Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

Limited spatiotemporal niche partitioning among mesocarnivores in Gorongosa National Park, Mozambique

Competition drives community composition and structure in many ecosystems. Spatial and temporal niche partitioning, in which competing species divide the environment in space or time, are mechanisms that may allow for coexistence among ecologically similar species. Such division of resources may be especially important for carnivores in African savannas, which support diverse carnivore assemblages. We used camera traps to explore patterns of spatial and temporal niche partitioning among four mesocarnivore species in Mozambique's Gorongosa National Park: large-spotted genet (Genetta maculata), African civet (Civettictis civetta), honey badger (Mellivora capensis) and marsh mongoose (Atilax paludinosus). We applied a multispecies occupancy model to evaluate spatial partitioning among mesocarnivores and to quantify the environmental factors that affect species-specific habitat use, including relative lion (Panthera leo) activity. We also analyzed the temporal activity overlap of the four focal species. We identified species-specific habitat covariates that influenced detection probabilities but found no evidence of spatial or temporal partitioning among mesocarnivores in the study system. Indeed, we found some evidence for spatial co-occurrence between two of our focal species: African civet and marsh mongoose. There may be limited competition among mesocarnivores in this system, perhaps due to niche and diet differentiation among these species and an abundance of resources. While we found limited evidence that lion activity impacts mesocarnivores, ongoing monitoring of intraguild interactions is vital as apex predator populations recover in the system. This study adds to a growing understanding of African mesocarnivore ecology and highlights the importance of understanding these dynamics for effective multispecies conservation and restoration.

An environmental habitat gradient and within-habitat segregation enable co-existence of ecologically similar bird species

Niche theory predicts that ecologically similar species can coexist through multidimensional niche partitioning. However, owing to the challenges of accounting for both abiotic and biotic processes in ecological niche modelling, the underlying mechanisms that facilitate coexistence of competing species are poorly understood. In this study, we evaluated potential mechanisms underlying the coexistence of ecologically similar bird species in a biodiversity-rich transboundary montane forest in east-central Africa by computing niche overlap indices along an environmental elevation gradient, diet, forest strata, activity patterns and within-habitat segregation across horizontal space. We found strong support for abiotic environmental habitat niche partitioning, with 55% of species pairs having separate elevation niches. For the remaining species pairs that exhibited similar elevation niches, we found that within-habitat segregation across horizontal space and to a lesser extent vertical forest strata provided the most likely mechanisms of species coexistence. Coexistence of ecologically similar species within a highly diverse montane forest was determined primarily by abiotic factors (e.g. environmental elevation gradient) that characterize the Grinnellian niche and secondarily by biotic factors (e.g. vertical and horizontal segregation within habitats) that describe the Eltonian niche. Thus, partitioning across multiple levels of spatial organization is a key mechanism of coexistence in diverse communities.

Disentangling Exploitative and Interference Competition on Forest Dwelling Salamanders

Exploitative competition and interference competition differ in the way access to resources is modulated by a competitor. Exploitative competition implies resource depletion and usually produces spatial segregation, while interference competition is independent from resource availability and can result in temporal niche partitioning. Our aim is to infer the presence of spatial or temporal niche partitioning on a two-species system of terrestrial salamanders in Northern Italy: Speleomantes strinatii and Salamandrina perspicillata. We conducted 3 repeated surveys on 26 plots in spring 2018, on a sampling site where both species are present. We modelled count data with N-mixture models accounting for directional interactions on both abundance and detection process. In this way we were able to disentangle the effect of competitive interaction on the spatial scale, i.e., local abundance, and from the temporal scale, i.e., surface activity. We found strong evidence supporting the presence of temporal niche partitioning, consistent with interference competition. At the same time, no evidence of spatial segregation has been observed.

Sunda Clouded Leopard Neofelis diardi (Cuvier, 1823) (Mammalia: Carnivora: Felidae) occupancy in Borneo: results of a pilot vehicle spotlight transect survey

