pressures. Mammal communities are threatened by many human activities but most of the time knowledge of the status of wildlife populations is lacking. In this study, we investigated two mammal communities, in the poorly studied country of Myanmar, characterized by similar environmental conditions but different levels of human pressure and habitat degradation. We found that the disturbed area hosted a community with a lower mammal diversity (species richness) but not altered in its functional composition (trophic niches and body mass) except for the lack of apex predators. There were also differences in the probability of occurrence of two species (Northern red muntjak and clouded leopard) with significantly lower values in the degraded area. The former being the target of hunting for bushmeat consumption and the latter vulnerable and threatened by human activities. These results increase our knowledge on the direct and indirect effects of human disturbance in tropical forest areas in Myanmar and give us important tools for future conservation actions.Tropical forests comprise a critically impacted habitat, and it is known that altered forests host a lower diversity of mammal communities. In this study, we investigated the mammal communities of two areas in Myanmar with similar environmental conditions but with great differences in habitat degradation and human disturbance. The main goal was to understand the status and composition of these communities in an understudied area like Myanmar at a broad scale. Using camera trap data from a three-year-long campaign and hierarchical occupancy models with a Bayesian formulation, we evaluated the biodiversity level (species richness) and different ecosystem functions (diet and body mass), as well as the occupancy values of single species as a proxy for population density. We found a lower mammal diversity in the disturbed area, with a significantly lower number of carnivores and herbivores species. Interestingly, the area did not show alteration in its functional composition. Almost all the specific roles in the community were present except for apex predators, thus suggesting that the effects of human disturbance are mainly effecting the communities highest levels. Furthermore, two species showed significantly lower occupancies in the disturbed area during all the monitoring campaigns: one with a strong pressure for bushmeat consumption and a vulnerable carnivore threatened by illegal wildlife trade.

Wildlife in the Anthropocene is increasingly spatially and temporally constrained by lethal and non-lethal human disturbance. For large carnivores with extensive space requirements, like wolves and Eurasian lynx, avoiding human disturbance in European landscapes is challenging when sufficient space with low disturbance is rarely available. Consequently, investigating behavioural adjustments to human presence is critical to understanding the capacity to adapt to human disturbance. We hypothesised that under low human disturbance conditions, large carnivores would adjust their temporal behaviours to make use of daytime, and when daytime human disturbance is high, they would opt for nocturnality. Using camera trap data from nine European study sites along a gradient in human disturbance, we analysed wolf and Eurasian lynx activity patterns. Our data spanned multiple years, 2014 – 2022, and we focused our analysis on September until April, when most large carnivore monitoring takes place. For wolves, our analysis revealed i) increased nocturnal behaviour, ii) decreased diurnal overlap with increasing human activity, and iii) a significant association between a higher probability of nocturnal activity and increasing human disturbance. For Eurasian lynx, we found iv) consistently nocturnal behaviours across all study sites, regardless of human disturbance, and v) no association between human disturbance and increased probability of being active during the night. Our results show that wolves can adjust to diurnal or cathemeral behaviours under low human disturbance, but shift to nocturnality when human disturbance increases. Eurasian lynx, however, consistently maintain their nocturnal behaviour, which we attribute to their principal hunting strategy of stalk and ambush. If human disturbance constrains large carnivore activity to nighttime, it could influence their interactions with prey, leading to cascading effects in the ecosystem. On the other hand, maintaining nocturnal behaviours in human-dominated landscapes may benefit large carnivore conservation, by decreasing negative interactions with humans thereby contributing to a landscape of coexistence.

Human disturbance has the potential to alter competitive interactions, favoring species better able to adapt to areas used by humans. One such species is the spotted hyena (Crocuta crocuta), which has been successful in human‐dominated areas throughout Africa. In addition, hyenas are frequently successful in kleptoparasiting prey brought down by other carnivore species (e.g., leopards [Panthera pardus]). In the Udzungwa Mountains of Tanzania, leopard density declines sharply close to human settlements, and hyenas are their only competitors. Using camera trap data and a spatio‐temporal occupancy model, we assessed the relative dominance of each species through spatial co‐occurrence, altered activity patterns and temporary site avoidance. We tested the hypothesis that hyenas gain a competitive advantage over leopards in human‐dominated areas due to their relatively higher tolerance for anthropogenic activities. We found that while hyena occupancy was best predicted by prey occupancy and not strongly affected by landscape factors associated with humans, leopards, especially male leopards, were less likely to be detected close to human settlements. Female leopards, which are smaller than males, exhibited activity shifts and temporary site avoidance in response to hyenas. In response to male leopards, hyenas shifted their activity patterns to become more active around dusk and dawn. These results suggest that while hyenas may be behaviorally dominant over female leopards, they are subordinate to male leopards. We found that male leopards and hyenas were less likely to co‐occur closer to people, especially where prey was scarce, suggesting subordinance of hyenas to male leopards may be mitigated by human disturbance. Furthermore, young male leopards shifted their activity patterns to be more diurnal in response to hyena presence, suggesting that dominance relationship between hyenas and leopards develops with age and is probably related to body size. These results indicate that human disturbance has the potential to affect the competitive relationship between leopards and hyenas in the Udzungwa Mountains, but that relationships will vary with sex and body size.

