Multi-species Occupancy Model Research Articles

Life on the edge: Considering ecotonal habitat for the conservation of alpine reptile metacommunities

Conservation planning focuses on core habitats, often overlooking ecotones, which can hold unrecognised potential for biodiversity conservation. This study focused on ecotonal habitat use in alpine reptile metacommunities, with emphasis on a grassland specialist, the critically endangered alpine she-oak skink, Cyclodomorphus praealtus. Survey transects in grasslands and woodlands in Kosciuszko National Park in the Australian Alps were used to investigate reptile occupancy and richness. Data was analysed using a multi-species occupancy model in relation to (1) distance from nearest grassland to assess grassland specialists' occupancy into woodland areas while accounting for imperfect detection, and (2) normalised difference vegetation index (NDVI) to assess the importance of high resource patches. Among the 11 reptile species detected, our hypothesis that grassland specialists would inhabit woodland ecotones was confirmed. The furthest occurrence of C. praealtus from the closest grassland was 41 m with a predicted occupancy of 0.06 (0.004 – 0.169 95 % Bayesian credible intervals) at 100 m. Contrary to conventional edge effect theories, our results revealed no increase in species richness nearer to the woodland ecotone from grasslands or with higher NDVI values. This study underscores the importance of including ecotonal buffers in ecological impact assessments and conservation plans for habitat specialists, that may still use ecotones of adjacent habitats. The findings emphasize the need for broader survey efforts beyond core habitats to capture the distribution of threatened species effectively. Incorporating ecotonal habitats into conservation strategies is crucial, particularly for specialist species whose dynamic use of ecotones may help safeguard them amidst predicted habitat transformation from anthropogenic influences and climate change.

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.

Ecologically informed priors improve Bayesian model estimates of species richness and occupancy for undetected species.

Detection error can bias observations of ecological processes, especially when some species are never detected during sampling. In many communities, the probable identity of these missing species is known from previous research and natural history collections, but this information is rarely incorporated into subsequent models. Here, I present prior aggregation as a method for including information from external sources in Bayesian hierarchical detection models. Prior aggregation combines information from multiple prior distributions, in this case, an ecologically informative, species-level prior, and an uninformative community-level prior. This approach incorporates external information into the model without sacrificing the advantages of modeling species in the context of the community. Using simulated data supplied to a multispecies occupancy model, I demonstrated that prior aggregation improves estimates of (1) metacommunity richness and (2) environmental covariates were associated with species-specific occupancy probabilities. When applied to a dataset of small mammals in Vermont, prior aggregation allowed the model to estimate occupancy correlates of the Eastern cottontail Sylvilagus floridanus, a species observed at several sites in the region but never captured. Prior aggregation can be used to improve the analysis of several important metrics in population and community ecology, including abundance, survivorship, and diversity.

Ungulate co-occurrence in a landscape of antagonisms

Protected areas largely now exist as coupled natural-human ecosystems where human activities are increasingly forcing wildlife to adjust behaviors. For many ungulate species that rely on protected areas for their persistence, they must balance these anthropogenic pressures amid natural regulators. Here, we investigated the pressures exerted from humans and livestock, apex predators, and within guild competitors on ungulate co-occurrence patterns in a fragile protected area complex in West Africa. Specifically, we used multi-species occupancy modeling to quantify co-occurrence among four ungulates (Tragelaphus scriptus, Redunca redunca, Kobus kob, Phacochoerus africanus) and applied structural equation models to discern the relative contributions of pressures on co-occurrence patterns. We observed a strong spatial gradient across with higher co-occurrence in the wetter western portion of our ~13,000 km2 study area. Co-occurrence patterns among ungulate dyads ranged from 0.15 to 0.49 with the smallest body sized pair showing highest levels of sympatry, warthog and reedbuck. We found that anthropogenic pressures, namely cattle had the greatest effect in reducing sympatry among wild ungulates more strongly than the presence of African lions that also exhibited negative effects. Humans, hyenas, and competitors showed positive effects on ungulate co-occurrence. In a region of the world ongoing rapid socio-ecological change with increasing threats from climate and environmental instability, protected areas in West Africa represent a major safeguard for wildlife and human livelihoods alike. Our findings highlight the need for effective interventions that focus on large carnivore conservation, habitat restoration, and containment of livestock grazing to promote the coexistence of biodiversity and socio-economic goals within the region.

