Multi-species Occupancy Model Research Articles

Landscape drivers of mammal habitat use and richness in a protected area and its surrounding agricultural lands

Protected areas (PAs) are key to conserving biodiversity and ecosystem services globally, but their effectiveness increasingly depends on the ability of the surrounding agricultural areas to support biodiversity and secure connectivity at the landscape level. This requires monitoring the broader multi-use landscapes in which PAs exist and identifying the landscape characteristics that support rich, functional wildlife communities. Here, we investigated the species richness and habitat use patterns of a mammal community in relation to different landscape variables and land use and land cover (LULC) types in a PA and its surrounding agricultural lands in the Cerrado. We first used a hierarchical multi-species occupancy model with input camera trap data and eight landscape variables (vegetation productivity, phenology, and heterogeneity, distance to water, roads and settlements, and the PA, slope, and elevation) to estimate the species richness and habitat use of 29 mammal species across the landscape. We then analyzed the relationships between the species richness and habitat use and the landscape variables at the site level, as well as the distribution of species at the landscape level in relation to the different natural and agricultural LULC types. We found that most species are present in the native forest areas across the landscape and that many species are also present in the croplands surrounding the PA. The results also showed that species’ habitat use was especially determined by the productivity and heterogeneity of the vegetation cover, with a particularly strong positive relation in grasslands and pastures. These results suggest that the private properties surrounding the PA might be playing an essential role in supporting biodiversity in this region and provide insights on management practices that could largely contribute to maintaining or promoting a multifunctional landscape, such as maintaining the remaining forests or increasing the productivity and the heterogeneity (e.g., by increasing tree cover) in pastures.

Simulated treatment effects on bird communities inform landscape-scale dry conifer forest management.

Human land use and climate change have increased forest density and wildfire risk in dry conifer forests of western North America, threatening various ecosystem services, including habitat for wildlife. Government policy supports active management to restore historical structure and ecological function. Information on potential contributions of restoration to wildlife habitat can allow assessment of tradeoffs with other ecological benefits when prioritizing treatments. We predicted avian responses to simulated treatments representing alternative scenarios to inform landscape‐scale forest management planning along the Colorado Front Range. We used data from the Integrated Monitoring in Bird Conservation Regions program to inform a hierarchical multispecies occupancy model relating species occupancy and richness with canopy cover at two spatial scales. We then simulated changes in canopy cover (remotely sensed in 2018) under three alternative scenarios, (1) a “fuels reduction” scenario representing landscape‐wide 30% reduction in canopy cover, (2) a “restoration” scenario representing more nuanced, spatially variable treatments targeting historical conditions, and (3) a reference, no‐change scenario. Model predictions showed areas of potential gains and losses for species richness, richness of ponderosa pine forest habitat specialists, and the ratio of specialists to generalists at two (1 km2 and 250 m2) spatial scales. Under both fuels reduction and restoration scenarios, we projected greater gains than losses for species richness. Surprisingly, despite restoration more explicitly targeting ecologically relevant historical conditions, fuels reduction benefited bird species richness over a greater spatial extent than restoration, particularly in the lower montane life zone. These benefits reflected generally positive species associations with moderate canopy cover promoted more consistently under the fuels reduction scenario. In practice, contemporary forest management is likely to lie somewhere between the fuels reduction and restoration scenarios represented here. Therefore, our results inform where and how active forest management can best support avian diversity. Although our study raises questions regarding the value of including landscape‐scale heterogeneity as a management objective, we do not question the value of targeting finer scale heterogeneity (i.e., stand and treatment level). Rather, our results combined with those from previous work clarify the scale at which targeting structural heterogeneity and historical reference conditions can promote particular ecosystem services.