The Sunda Clouded Leopard Neofelis diardi on Borneo is threatened principally by deforestation for oil palm plantations and the indiscriminate use of illegal trapping. Sunda Clouded Leopard populations are decreasing across their range, and the species has been categorised as Vulnerable on the IUCN Red List. Despite the persistence of threats and numerous surveys in recent years, information on its ecology is still limited. Most studies to date have relied on the use of camera traps as their primary sampling tool, as it is challenging otherwise to gather data on Sunda Clouded Leopards. This study aimed to test the feasibility of estimating the Sunda Clouded Leopard occupancy using a different approach. We conducted vehicle spotlight transect surveys in a mixed-use forest reserve and logging concession in Sabah. We drove a cumulative total of 8,433 km of transects at night and documented the occurrence of Sunda Clouded Leopards in eight out of 31 predetermined long-distance transects, yielding a relatively low naïve occupancy rate (nO = 0.26). When accounting for imperfect detection (ρ = 0.15), null occupancy of Sunda Clouded Leopards appeared much higher (ᴪ = 0.55), though our parameter estimates lacked relative precision. Despite this, our results suggest there may be potential to further refine and adapt a basic, cost-effective monitoring approach in a local mixed-use reserve with the help of concession managers and additional improvements to study design. We caution, however, that not all study sites may be suited for this type of approach and strongly advise the development of pilot studies to evaluate their overall feasibility.

Pathways to global-change effects on biodiversity: new opportunities for dynamically forecasting demography and species interactions

In structured populations, persistence under environmental change may be particularly threatened when abiotic factors simultaneously negatively affect survival and reproduction of several life cycle stages, as opposed to a single stage. Such effects can then be exacerbated when species interactions generate reciprocal feedbacks between the demographic rates of the different species. Despite the importance of such demographic feedbacks, forecasts that account for them are limited as individual-based data on interacting species are perceived to be essential for such mechanistic forecasting-but are rarely available. Here, we first review the current shortcomings in assessing demographic feedbacks in population and community dynamics. We then present an overview of advances in statistical tools that provide an opportunity to leverage population-level data on abundances of multiple species to infer stage-specific demography. Lastly, we showcase a state-of-the-art Bayesian method to infer and project stage-specific survival and reproduction for several interacting species in a Mediterranean shrub community. This case study shows that climate change threatens populations most strongly by changing the interaction effects of conspecific and heterospecific neighbours on both juvenile and adult survival. Thus, the repurposing of multi-species abundance data for mechanistic forecasting can substantially improve our understanding of emerging threats on biodiversity.

Inferring predator-prey interactions from camera traps: A Bayesian co-abundance modeling approach

Predator-prey dynamics are a fundamental part of ecology, but directly studying interactions has proven difficult. The proliferation of camera trapping has enabled the collection of large datasets on wildlife, but researchers face hurdles inferring interactions from observational data. Recent advances in hierarchical co-abundance models infer species interactions while accounting for two species' detection probabilities, shared responses to environmental covariates, and propagate uncertainty throughout the entire modeling process. However, current approaches remain unsuitable for interacting species whose natural densities differ by an order of magnitude and have contrasting detection probabilities, such as predator-prey interactions, which introduce zero inflation and overdispersion in count histories. Here, we developed a Bayesian hierarchical N-mixture co-abundance model that is suitable for inferring predator-prey interactions. We accounted for excessive zeros in count histories using an informed zero-inflated Poisson distribution in the abundance formula and accounted for overdispersion in count histories by including a random effect per sampling unit and sampling occasion in the detection probability formula. We demonstrate that models with these modifications outperform alternative approaches, improve model goodness-of-fit, and overcome parameter convergence failures. We highlight its utility using 20 camera trapping datasets from 10 tropical forest landscapes in Southeast Asia and estimate four predator-prey relationships between tigers, clouded leopards, and muntjac and sambar deer. Tigers had a negative effect on muntjac abundance, providing support for top-down regulation, while clouded leopards had a positive effect on muntjac and sambar deer, likely driven by shared responses to unmodelled covariates like hunting. This Bayesian co-abundance modeling approach to quantify predator-prey relationships is widely applicable across species, ecosystems, and sampling approaches and may be useful in forecasting cascading impacts following widespread predator declines. Taken together, this approach facilitates a nuanced and mechanistic understanding of food-web ecology.

Tropical forest dung beetle-mammal dung interaction networks remain similar across an environmental disturbance gradient

Conservation outcomes could be greatly enhanced if strategies addressing anthropogenic land-use change considered the impacts of these changes on entire communities as well as on individual species. Examining how species interactions change across gradients of habitat disturbance allows us to predict the cascading consequences of species extinctions and the response of ecological networks to environmental change. We conducted the first detailed study of changes in a commensalist network of mammals and dung beetles across an environmental disturbance gradient, from primary tropical forest to plantations, which varied in above-ground carbon density (ACD) and mammal communities. Mammal diversity changed only slightly across the gradient, remaining high even in oil palm plantations and fragmented forest. Dung beetle species richness, however, declined in response to lower ACD and was particularly low in plantations and the most disturbed forest sites. Three of the five network metrics (nestedness, network specialization, and functionality) were significantly affected by changes in dung beetle species richness and ACD, but mammal diversity was not an important predictor of network structure. Overall, the interaction networks remained structurally and functionally similar across the gradient, only becoming simplified (i.e., with fewer dung beetle species and fewer interactions) in the most disturbed sites. We suggest that the high diversity of mammals, even in disturbed forests, combined with the generalist feeding patterns of dung beetles, confer resilience to the commensalist dung beetle-mammal networks. This study highlights the importance of protecting logged and fragmented forests to maintain interaction networks and potentially prevent extinction cascades in human-modified systems.