Forest structure mediates occupancy and extinction of vertebrate prey species on the trailing edge of the boreal forest

Climate change is expected to shift the distributions of global biomes. High latitude biomes, such as the boreal forest, are among the most vulnerable and serve as a bellwether for the effects of climate change on other ecosystems. We examined patterns of occupancy, local extinction, and abundance in a guild of forest-associated vertebrate prey species on the southern margin of the boreal forest in Minnesota (USA). We used multi-season, multi-state, and multi-species occupancy modeling approaches to determine the effects of land cover, forest structural characteristics, and climatic variation on two boreal-associated species, spruce grouse (Canachites canadensis) and snowshoe hare (Lepus americanus), and a forest generalist, ruffed grouse (Bonasa umbellus). Occupancy, abundance, and extinction of spruce grouse was strongly associated with landscape-scale characteristics. In particular, deciduous forest cover may govern their southern range limit. Broadly, forest understory structure played a significant role in occupancy, extinction, and abundance patterns of all three species, with ruffed and spruce grouse generally associated with vegetation density in the lower and mid-canopy layer (5.00–15.00 m) and snowshoe hare associated with density in the shrub layer (1.37–5.00 m) in winter. Co-occurrence varied annually but was greatest in mixed forests during an uncharacteristically warm and snow-sparse year. Climatic variables (winter temperature and snowfall) were associated with extinction probabilities for all three species, but the effect was generally weaker than that of forest structure. Our results suggest that forest management practices that promote dense understory structure may help provide climate refugia for vertebrate prey species in boreal forest ecosystems.

From backyard to backcountry: changes in mammal communities across an urbanization gradient

Abstract Urbanization often results in biodiversity loss and homogenization, but this result is not universal and there is substantial variability in the spatiotemporal effects of urbanization on wildlife across cities and taxa. Areas with lower population and housing density are some of the fastest-growing regions in the western United States; thus, more research in these areas could offer additional insight into the effects of urbanization on wildlife and the potential importance of wild spaces in maintaining a diverse biotic community surrounding developed areas. To address this need, we conducted a study to identify the effects of urbanization (i.e. housing density) on mammals along a housing density gradient from wilderness to suburbia in Missoula, Montana. We deployed 178 motion-activated trail cameras at random sites within urban/suburban, exurban, rural, and wild regions from May to October 2019 to 2020. We identified all mammals >150 g, then evaluated how housing density influenced: (i) occupancy and (ii) species richness using multispecies occupancy models; (iii) relative abundance using Poisson models; and (iv) diel activity patterns using kernel density estimation and logistic regression. Urbanization was the strongest driver of mammal distribution, with a linear decline in mammal species richness as housing density increased. Urbanization also had strong effects on occupancy and detection rates, with larger-bodied mammals generally having stronger negative associations. Overall, mammal relative abundance was highest in suburban regions; however, this effect was largely driven by White-tailed Deer. Natural environmental factors explained most changes in mammal nocturnal activity; however, urbanization strongly affected nocturnality in some species, with Black Bear and White-tailed Deer becoming more nocturnal and Red Fox and Northern Raccoon becoming less nocturnal as housing density increased. While our study confirms that some mammals can live and thrive in developed areas, it emphasizes the importance of maintaining wild areas for those species that cannot.