Short-term benefits of prescribed fire to bird communities of dry forests

BackgroundLow-severity prescribed fire is an important tool to manage fire-maintained forests across North America. In dry conifer forests of the western USA, prescribed fire is often used to reduce fuel loads in forests characterized historically by mixed- and low-severity fire regimes. Understanding the ecological effects of prescribed fire treatments is important for predicting the impacts of these management actions on wildlife communities. Few studies, however, have estimated small landbird responses to forest treatments at spatial scales relevant to their ecology or have examined potential differences in treatment effects applied within historically mixed- vs. low-severity fire regimes. Therefore, we evaluated prescribed fire treatment effects and relationships with burn severity for avian communities in dry conifer forests dominated by ponderosa pine (Pinus ponderosa) located on seven national forests in the interior western USA. We surveyed birds for 1–4 years and 1–3 years before and after prescribed fire treatments at mixed- and low-severity fire regime locations, respectively, following a before-after, control-impact study design — 8 paired control-treatment units in mixed-severity locations (16 total study units with 320 survey points) and 4 paired control-treatment units in low-severity locations (10 total study units with 278 survey points). Using a Bayesian hierarchical multi-species occupancy model, we investigated responses to prescribed fire treatments by a community of 95 bird species.ResultsWe found statistically supported treatment effects and/or burn severity relationships for 33 species primarily in mixed-severity locations. The data supported positive treatment effects at mixed-severity locations for 9 species (American robin [Turdus migratorius], western bluebird [Sialia mexicana], hairy woodpecker [Dryobates villosus], black-backed woodpecker [Picoides arcticus], American three-toed woodpecker [Picoides dorsalis], house wren [Troglodytes aedon], dusky flycatcher [Empidonax oberholseri], western wood-pewee [Contopus sordidulus], gray flycatcher [Empidonax wrightii]), whose occupancy was more likely after treatment at the most severely burned units, and a negative effect for one species (ruby-crowned kinglet [Corthylio calendula]), whose occupancy was less likely after treatment at the most severely burned units. At low-severity locations, only two species exhibited treatment effects, both negative (red-faced warbler [Cardellina rubrifrons] and lark sparrow [Chondestes grammacus]). We also found supported occupancy relationships with burn severity post-treatment (i.e., regardless of species distribution before treatment) for 29 species, most of which were consistent with their life histories (e.g., patterns of positive relationships for cavity-nesting, bark insectivores and negative relationships for open-nesting, foliage insectivores). Stronger responses to prescribed fire treatments at mixed-severity locations were unexpected because prescribed fire applications were more similar to historical wildfires characteristic of low-severity fire regimes.ConclusionsBird populations in historically low-severity locations may be relatively unresponsive to prescribed fire because fire there is typically more frequent and regular. By comparison, fire events in forests characterized by a mixed-severity regime are less common, potentially eliciting more responses to an infrequent opportunity, even by species that are strongly associated with recently burned forests by wildfire. Our results suggest that fire management activities intended to reduce fuels and lower the risk of high-severity wildfire can also be effective in creating habitat for some fire specialists at least in the short term.

Measuring protected-area effectiveness using vertebrate distributions from leech iDNA

Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas.

Carnivores in color: pelt color patterns among carnivores in Idaho

Abstract Pelt color serves many functions from signaling to crypsis to thermoregulation and its purpose has been a lively source of debate in biology for over a century. Determining the effects of both habitat and human influences on pelt color patterns can be difficult. We made novel use of a multispecies occupancy model by defining “pelt color” as “species.” We then used this model to test predictions and estimate pelt color patterns concurrently for three carnivore species in Idaho, United States. We predicted pelt patterns of all three carnivores would be affected by environmental variables as well as human disturbance. Areas of Idaho where baiting was allowed and preferential harvest possible did not explain pelt patterns in black bears and neither did forest cover. Road density was positively associated with detection probability but negatively associated with occupancy of both black and brown pelt bears, however. Gray pelt wolves were found more often in areas with higher road densities than black wolves. As predicted, black, but not gray, wolves were positively associated with forest cover. Both red and black pelt foxes were positively associated with increasing elevation and road density. Black pelt foxes were negatively associated with forest cover, mirroring the habitat use described for native black pelt foxes. We demonstrate how using noninvasively collected data and extending multispecies occupancy models can allow biologists to study the distribution of different pelt colors in wild populations.