Site occupancy models (SOMs) are a common tool for studying the spatial ecology of wildlife. When observational data are collected using passive monitoring field methods, including camera traps or autonomous recorders, detections of animals may be temporally autocorrelated, leading to biased estimates and incorrectly quantified uncertainty. We presently lack clear guidance for understanding and mitigating the consequences of temporal autocorrelation when estimating occupancy models with camera trap data. We use simulations to explore when and how autocorrelation gives rise to biased or overconfident estimates of occupancy. We explore the impact of sampling design and biological conditions on model performance in the presence of autocorrelation, investigate the usefulness of several techniques for identifying and mitigating bias and compare performance of the SOM to a model that explicitly estimates autocorrelation. We also conduct a case study using detections of 22 North American mammals. We show that a join count goodness‐of‐fit test previously proposed for identifying clustered detections is effective for detecting autocorrelation across a range of conditions. We find that strong bias occurs in the estimated occupancy intercept when survey durations are short and detection rates are low. We provide a reference table for assessing the degree of bias to be expected under all conditions. We further find that discretizing data with larger windows decreases the magnitude of bias introduced by autocorrelation. In our case study, we find that detections of most species are autocorrelated and demonstrate how larger detection windows might mitigate the resulting bias. Our findings suggest that autocorrelation is likely widespread in camera trap data and that many previous studies of occupancy based on camera trap data may have systematically underestimated occupancy probabilities. Moving forward, we recommend that ecologists estimating occupancy from camera trap data use the join count goodness‐of‐fit test to determine whether autocorrelation is present in their data. If it is, SOMs should use large detection windows to mitigate bias and more accurately quantify uncertainty in occupancy model parameters. Ecologists should not use gaps between detection periods, which are ineffective at mitigating temporal structure in data and discard useful data.

Grain (size of sampling units) affects the spatial resolution at which ecological patterns can be observed and analysed, and potentially has an important effect on the results of broad‐scale studies on diversity gradients. Here we examine the effect of grain on patterns of species richness and turnover in lowland rainforests of western Amazonia (Peru and Colombia). We inventoried pteridophytes (ferns and lycophytes), melastomes (Melastomataceae) and palms (Arecaceae) in four line transects of 22–29 km length. Different grains were obtained by aggregating original 100‐m‐long sampling units into larger segments up to 19.2 km long. With any given grain and plant group, local species richness varied considerably both within and among transects, and a transect segment that was species‐rich with one grain could be relatively species‐poor with another. Which transect had the highest vs lowest mean species richness per sampling unit (α richness) differed among plant groups. It also varied to some degree with grain, as transects differed in how rapidly local species richness increased with increasing grain. Patterns of species turnover were more consistently correlated among plant groups than patterns of species richness were, and NMDS ordinations were rather similar with all grains and plant groups. Floristic heterogeneity within the Amazonian terra firme rainforest seems to contain a general compositional pattern that is sufficiently robust to be detectable with various sampling schemes, but patterns of species richness appear more case‐specific. Therefore, using one plant group as an indicator for patterns in other plant groups can be expected to work better for species turnover than for species richness.