Intraguild dynamics of understudied carnivores in a human-altered landscape

Mesocarnivores constitute a diverse and often abundant group of species, which are increasingly occupying hweigher trophic levels within multi-use landscapes. Yet, we know relatively little about their interactions with each other, especially in human-altered areas. Using camera trap data collected in a forestry concession in the Greater Gorongosa ecosystem of central Mozambique, we examined the spatiotemporal relationships and potential for intraguild competition among three understudied African carnivores: African civets (Civettictis civetta), bushy-tailed mongooses (Bdeogale crassicauda), and large-spotted genets (Genetta maculata). After accounting for habitat preferences and tolerance to anthropogenic factors, we found that African civets and bushy-tailed mongooses avoid each other spatially and temporally. Additionally, civets and mongooses were also both more likely to use sites farther away from human settlements, possibly decreasing the total available habitat for each species if competition is driving this spatial partitioning. In contrast, we did not find evidence for spatial or temporal partitioning between large-spotted genets and African civets, but bushy-tailed mongooses altered their activity patterns where they co-occurred with genets. Our study contributes to scant ecological knowledge of these mesocarnivores and adds to our understanding of community dynamics in human-altered ecosystems.

Effects of law enforcement and community outreach on mammal diversity in a biodiversity hotspot

Management activities such as law enforcement and community outreach are thought to affect conservation outcomes in protected areas, but their importance relative to intrinsic environmental characteristics of the parks and extrinsic human pressures surrounding the parks have not been explored. Furthermore, it is not clear which is more related to conservation outcomes-the management itself or local people's perceptions of the management. We measured objective (reports by park staff) and subjective (reports by local people) levels of community outreach and law enforcement based on responses to 374 questionnaires. We estimated mammal abundance and diversity of 6 protected areas based on data from 115 camera traps in Xishuangbanna, southwest China, a biodiversity hotspot with high hunting and land-conversion pressures. We then examined correlations among them and found that local people's perception of law enforcement was positively related to the local abundance of 2 large, hunted species, wild boar (Sus scrofa) (β = 15.22) and muntjac (Muntiacus vaginalis) (β = 14.82), but not related to the abundance of smaller mammals or to objective levels of enforcement. The subjective frequency of outreach by park staff to local communities (β = 3.42) and park size (β = 3.28) were significantly and positively related to mammal species richness, whereas elevation, human population density, and subjective frequency of law enforcement were not. We could not conclude that community outreach and law enforcement were directly causing increased mammal abundance and diversity. Nevertheless, the patterns we detected are some of the first empirical evidence consistent with the idea that biodiversity in protected areas may be more positively and strongly related to local perceptions of the intensity of park management than to either intrinsic (e.g., elevation, park size) or extrinsic (e.g., human population density) environmental factors.

Diversity and size-structured persistence of tropical carnivores in a small, isolated protected area

Protected areas are critical to biodiversity conservation. Yet many protected areas around the world are very small, and population persistence can be compromised in small habitat patches, particularly for large species. But we do not know how small is too small for long-term population viability, or the degree to which habitat area effects vary with mammal body size, for most tropical species. Here, diversity and species occurrence were assessed in a small national park that has long been isolated from other forest patches. The two largest Bornean carnivores, the Sunda clouded leopard (Neofelis diardi) and sun bear (Helarctos malayanus), may be locally extinct, but 12 smaller carnivores appear to be persisting. The banded civet (Hemigalus derbyanus), the Malay civet (Viverra tangalunga) and the leopard cat (Prionailurus bengalensis) had relatively high occurrence rates and were found in all habitat types, though were more common in hill (banded civet) or lowland (common palm civet) forest (LF). Occurrence probabilities for all of these species and the common palm civet (Paradoxurus hermaphroditus) were lower in areas more accessible to humans. Detection rates and estimated diversity suggest that this park has a small carnivore assemblage equivalent to those of much larger areas. These are the first results demonstrating size-specific vulnerability to area effects in Southeast Asian carnivores.