The effect of urbanization on spatiotemporal interactions between gray foxes and coyotes

AbstractInteractions between species can influence their distribution and fitness, with potential cascading ecosystem effects. Human disturbance can affect these competitive dynamics but is difficult to measure due to potential simultaneous spatial and temporal responses. We used camera traps with a multispecies occupancy model incorporating a continuous‐time detection process to evaluate spatial and temporal interactions between two competing carnivore species, coyote (Canis latrans) and gray fox (Urocyon cinereoargenteus), along an urbanization gradient. Coyotes were less likely to occupy high housing density sites than gray foxes, but the two species were more likely to co‐occur in suburban forest fragments. Gray foxes were less likely to occupy low housing density sites in the presence of coyotes, shifted their activity patterns to be more nocturnal when coyotes were present and avoided sites recently used by coyotes. These effects were most pronounced where forest cover was low, suggesting these shifts are not necessary where forest cover is high, perhaps due to the gray fox's ability to climb trees. Gray foxes did not spatially or temporally avoid coyotes moving through the suburban matrix nor did precipitation mediate temporal avoidance in suburban habitats (i.e., by washing away scent), possibly because coyotes are less likely to establish territories at high housing densities, and thus less likely to scent mark. As reports of gray fox declines in portions of North America mount and coyotes are implicated, our results suggest that preserving tree cover could be important for gray fox persistence. At least 50% of forest cover in a 1 km radius resulted in lower coyote occupancy with gray fox occupancy rising to ≥0.1, suggesting a good benchmark for management.

Habitat use by the island lemurs of Nosy Be, Madagascar.

Madagascar's lemurs are threatened by forest loss, fragmentation, and degradation. Many species use flexible behaviors to survive in degraded habitat, but their ability to persist in very small areas may be limited. Insular lemurs, like those found on Nosy Be, an island off the northwestern coast of Madagascar, are at heightened risk of sudden population declines and extirpation. Nosy Be is home to two Critically Endangered species-the endemic Nosy Be sportive lemur (Lepilemur tymerlachsoni) and Claire's mouse lemur (Microcebus mamiratra)-as well as the Endangered black lemur (Eulemur macaco). Most of the remaining forest on Nosy Be is protected by the 862-ha Lokobe National Park. To document how Nosy Be lemurs use their restricted habitat, we conducted vegetation and reconnaissance surveys on 53 transects in and around Lokobe. We collected data on tree size, canopy cover, understory visibility, and elevation for 248 lemur sightings. We used a spatially explicit, multi-species occupancy model to investigate which forest-structure variables are important to lemurs. Our results represent some of the first data on habitat use by insular lemurs. Black lemurs preferred significantly larger trees and areas with less dense understory. They also occurred significantly less outside of Lokobe National Park, even when accounting for sampling effort and geography. The distributions of the sportive and mouse lemurs were not related to the forest structure variables we documented, but they did negatively predict each other-perhaps because their habitat requirements differ. These results also underscore the importance of the national park to protecting the black lemur population on Nosy Be and raise questions about what factors do influence the distribution of Nosy Be's smaller lemurs. Close monitoring is needed to prevent these populations and the ecosystem services they provide from disappearing, as have other island lemurs.

Trade-off between deep learning for species identification and inference about predator-prey co-occurrence: Reproducible R workflow integrating models in computer vision and ecological statistics

Deep learning is used in computer vision problems with important applications in several scientific fields. In ecology for example, there is a growing interest in deep learning for automatizing repetitive analyses on large amounts of images, such as animal species identification. However, there are challenging issues toward the wide adoption of deep learning by the community of ecologists. First, there is a programming barrier as most algorithms are written in Python while most ecologists are versed in R. Second, recent applications of deep learning in ecology have focused on computational aspects and simple tasks without addressing the underlying ecological questions or carrying out the statistical data analysis to answer these questions. Here, we showcase a reproducible R workflow integrating both deep learning and statistical models using predator-prey relationships as a case study. We illustrate deep learning for the identification of animal species on images collected with camera traps, and quantify spatial co-occurrence using multispecies occupancy models. Despite average model classification performances, ecological inference was similar whether we analysed the ground truth dataset or the classified dataset. This result calls for further work on the trade-offs between time and resources allocated to train models with deep learning and our ability to properly address key ecological questions with biodiversity monitoring. We hope that our reproducible workflow will be useful to ecologists and applied statisticians. All material (source of the Rmarkdown notebook and auxiliary files) is available from this https URL.