Frequent prescribed burns reduce mammalian species richness and occurrence in longleaf pine sandhills

Prescribed fire is a critical forest management tool, the frequency and size of which can alter the composition of wildlife communities. In the longleaf pine ecosystem of the southeastern United States, frequent prescribed fire (1–3 year fire interval) is used to replicate natural processes that prevent woody encroachment and transition to alternate states. However, we have little understanding of how different scales and frequencies of fire influence medium and large mammals. To address this knowledge gap, we assessed the homogenizing influence of prescribed fire on mammal community composition at different fire frequencies and scales. We set 110 camera trap grids containing 990 individual camera points across conservation lands in north Florida and the Florida panhandle. We used a Bayesian multi-species occupancy modeling approach to assess the relationship between fire frequency and the occurrence of 11 mammal species across three spatial scales (0.2 ha, 12.57 ha, and 176.71 ha). Species richness was negatively associated with increased burn frequency at all scales and community occurrence was negatively associated with increased burn frequency at the two largest scales. Non-native nine-banded armadillos were negatively associated with increased burn frequency at all scales and non-native feral hogs were negatively associated with increased burn frequency at the two largest scales. Raccoons and opossums, both known nest predators, were negatively associated with increased burn frequency at the two largest scales. Our results indicate that prescribed fire applied at 1–3 year intervals could be used to reduce the occurrence of most non-native mammals and several prolific nest predators in longleaf pine sandhills, particularly at larger scales. However, these perceived benefits must be weighed against the concurrent loss of the ecosystem services and functions native generalist species provide.

Wildlife response to management regime and habitat loss in the Terai Arc Landscape of Nepal

The establishment of protected areas and buffer zones has been widely adopted in many countries to mitigate biodiversity loss. However, in contrast to the growing evidence about the beneficial impacts of protected areas, ecological outcomes of buffer zones have rarely been measured. Here, we use data from a large camera trap survey and multi-species occupancy modelling to assess the effectiveness of different management regimes (Bardia National Park, its buffer zone, and areas outside the buffer zone) at safeguarding wildlife in the Terai Arc Landscape of Nepal. Using areas outside the buffer zone as the counterfactual to compare occurrence probability of 25 mammal species >1 kg, we revealed a positive effect of the national park and the buffer zone on seven and six species, respectively. Three species had greater occurrence probability outside the buffer zone than in the national park, but no species had greater occurrence probability outside the buffer zone than inside the buffer zone. Analysis of species richness indicated that management regime differentially affects species groups. For non-threatened and herbivorous species, the buffer zone performed better than areas outside the buffer zone and similar to, or better than, the national park. However, for threatened species and large animalivores (carnivores and insectivores) the national park outperformed the other management regimes. Our results also suggest that the buffer zone partially mitigated the impacts of habitat loss outside the national park, indicating that management regime may play a role in modulating the effect of agriculture on wildlife in human-dominated landscapes in Nepal.

Evaluating temporal turnover in avian species richness in a Mediterranean semiarid region: Different responses to elevation and forest cover

AbstractAimWhen studying the effects of global change on biodiversity, it is far more common for the effects of climate change and land‐use changes to be assessed separately rather than jointly. However, the effects of land‐use changes in recent decades on species richness in areas affected by climate change have been less studied. We assess the temporal turnover in species richness of an avian community between a historical period and a modern one as a consequence of global change.LocationSemiarid Mediterranean ecosystem (southeastern Spain).MethodWe fitted a hierarchical multispecies occupancy model for each period (1991–1992, and 2012–2017), obtaining avian species‐specific estimates of occupancy probability in relation to environmental covariates (elevation and forest cover). We analyse the relationships between changes in the bird community and environmental variables, analysing the temporal turnover of the species richness and the richness‐based species‐exchange ratio.ResultsThe estimated species richness accounting for detectability was higher than observed species richness, and decreased in the more recent period. Following our hypotheses, we observed a dual pattern of species richness increase associated with different elevations, showing different species turnover rates due to the joint effects of climate change and land‐use change. There is a trend towards greater species richness with higher elevations that is associated with climate change, where the species turnover rate is low. Also, species richness increased towards lower elevations, but with a high turnover rate. The latter can be due to species expansions throughout new habitat configurations in bordering forest systems associated with anthropic land‐use changes.ConclusionsOur study is of great interest to understand the temporal turnover of avian species richness associated with areas experiencing both climate and land‐use change.