Post-fire succession is an ideal case for studying effects of disturbance on community assembly, and the key is to disentangle the contributions of assembly processes to the variation of community composition, namely beta diversity, and the contingent scales. The central Yunnan Plateau of Southwest China is characterized by monsoon related seasonal drought, and frequent forest fires. We sampled five fire sites burned in different years and a middle aged forest, measured species composition dissimilarity and its species turnover and nestedness components, within each fire site and across all sites. Results indicated species turnover as the primary component of beta diversity within all communities. There was no trend of change with year-since-fire (YSF) in beta diversity among early post-fire communities, but beta diversity in the middle aged community was significantly higher. Species turnover patterns across fire sites revealed a weak dispersal limit effect, which was stronger at lower than upper slope position for woody plants, and reverse for herbs. At the site scale, the species dissimilarity and turnover both enlarged with increasing slope position difference, especially in the middle-aged community, but the species nestedness had no consistent trend among sites, except a decreasing trend in the middle-aged forest. (Partial) Mantel tests indicated habitat filtering [primarily indicating total nitrogen (TN) and slope position] played a much stronger role than dispersal limit and YSF (indicating competition intensity) for the post-fire forest assembly at the landscape scale, for both woody and herbaceous layers. However, at the site scale, Mantel tests indicated a diminishing effect of soil nutrient filtering with increasing YSF, while effects of topography and spatial distance in the middle aged community was stronger. This divergence suggests the primary assembly mechanism gradually shift away from the soil constraint. While the seasonal drought and the mountain topography dominate the environmental legacy, our results imply that fires may reinforce a priority effect in the forests assembly in this region, by creating a habitat filtering (e.g., moisture and nitrogen limitation) effect on species composition in post-fire communities.

Richness, diversity, and factors influencing occupancy of mammal communities across human-modified landscapes in Colombia

Summary 1. Biotic homogenization (BH), a dominant process shaping the response of natural communities to human disturbance, reflects both the expansion of exotic species at large scales and other mechanisms that often operate at smaller scales. 2. Here, we examined the relationship between BH in plant communities and spatio-temporal landscape disturbance (habitat fragmentation and surrounding habitat conversion) at a local scale (1 km²), using data from a standardized monitoring programme in France. We quantified BH using both a spatial partitioning of taxonomic diversity and the average habitat specialization of communities, which informs on functional BH. 3. We observed a positive relationship between local taxonomic diversity and landscape fragmentation or instability. This increase in local taxonomic diversity was, however, paralleled by a decrease in average community specialization in more fragmented landscapes and in more unstable landscapes around forest sites. The decrease in average community specialization suggests that landscape disturbance causes functional BH, but there was limited evidence for concurrent taxonomic BH. 4. Synthesis. Our results show that landscape disturbance is partly responsible for functional BH at small scales via the extirpation of specialist species, with possible consequences for ecosystem functioning. However, this change in community composition is not systematically associated with taxonomic BH. This has direct relevance in designing biodiversity indicators: metrics incorporating species sensitivity to disturbance (such as species specialization to habitat) appear much more reliable than taxonomic diversity for documenting the response of communities to disturbance.

We present the first community-level study of the associations of both roads and other human disturbances with the distribution of mammals in Gabon (central Africa). Our study site was in an oil concession within a littoral mosaic landscape. We conducted surveys along 199 line transects and installed camera traps on 99 of these transects to document mammal presence and abundance. We used generalized linear mixed-effect models to document associations between variables related to the ecosystem (land cover, topography, and hydrology), roads (coating, width of rights of way, condition, type of vehicle used on the road, traffic level, affiliation of users, and general type of road), and other human disturbances (urbanization, agriculture, hunting, logging, gathering, and industrial activities) and the abundance or presence of 17 species or groups of mammals including elephant (Loxodonta cyclotis), buffalo (Syncerus caffer), sitatunga (Tragelaphus spekei), red river hog (Potamochoerus porcus), smaller ungulates, gorilla (Gorilla gorilla), chimpanzee (Pan troglodytes), side-striped jackal (Canis adustus), carnivores, monkeys, and large rodents. Some types of roads and other human disturbances were negatively associated with the abundance or presence of elephants, buffalos, gorillas, sitatungas, some monkeys, and duikers. The pattern of associations of mammals with roads and other human disturbances was diverse and included positive associations with road presence (red river hog, some monkeys, and duikers), agriculture (sitatunga, small carnivores, and large rodents) and industrial activities (sitatunga, red river hog, red duikers, and side-striped jackal). Our results suggest that the community of mammals we studied was mostly affected by hunting, agriculture, and urbanization, which are facilitated by road presence. We recommend increased regulation of agriculture, hunting, and road building in the area.Distribución de una Comunidad de Mamíferos en Relación a Carreteras y Otras Perturbaciones Humanas en Gabón, Africa CentralResumenPresentamos el primer estudio a nivel de comunidad de la relación entre carreteras y otras perturbaciones humanas con la distribución de mamíferos en Gabón (África central). Nuestro sitio de estudio está dentro de una concesión petrolera en un paisaje litoral heterogéneo. Realizamos muestreos a lo largo de 199 transectos lineales e instalamos cámaras trampa en 99 de ellos para documentar la presencia y abundancia de mamíferos. Utilizamos modelos lineales generalizados con efectos mixtos para documentar las asociaciones entre variables relacionadas con el ecosistema (cobertura de suelo, topografía e hidrología), carreteras (tipo de revestimiento, ancho de derecho de vía, condición, tipo de vehículos que utilizan la carretera, nivel de tráfico, afiliación de los usuarios y el tipo general de carretera) y otras perturbaciones humanas (urbanización, agricultura, caza, tala, recolecta y actividades industriales) y la abundancia o presencia de 17 especies o grupos de mamíferos incluyendo elefantes (Loxodonta cyclotis), búfalo (Syncerus caffer), sitatunga (Tragelaphus spekei), cerdo rojo de río (Potomochoerus porcus), ungulados pequeños, gorila (Gorilla gorilla), chimpancé (Pan troglodytes), chacal con rayas a los lados (Canis adustus), carnívoros, monos y roedores de talla grande. Ciertos tipos de carreteras y otras perturbaciones humanas estuvieron asociadas negativamente con la abundancia o presencia de elefantes, búfalos, gorilas, sitatungas, algunos monos y antílopes. Los patrones de asociación de mamíferos con carreteras y otras perturbaciones humanas fueron diversos e incluyen asociaciones positivas con la presencia de carreteras (cerdo rojo de río, algunos monos y antílopes), agricultura (sitatunga, carnívoros pequeños y roedores de talla grande) y actividades industriales (sitatunga, cerdo rojo de río, antílope rojo y chacal con rayas a los lados). Nuestros resultados sugieren que la comunidad de mamíferos que estudiamos fue afectada principalmente por la caza, agricultura y urbanización, que son facilitadas por la presencia de carreteras. Recomendamos una mayor regulación de la agricultura, caza y construcción de carreteras en el área.