Turnover-driven loss of forest-dependent species changes avian species richness, functional diversity, and community composition in Andean forest fragments

Andean forests, a hotspot of biodiversity, have suffered extensive fragmentation, yet we have little understanding of how this process has affected biodiversity. We surveyed bird communities across a gradient of fragment sizes (10–170 ha) and a continuous forest reference site in the Colombian Western Andes. Using a multi-species occupancy model to combine survey data from audio-visual transect surveys, mist netting, and playbacks for owls, we estimated alpha and beta taxonomic and functional diversity. We asked whether (1) habitat amount (patch size), edge effects, or selective logging affect bird occupancy and drive changes to diversity, (2) functional and taxonomic diversity respond similarly to fragmentation, and (3) compositional changes result from species turnover or nested species loss. Species richness declined with decreasing habitat amount, increasing edge density, and increasing disturbance through selective logging. These effects were driven by the loss of forest-dependent species, which were also area sensitive: 30 such species were absent from fragments, even the largest ones (>150 ha). Area-sensitive species were also edge sensitive and increased in occupancy in unlogged forest. We further found high beta diversity (0.78) driven by species turnover (85% of dissimilarity) along the gradient. Despite extensive turnover to non-forest species within functional groups, functional trait richness and dispersion significantly declined with habitat amount. Small fragments may mimic the structure and composition of early-successional Andean forests, driving spatial turnover patterns favoring disturbance-adapted species at the expense of primary-forest specialists. Large forest reserves are therefore required to conserve forest-dependent Andean birds.

Using interview surveys and multispecies occupancy models to inform vertebrate conservation.

Species distribution data are an essential biodiversity variable requiring robust monitoring to inform wildlife conservation. Yet, such data remain inherently sparse because of the logistical challenges of monitoring biodiversity across broad geographic extents. Surveys of people knowledgeable about the occurrence of wildlife provide an opportunity to evaluate species distributions and the ecology of wildlife communities across large spatial scales. We analyzed detection histories of 30 vertebrate species across the Western Ghats biodiversity hotspot in India, obtained from a large-scale interview survey of 2318 people who live and work in the forests of this region. We developed a multispecies occupancy model that simultaneously corrected for false-negative (non-detection) and false-positive (misidentification) errors that interview surveys can be prone to. Using this model, we integrated data across species in composite analyses of the responses of functional species groups (based on disturbance tolerance, diet, and body mass traits) to spatial variation in environmental variables, protection, and anthropogenic pressures. We observed a positive association between forest cover and the occurrence of species with low tolerance of human disturbance. Protected areas were associated with higher occurrence for species across different functional groups compared with unprotected lands. We also observed the occurrence of species with low disturbance tolerance, herbivores, and large-bodied species was negatively associated with developmental pressures, such as human settlements, energy production and mining, and demographic pressures, such as biological resource extraction. For the conservation of threatened vertebrates, our work underscores the importance of maintaining forest cover and reducing deforestation within and outside protected areas, respectively. In addition, mitigating a suite of pervasive human pressures is also crucial for wildlife conservation in one of the world's most densely populated biodiversity hotspots.