Spatial and temporal niche overlap of aardwolves and aardvarks in Serengeti National Park, Tanzania.

Species interactions can influence species distributions, but mechanisms mitigating competition or facilitating positive interactions between ecologically similar species are often poorly understood. Aardwolves (Proteles cristata) and aardvarks (Orycteropus afer) are nocturnal, insectivorous mammals that co-occur in eastern and southern Africa, and knowledge of these species is largely limited to their nutritional biology. We used aardwolf and aardvark detections from 105 remote cameras during 2016-2018 to assess their spatial and temporal niche overlap in the grasslands of Serengeti National Park, Tanzania. Using a multispecies occupancy model, we identified a positive interaction between occupancy probabilities for aardwolves and aardvarks. Slope, proportion of grassland and termite mound density did not affect the occupancy probabilities of either species. The probability of aardwolf, but not aardvark, occupancy increased with distance to permanent water sources, which may relate to predation risk avoidance. Diel activity overlap between aardwolves and aardvarks was high during wet and dry seasons, with both species being largely nocturnal. Aardwolves and aardvarks have an important ecological role as termite consumers, and aardvarks are suggested to be ecosystem engineers. Our results contribute to a better understanding of the spatial and temporal niche of insectivores like aardwolves and aardvarks, suggesting high spatial and temporal niche overlap in which commensalism occurs, whereby aardwolves benefit from aardvark presence through increased food accessibility.

Estimating relative species abundance using fossil data identified to different taxonomic levels

Site‐occupancy modelling is widely used in ecology for understanding species distribution, habitat‐use and community changes but its application is still limited in paleoecology, where incomplete detection is also routine. Here, we make extensive expansions to an earlier multispecies occupancy model used to estimate the dynamics of relative species abundance in fossil communities. These expansions include incorporating counts of individuals at sites, explicitly allowing for the inclusion of specimens assignable to genus – but not species‐level, a situation common in paleontology, and modelling regional presence/absence. We provide simulations to check the performance of this new model, as well as simulations to quantify the benefits of using individual count data versus subsample occupancy data, and model estimates versus face‐value (raw) estimates, respectively. We also provide an empirical case study using occupancy data from a community of marine benthic colonial animals preserved in the Pleistocene of New Zealand. We find that the new model performs well, especially when it comes to recovering relative abundance dynamics and that it is well worth the effort to both collect individual count data and to include individuals unidentified to species‐level in the site‐occupancy modelling framework. This extended model can be widely applied in paleoecological settings and is necessary when both the average and uncertainty values of relative abundance dynamics need to be robustly estimated.

Tropical forest mammal occupancy and functional diversity increase with microhabitat surface area.

Many animal-environment interactions are mediated by the physical forms of the environment, especially in tropical forests, where habitats are structurally complex and highly diverse. Higher structural complexity, measured as habitat surface area, may provide increased resource availability for animals, leading to higher animal diversity. Greater habitat surface area supports increased animal diversity in other systems, such as coral reefs and forest canopies, but it is uncertain how this relationship translates to communities of highly mobile, terrestrial mammal species inhabiting forest floors. We tested the relative importance of forest floor habitat structure, encompassing vegetation and topographic structure, in determining species occupancy and functional diversity of medium to large mammals using data from a tropical forest in the Udzungwa Mountains of Tanzania. We related species occupancies and diversity obtained from a multispecies occupancy model with ground-level habitat structure measurements obtained from a novel head-mounted active remote sensing device, the Microsoft HoloLens. We found that habitat surface area was a significant predictor of mean species occupancy and had a significant positive relationship with functional dispersion. The positive relationships indicate that surface area of tropical forest floors may play an important role in promoting mammal occupancy and functional diversity at the microhabitat scale. In particular, habitat surface area had higher mean effects on occupancy for carnivorous and social species. These results support a habitat surface area-diversity relationship on tropical forest floors for mammals.