A variety of factors can affect the biodiversity of tropical mammal communities, but their relative importance and directionality remain uncertain. Previous global investigations of mammal functional diversity have relied on range maps instead of observational data to determine community composition. We test the effects of species pools, habitat heterogeneity, primary productivity and human disturbance on the functional diversity (dispersion and richness) of mammal communities using the largest standardized tropical forest camera trap monitoring system, the Tropical Ecology Assessment and Monitoring (TEAM) Network. We use occupancy values derived from the camera trap data to calculate occupancy-weighted functional diversity and use Bayesian generalized linear regression to determine the effects of multiple predictors. Mammal community functional dispersion increased with primary productivity, while functional richness decreased with human-induced local extinctions and was significantly lower in Madagascar than other tropical regions. The significant positive relationship between functional dispersion and productivity was evident only when functional dispersion was weighted by species' occupancies. Thus, observational data from standardized monitoring can reveal the drivers of mammal communities in ways that are not readily apparent from range map-based studies. The positive association between occupancy-weighted functional dispersion of tropical forest mammal communities and primary productivity suggests that unique functional traits may be more beneficial in more productive ecosystems and may allow species to persist at higher abundances.

Human activities generally increase trophic overlap in predator guilds through resource subsidies, whereas the effects on whether sympatric species overlap or separate their niches are context-dependent. Mesocarnivores (order Carnivora, Mammalia) are often adaptive and tolerant to human activities, allowing them to establish populations in human-modified landscapes. Here, we examined how trophic niche overlaps between the wide-ranging mesocarnivores, the red fox (Vulpes vulpes) and sympatric martens (genus Martes), are influenced by geo-environmental and anthropogenic factors, using a systematic literature review and meta-analysis at the Eurasian continental scale. We hypothesized that the extent of trophic overlap would increase in areas with greater human disturbance and less productive environments associated with resource availability. We included a total of 35 publications with 76 observations from continental Europe and Japan and then calculated the relative trophic overlap. Their trophic overlaps were relatively high because they shared common resources, such as small mammals, invertebrates, and fruits. Contrary to our predictions, multivariate statistical modeling demonstrated that trophic overlaps declined with increasing human disturbance and decreasing vegetative landscapes. Our findings indicate that human disturbances forced their resource use to separate, potentially due to resource depletion by land modifications and intense human activities, whereas vegetated habitats moderated direct and indirect competition. Based on these results, we conclude that patterns in trophic interactions largely depend on spatiotemporal resource availabilities. We suggest that maintaining regional resource abundance is crucial for successful sympatry in competing carnivores and for balancing stable intraguild interactions in human-modified landscapes.