Perceived risk structures the space use of competing carnivores

Abstract Competition structures ecological communities. In carnivorans, competitive interactions are disproportionately costly to subordinate carnivores who must account for the risk of interspecific killing when foraging. Accordingly, missed opportunity costs for meso-carnivores imposed by risk can benefit the smallest-bodied competitors. However, the extent to which the risk perpetuates into spatial partitioning in hierarchically structured communities remains unknown. To determine how risk-avoidance behaviors shape the space-use of carnivore communities, we studied a simple community of carnivores in northern Patagonia, Argentina: pumas (Puma concolor; an apex carnivore), culpeo foxes (Lycalopex culpaeus; a meso-carnivore), and chilla foxes (Lycalopex griseus; a small carnivore). We used multi-species occupancy models to quantify the space use within the carnivore community and giving-up densities to understand the behaviors that structure space use. Notably, we applied an analytical framework that tests whether the actual or perceived risk of predation most strongly influences the space use of subordinate carnivores although accounting for their foraging and vigilance behaviors. We found that there was a dominance hierarchy from the apex carnivore through the meso-carnivore to the subordinate small carnivore, which was reflected in space. Although both meso- and small carnivores exhibited similar predator avoidance behavioral responses to apex carnivores, the habitat associations of apex carnivores only altered meso-carnivore space use. The biases in risk management we observed for meso-carnivores likely translates into stable co-existence of this community of competing carnivores. We believe our analytical framework can be extended to other communities to quantify the spatial-behavioral tradeoffs of risk.

A penalized likelihood for multispecies occupancy models improves predictions of species interactions.

Multispecies occupancy models estimate dependence among multiple species of interest from patterns of co-occurrence, but problems associated with separation and boundary estimates can lead to unreasonably large estimates of parameters and associated standard errors when species are rarely observed at the same site or when data are sparse. In this paper, we overcome these issues by implementing a penalized likelihood, which introduces a small bias in parameter estimates in exchange for a potentially large reduction in variance. We compare parameter estimates obtained from both penalized and unpenalized multispecies occupancy models fit to simulated data that exhibit various degrees of separation and to a real-word data set of bird surveys with little apparent overlap between potentially interacting species. Our simulation results demonstrate that penalized multispecies occupancy models did not exhibit boundary estimates and produced lower bias, lower mean squared error, and improved inference relative to unpenalized models. When applied to real-world data, our penalized multispecies occupancy model constrained boundary estimates and allowed for meaningful inference related to the interactions of two species of conservation concern. To facilitate the use of our penalized multispecies occupancy model, the techniques demonstrated in this paper have been integrated into the unmarked package in R programing language.

Landscape Structure and Seasonality: Effects on Wildlife Species Richness and Occupancy in a Fragmented Dry Forest in Coastal Ecuador

Despite high fragmentation and deforestation, little is known about wildlife species richness and occurrence probabilities in tropical dry forest (TDF) landscapes. To fill this gap in knowledge, we used a Sentinel-2-derived land-cover map, Normalized Difference Vegetation Index (NDVI) data and a multi-species occupancy model to correct for detectability to assess the effect of landscape characteristics on medium and large mammal occurrence and richness in three TDF areas that differ in disturbance and seasonality in Ecuador. We recorded 15 species of medium and large mammals, distributed in 12 families; 1 species is critically Endangered, and 2 are Near-Threatened. The results indicate that species occupancy is related to low forest cover and high vegetation seasonality (i.e., high difference in NDVI between the wet and dry seasons). We believe that the apparent negative effect of forest cover is an indicator of species tolerance for disturbance. The three sampling areas varied from 98% to 40% forest cover, yet species richness and occupancy were not significantly different among them. Vegetation seasonality indicates that more seasonal forests (i.e., those where most tree species lose their leaves during the dry season) tend to have higher mammal species occupancy compared to less seasonal, semi-deciduous forests. Overall, occupancy did not vary between the dry and wet seasons, but species-specific data indicate that some species exhibit higher occupancy during the wet season. This research offers a good understanding of mammal species’ responses to habitat disturbance and fragmentation in TDFs and provides insights to promote their conservation.