Integrating existing data to assess the risk of an expanding land use change on mammals

ContextLand-use change, including agricultural expansion, is one of the major drivers of biodiversity loss globally. Given the rapid pace of land-use change, data-driven, strategic, and dynamic conservation planning is imperative.ObjectivesWe present an exemplar application of using existing data to inform conservation planning. Specifically, we developed a systematic approach for identifying areas of conservation concern due to cannabis cultivation in California, USA.MethodsWe used three existing datasets: (1) camera trap data from ten projects (n = 1186); (2) the locations of cannabis cultivation sites eradicated by law enforcement (n = 834); and (3) the locations of cultivation licenses (n = 4366). We analyzed this data using multi-species occupancy models to estimate the occupancy and richness of 30 species, and maximum entropy models to estimate the risk of unlicensed and trespass cultivation. We then identified areas of overlap and determined the percent of suitable habitat potentially impacted by cannabis cultivation.ResultsCannabis cultivation was estimated to overlap 39–74% of suitable habitat for special status species. Private land cultivation tended to have a larger influence on generalist species whereas trespass cultivation had the largest potential influence on fisher (Pekania pennanti), a special status species.ConclusionsOur results can be used to prioritize eradication, restoration, and remediation activities; to target mitigation efforts; and to guide the placement of new, licensed cultivation. Our approach demonstrates the utility of aggregating existing biological and socioeconomic data to inform conservation planning and is broadly applicable to other data sources and ecological stressors.

Occupancy of Bombus affinis (Hymenoptera: Apidae) in Minnesota is highest in developed areas when standardized surveys are employed.

Mounting evidence of bumble bee declines and the listing of the rusty patched bumble bee (Bombus affinis Cresson) as federally endangered in the United States in 2017 and Canada in 2012 has stimulated an interest in monitoring and conservation. Understanding the influence of land use on occupancy patterns of imperiled species is crucial to successful recovery planning. Using detection data from community surveys, we assessed land use associations for 7 bumble bee species in Minnesota, USA, including B. affinis. We used multispecies occupancy models to assess the effect of 3 major land use types (developed, agricultural, and natural) within 0.5 and 1.5 km on occupancy of 7 Bombus (Hymenoptera: Apidae) species, while accounting for detection uncertainty. We found that B. affinis occupancy and detection were highest in developed landscapes and lowest in agricultural landscapes, representing an inverse relationship with the relative landcover ratios of these landscapes in Minnesota. Occupancy of 2 bumble bee species had strong positive associations with natural landscapes within 1.5 km and 2 species had strong negative associations with agricultural landscapes within 1.5 km. Our results suggest that best practices for imperiled Bombus monitoring and recovery planning depends upon the surrounding major land use patterns. We provide recommendations for urban planning to support B. affinis based on conservation success in the metropolitan areas of Minneapolis-St. Paul. We also encourage substantial survey effort be employed in agricultural and natural regions of the state historically occupied by B. affinis to determine the current occupancy state.

Urbanization, climate and species traits shape mammal communities from local to continental scales.

Human-driven environmental changes shape ecological communities from local to global scales. Within cities, landscape-scale patterns and processes and species characteristics generally drive local-scale wildlife diversity. However, cities differ in their structure, species pools, geographies and histories, calling into question the extent to which these drivers of wildlife diversity are predictive at continental scales. In partnership with the Urban Wildlife Information Network, we used occurrence data from 725 sites located across 20 North American cities and a multi-city, multi-species occupancy modelling approach to evaluate the effects of ecoregional characteristics and mammal species traits on the urbanization-diversity relationship. Among 37 native terrestrial mammal species, regional environmental characteristics and species traits influenced within-city effects of urbanization on species occupancy and community composition. Species occupancy and diversity were most negatively related to urbanization in the warmer, less vegetated cities. Additionally, larger-bodied species were most negatively impacted by urbanization across North America. Our results suggest that shifting climate conditions could worsen the effects of urbanization on native wildlife communities, such that conservation strategies should seek to mitigate the combined effects of a warming and urbanizing world.