Bird occupancy in intensively managed agroecosystems under large-scale organic and conventional farming in Argentina: A multi-species approach

Several studies in European and North American agroecosystems conclude that organic farming benefits birds compared to conventional farming. Nevertheless, there are some biases toward these geographic regions and farm size. Argentinian agroecosystems are particularly homogeneous with large arable fields and sparse uncultivated field margins (i.e. large-scale homogenous cropping systems). In Argentina only 0.55% of the total farmland is under organic farming. Thus, our aims were to assess differences in bird occupancy between organic versus conventional farming regimes, and whether bird occupancy varied in relation to annual crop proportion in both farming regimes in central Argentina agroecosystems. We surveyed 156 points in farms under conventional and 154 in organic farming regimes during two bird-breeding seasons. We used multi-species occupancy models with a Bayesian approach to estimate bird occupancy. We observed that the type of farming regime (organic in relation to conventional) had a weak effect on avian occupancy, varying by species and groups. Probability of occupancy was higher for a few insectivorous and omnivorous species but lower for carnivores in organic farms in relation to conventional ones. The proportion of annual crops was positively correlated with occupancy of an insectivore aerial forager, some insectivore foliage gleaners, a granivore, and some omnivorous species in organic farms, but not conventional farms. This work contributes to reducing geographic and small-scale heterogeneous cropping system biases in the avian agroecological literature. Our results, together with future studies needed to assess landscape configuration and composition, and resource availability for birds in each farming regime, will allow the evaluation of organic farming as a tool for the conservation of bird species in large-scale homogeneous cropping systems in temperate regions.

Determining Community-level Carnivore Response to Landscape Factors in Bukit Barisan Selatan National Park, Sumatra, Indonesia.

Researchers are challenged to understand the distribution of biodiversity on the landscape or determine if community-level assemblages respond to landscape variability. Canonical ordinations and multispecies occupancy modeling are often utilized and differ in their analytical scale and technique. Community-level data for carnivores (n=18) from camera trapping data (n=60) were tested for their collective response to covariates (distance to villages, roads, plantations, streams, and also topographic variables for elevation and slope) in Bukit Barsan Selatan National Park. Redundancy analysis (RDA) results confirmed that the carnivore community responded to the anthropogenic covariates, with carnivore detections being higher in areas at a high distance from roads and plantations medium distance villages. Then, multispecies occupancy models (MSOM), a comparatively finer temporal scale analysis that incorporated imperfect detections, were compared to RDA. We fit four models (full, anthropogenic, natural, and null) that were mainly inconclusive. In some MSOM models, the carnivore community did respond to environmental covariates, although the coefficients did not show a consistent response between seasons or years. These results indicate that RDA was able to detect broad-scale covariate effects that were not able to be modeled by MSOM and that these scaling and imperfect detection issues should be considered when attempting to understand landscape community diversity.

Amphibian population responses to mitigation: Relative importance of wetland age and design

Wetland creation is a common practice to mitigate for the loss of natural wetlands. However, there is still uncertainty about how effectively created wetlands replace habitat provided by natural wetlands. This uncertainty is due in part because post-construction monitoring of biological communities, and vertebrates especially, is rare and typically short-term (<5 years). We estimated occupancy of 4 amphibian species in 8 created mitigation wetlands, 7 impacted wetlands, and 7 reference wetlands in the Greater Yellowstone Ecosystem in Wyoming, USA. Mitigation wetlands were created to replace wetland habitat that was lost during road construction and ranged in age from 1 to 10 years when sampled. Impacted wetlands were natural wetlands partially filled by road construction and were adjacent to a highway. We sampled for amphibian larvae during 6 summers from 2013 to 2020 and used multi-species occupancy models that estimated detection and occupancy of each of 4 amphibian species to determine how amphibian responses changed over time, especially in mitigation wetlands. Occupancy did not differ between impacted and reference wetlands for any of the 4 amphibian species. Western Toads (Anaxyrus boreas) were most common (although briefly) in created wetlands, and occupancy of Columbia Spotted Frogs (Rana luteiventris), Western Tiger Salamanders (Ambystoma mavortium), and Boreal Chorus Frogs (Pseudacris maculata) was lower in created wetlands than in impacted or reference wetlands. Individual wetland area was positively associated with occupancy for all 4 species and wetland vegetation cover was positively associated with Boreal Chorus Frog and Columbia Spotted Frog occupancy; these results emphasize the importance of design characteristics when planning mitigation wetlands. The link between wetland age and occupancy was complex and included threshold and quadratic relationships for three of the four species, but only Boreal Chorus Frog occupancy was still increasing slowly at the end of our study. Our results indicate created wetlands did not attain the suitability of impacted and natural wetlands for local amphibians, even several years after construction. The complex relationships between wetland age and species-specific occupancy illustrate the importance of long-term monitoring in describing population responses to the construction of wetlands as mitigation for wetland loss.

Marginal support for a trophic cascade among sympatric canids in peripheral wolf range.

Trophic cascades reportedly structure ecological communities through indirect species interactions. Though the predator-herbivore-autotroph relationship has received much attention, mechanistic evidence supporting intraguild trophic cascades is rare. We established 348 remote camera sites (1 August-5 September 2019) across seven study areas of varying wolf (Canis lupus) density including one study area where wolves were absent in northern Michigan, USA. Using multi-species occupancy modeling at species-relevant spatial scales, we evaluated the hypothesis that increased wolf occurrence suppresses coyote (C. latrans) occurrence with corresponding increased red fox (Vulpes vulpes) occurrence mediated by land cover edge density, human presence, and temporal partitioning. Remote cameras recorded >600,000 images and included 6,370, 10,137, and 4,876 detections of wolves, coyotes, and foxes, respectively. Fox occupancy probability was more than three times as high (0.29) at camera sites where wolves were present, relative to sites wolves were absent (0.09). Pairwise species interactions supported expected size-based dominance patterns among canids and insignificant effects were directionally consistent with reported reduced strength of top-down effects in peripheral wolf range. Increased edge density also increased co-occurrence of coyote and wolves, likely a function of increased prey availability and refugia for coyotes. Though foxes occurred in spatial proximity to wolves, competition was limited by greater temporal partitioning than observed between coyotes and foxes that were spatially segregated. Collectively, our results provide marginal support for the reported trophic cascade among wolves, coyotes, and foxes wherein top-down effects may be reduced near the edge of current wolf distributions. As predators continue to recolonize portions of their historic range, knowledge of the effects on intraguild predators has implications for species management and predicting prey population responses.

Intermediate fire severity diversity promotes richness of forest carnivores in California

AbstractAimFire can strongly influence ecosystem function, and human activities are disrupting fire activity at the global scale. Ecological theory and a growing body of literature suggest that a mixed severity fire regime promotes biodiversity in western North America. Some researchers advocate the use of pyrodiversity (i.e. heterogeneity in aspects of the fire regime such as time since fire or severity) as a conservation index to be maximized. Others caution against this approach arguing that the index oversimplifies fire–biodiversity interactions across trophic, spatial and temporal scales. We evaluated the effects of several landscape‐scale pyrodiversity indices, and their severity and time‐since‐fire components, on species richness of forest carnivores.LocationNorthern California, United States.MethodsWe gathered data on fire history and mammal occurrence from camera trap surveys at 1,451 sites across Northern California public and private forestlands during 2009–2018. We used these data to model the effects of fire severity diversity, and its components (i.e. low, moderate and high severity wildfires), on carnivore richness at short (10 years) and longer (25 years) timeframes. We repeated the modelling using a measure of time‐since‐fire diversity and its components (&lt;10 years, 10–20 years, 20–30 years, 30–40 years, 40–100 years). We used Bayesian multispecies occupancy modelling to correct for imperfect measurement of species richness.ResultsWe found that carnivore richness was highest at locations with intermediate fire severity diversity (0.46, 90%CI: 0.40–0.52) calculated using Simpson's Measure of Evenness (range: 0–1) for the 10‐year timeframe, and the results were almost identical yet less precise for the longer timeframe. When we separated fire severity diversity into its components, we found that carnivore richness was highest at locations where 17% (90%CI: 4–20) of the landscape had experienced low severity burns over the past decade. In contrast, we found no association between time‐since‐fire diversity and carnivore richness, however, an intermediate amount of one of the components (e.g., the total amount of fire in the past 10 years) was positively associated with carnivore richness. Our results are consistent with a mixed severity fire regime wherein there is a greater extent of low severity than high severity fire.Main conclusionsOverall our results suggest that carnivores would benefit from landscapes managed for greater, but not maximal, fire severity diversity. Our results also suggest that prescribed, low severity burns may provide ecological services to wildlife not otherwise provided by silviculture in a managed forest landscape.