Scenario planning and multispecies occupancy models reveal positive avian responses to restoration of afforested woodlands

Scenario planning is a powerful approach for assessing restoration outcomes under alternative futures. However, developing plausible scenarios remains daunting in complex systems like ecological communities. Here, we used Bayesian multispecies occupancy modeling to develop scenarios to assess woodland restoration outcomes in afforested communities in seven wildlife management areas in Arkansas, U.S.A. Our objectives were (1) to define plausible woodland restoration and afforestation scenarios by quantifying historic ranges of variation in mean tree cover and tree cover heterogeneity from 1986 to 2021 and (2) to predict changes in bird species richness and occupancy patterns for six species of greatest conservation need under two future scenarios: complete afforestation (100% tree cover) and woodland restoration (based on remotely sensed historic tree cover). Using 35 years of remotely sensed tree cover data and 6 years of bird monitoring data, we developed multispecies occupancy models to predict future bird species richness and occupancy under the complete afforestation and woodland restoration scenarios. Between 1986 and 2021, tree cover increased in all study areas—with one increasing 70%. Under the woodland restoration scenario, avian species richness increased up to 20%, and four of six species of greatest conservation need exhibited gains in occupancy probability. The complete afforestation scenario had negligible effects on richness and occupancy. Overall, we found decreasing tree cover to historic levels prior to widespread afforestation would provide community‐level benefits and would do little harm even to forest‐dependent species of conservation concern. Applying multispecies occupancy modeling within a scenario planning framework allows for comparing multiscale trade‐offs between plausible futures.

Using integrated multispecies occupancy models to map co‐occurrence between bottlenose dolphins and fisheries in the Gulf of Lion, French Mediterranean Sea

In the Mediterranean Sea, interactions between marine species and human activities are prevalent. The coastal distribution of bottlenose dolphins Tursiops truncatus and the predation pressure they put on fishing stocks lead to regular interactions with fisheries. Multispecies occupancy models are a relevant framework to estimate co‐occurrence between two (or more) species while accounting for false negatives and potential interspecific dependance although requiring substantial quantity of data to fit. Here, we extended multispecies occupancy model to integrate multiple datasets to map spatial co‐occurrence between trawlers and bottlenose dolphins in the Gulf of Lion, French Mediterranean Sea combining data from aerial surveys and boat surveys at a large spatial scale. The integrated multispecies occupancy model produced more precise estimate than single‐dataset multispecies occupancy models. Our results support that both integrated and multispecies frameworks are relevant to map distribution and understand species interactions in our case study. Besides, our application of multispecies occupancy models to bottlenose dolphins and fishing trawlers enabled to map co‐occurrence probability, which open promising avenues in the understanding of interactions between human activities and marine mammals that occur at large spatial scales.

Dietary and habitat specialization, eye size, clutch size, and aerial lifestyle predict avian fragmentation sensitivity in an Andean biodiversity hotpot