Living in the concrete jungle: carnivore spatial ecology in urban parks.

People and wildlife are living in an increasingly urban world, replete with unprecedented human densities, sprawling built environments, and altered landscapes. Such anthropogenic pressures can affect multiple processes within an ecological community, from spatial patterns to interspecific interactions. We tested two competing hypotheses, human shields vs. human competitors, to characterize how humans affect the carnivore community using multispecies occupancy models. From 2017 to 2020, we conducted the first camera survey of city parks in Detroit, Michigan, and collected spatial occurrence data of the local native carnivore community. Our 12,106–trap night survey captured detection data for coyotes (Canis latrans), red foxes (Vulpes vulpes), raccoons (Procyon lotor), and striped skunks (Mephitis mephitis). Overall occupancy varied across species (Ψcoyote = 0.40, Ψraccoon = 0.54, Ψred fox = 0.19, Ψstriped skunk = 0.09). Contrary to expectations, humans did not significantly affect individual occupancy for these urban carnivores. However, co‐occurrence between coyote and skunk increased with human activity. The observed positive spatial association between an apex and subordinate pair supports the human shield hypothesis. Our findings demonstrate how urban carnivores can exploit spatial refugia and coexist with humans in the cityscape.

Multi‐Species Occupancy Modeling Provides Novel Insights into Amphibian Metacommunity Structure and Wetland Restoration

A fundamental goal of community ecology is to understand species-habitat relationships and how they shape metacommunity structure. Recent advances in occupancy modeling enable habitat relationships to be assessed for both common and rare species within metacommunities using multi-species occupancy models (MSOM). These models account for imperfect species detection and offer considerable advantages over other analytical tools commonly used for community analyses under the elements of metacommunity structure (EMS) framework. Here, we demonstrate that MSOM can be used to infer habitat relationships and test metacommunity theory, using amphibians. Repeated frog surveys were undertaken at 55 wetland sites in southeastern Australia. We detected 11 frog species from three families (Limnodynastidae, Myobatrachidae, and Pelodryadidae). The rarest species was detected at only one site whereas the most common species was detected at 42 sites (naive occupancy rate 0.02-0.76). Two models were assessed representing two competing hypotheses; the best-supported model included the covariates distance to the nearest site (connectivity), wetland area, presence of the non-native eastern mosquitofish (Gambusia holbrooki), proportion cover of emergent vegetation, an interaction term between Gambusia and emergent vegetation cover, and the proportion canopy cover over a site. Hydroperiod played no detectable role in metacommunity structure. We found species-habitat relationships that fit with current metacommunity theory: occupancy increased with wetland area and connectivity. There was a strong negative relationship between occupancy and the presence of predatory Gambusia, and a positive interaction between Gambusia and emergent vegetation. The presence of canopy cover strongly increased occupancy for several tree frog species, highlighting the importance of terrestrial habitat for amphibian community structure. We demonstrated how responses by amphibians to environmental covariates at the species level can be linked to occupancy patterns at the metacommunity scale. Our results have clear management implications: wetland restoration projects for amphibians and likely other taxa should maximize wetland area and connectivity, establish partial canopy cover, and eradicate Gambusia or provide aquatic vegetation to mitigate the impact of this non-native fish. We strongly advocate the use of MSOM to elucidate the habitat drivers behind animal occupancy patterns and to derive unbiased occupancy estimates for monitoring programs.