The fragmentation of tropical forests remains a major driver of avian biodiversity loss, particularly for insectivores, yet the mechanisms underlying area sensitivity remain poorly understood. Studies in lowland systems suggest that loss of food resources, changes to light microenvironments, increased nest predation, and dispersal limitation are possible mechanisms, but these are untested for montane tropical bird communities. In this study, we related avian functional traits to area sensitivity (quantified using beta estimates from a multi-species occupancy model) to test the above four hypotheses for a cloud forest bird community (both resident species and just resident insectivores) in the Colombian Western Andes. We found that species with more specialized diets and those that use the canopy and subcanopy (loss of food hypothesis), larger relative eye sizes (light microhabitat hypothesis), and larger clutch sizes (nest predation hypothesis) were significantly more area sensitive. By contrast, there was no support for the dispersal limitation hypothesis; instead, we found that insectivores with more pointed wing shapes, and more aerial lifestyles, were significantly more fragmentation sensitive. These results suggest that reduced vegetation structure, loss of late-successional plant species, and loss of epiphytic plants may reduce food availability in fragments. Similarly, the ability to tolerate higher light intensity near fragment edges, or when traversing matrix habitat, may be important for persistence in fragments and suggests that habitat configuration may be of special importance in fragmented Andean landscapes. Overall, a lack of information on foraging, movement, and breeding ecology complicates avian conservation in the Andes.

Joint species distribution models with imperfect detection for high-dimensional spatial data.

Determining the spatial distributions of species and communities is a key task in ecology and conservation efforts. Joint species distribution models are a fundamental tool in community ecology that use multi-species detection-nondetection data to estimate species distributions and biodiversity metrics. The analysis of such data is complicated by residual correlations between species, imperfect detection, and spatial autocorrelation. While many methods exist to accommodate each of these complexities, there are few examples in the literature that address and explore all three complexities simultaneously. Here we developed a spatial factor multi-species occupancy model to explicitly account for species correlations, imperfect detection, and spatial autocorrelation. The proposed model uses a spatial factor dimension reduction approach and Nearest Neighbor Gaussian Processes to ensure computational efficiency for data sets with both a large number of species (e.g., >100) and spatial locations (e.g., 100,000). We compared the proposed model performance to five alternative models, each addressing a subset of the three complexities. We implemented the proposed and alternative models in the spOccupancy software, designed to facilitate application via an accessible, well documented, and open-source R package. Using simulations, we found that ignoring the three complexities when present leads to inferior model predictive performance, and the impacts of failing to account for one or more complexities will depend on the objectives of a given study. Using a case study on 98 bird species across the continental US, the spatial factor multi-species occupancy model had the highest predictive performance among the alternative models. Our proposed framework, together with its implementation in spOccupancy, serves as a user-friendly tool to understand spatial variation in species distributions and biodiversity while addressing common complexities in multi-species detection-nondetection data.

Mammalian resistance to megafire in western U.S. woodland savannas

AbstractIncreasingly frequent megafires are dramatically altering landscapes and critical habitats around the world. Across the western United States, megafires have become an almost annual occurrence, but the implication of these fires for the conservation of native wildlife remains relatively unknown. Woodland savannas are among the world's most biodiverse ecosystems and provide important food and structural resources to a variety of wildlife, but they are threatened by megafires. Despite this, the great majority of fire impact studies have only been conducted in coniferous forests. Understanding the resistance and resilience of wildlife assemblages following these extreme perturbations can help inform future management interventions that limit biodiversity loss due to megafire. We assessed the resistance of a woodland savanna mammal community to the short‐term impacts of megafire using camera trap data collected before, during, and after the fire. Specifically, we utilized a 5‐year camera trap data set (2016–2020) from the Hopland Research and Extension Center to examine the impacts of the 2018 Mendocino Complex Fire, California's largest recorded wildfire at the time, on the distributions of eight observed mammal species. We used a multispecies occupancy model to quantify the effects of megafire on species' space use, to assess the impact on species size and diet groups, and to create robust estimates of fire's impacts on species diversity across space and time. Megafire had a negative effect on the detection of certain mammal species, but overall, most species showed high resistance to the disturbance and returned to detection and site use levels comparable to unburned sites by the end of the study period. Following megafire, species richness was higher in burned areas that retained higher canopy cover relative to unburned and burned sites with low canopy cover. Fire management that prevents large‐scale canopy loss is critical to providing refugia for vulnerable species immediately following fire in oak woodlands, and likely other mixed‐forest landscapes.