Two-species occupancy models: a new parameterization applied to co-occurrence of secretive rails

Red foxes avoid apex predation without increasing fear

Apex predators structure ecosystems by hunting mesopredators and herbivores. These trophic cascades are driven not only by the number of animals they kill, but also by how prey alter their behaviors to reduce risk. The different levels of risk navigated by prey has been likened to a “landscape of fear.” In Australia, dingoes are known to suppress red fox populations, driving a trophic cascade. However, most of what we know of this relationship comes from circumstances where predators are persecuted, which can affect their social and trophic interactions. Utilizing camera traps, we monitored fox behavior when accessing key resource points used by territorial dingoes, in a region where both predators are protected. We predicted that foxes would avoid and be more cautious in areas of high dingo activity. Indeed, foxes avoided directly encountering dingoes. However, contrary to our expectations, foxes were not more cautious or vigilant where dingo activity was high. In fact, fox activity and scent-marking rates increased where dingo scent-marking was concentrated. Further, foxes were increasingly confident with increasing levels of conspecific activity. Our results suggest that responses to the threat of predation are more complex than fear alone. In socially stable conditions, it is possible that prey may develop knowledge of their predators, facilitating avoidance, and reducing fear.

The status and ecology of the sand cat in the Uruq Bani Ma’arid Protected Area, Empty Quarter of Saudi Arabia

The sand cat is one of the world’s least studied small cats. Our camera-trap survey, one of the largest undertaken in a desert system, generated over 1500 images of the species across 100 camera-traps distributed systematically over the 2400 km2 core area of the Uruq Bani Ma’arid Protected Area of the Empty Quarter, Saudi Arabia. The study revealed a much more significant and widespread sand cat population in the ecosystem than previously understood. Sand cats were detected across one-third of the core area in all major habitats, comprising escarpment plateau, sand dunes and interdunal gravel valleys. The species showed a marginal preference for the interior parallel dune system with interspersed gravel valleys where they also preferred sand dunes over the gravel valley in the hot season. There was no evidence of strong spatial interactions with other predators. The ecosystem’s larger predators (Arabian red fox and honey badger, and all records of wild and feral cats) were primarily associated with the escarpment plateau. The smaller Rueppell’s fox was the only other carnivore more consistently present in the main dune system. Sand cats were strictly nocturnal and 14% more active in the hot season than the cool season.

Exotic Prey Facilitate Coexistence between Pumas and Culpeo Foxes in the Andes of Central Chile

Coexistence between species with similar ecological niches implies species must segregate along one or more niche axes to survive. Space, time, and trophic resources are regarded as the principal axes upon which species segregate. We examined segregation along these niche axes to determine mechanisms underlying coexistence between the two main predators, puma (Puma concolor) and culpeo foxes (Lycalopex culpaeus) in the Andes of Central Chile. We used occupancy modeling to examine space use and overlap, Kernel Density Estimation to determine temporal activity patterns and overlap, and analysis of prey remains in feces to assess diet breadth and similarity. We found high spatial overlap and positive associations between detection of the carnivores lending little support for spatial segregation. Similarly, we found high nocturnal, temporal overlap between pumas and foxes that matched peaks in activity of prey. In contrast, we found relatively low dietary overlap indicating niche segregation likely occurs along the dietary axis. The Puma diet was dominated by introduced, exotic hares and foxes appeared to shift away from hares to rabbits, small mammals, and seeds. Given that lagomorphs are the main dietary resource for pumas in particular, management decisions regarding the control or eradication of such exotic species could negatively affected puma survival.

Spatiotemporal co-occurrence and overlap of two sympatric mongoose species in an urban environment

Small carnivores are becoming increasingly common in urban areas. What has received less attention is whether and how resource partitioning among sympatric species in urban areas facilitates their coexistence. We examined the spatial, temporal and combined spatiotemporal occurrence and overlap of co-existing yellow mongoose Cynictis penicillata and slender mongoose Galerella sanguinea in an urban estate in South Africa. The reserve comprised two parts, an Eco-Estate where human residential and natural areas are interspersed and wildlife has greater contact with people, and a Nature Estate, where contact is reduced by palisade fencing between people and natural areas. Using photographic data from camera traps collected over 11 consecutive months, we found a moderate level of spatial overlap between the mongoose species. Differences between the species occurred at a finer habitat scale: yellow mongooses were more common in open habitats located near human residents whereas the slender mongooses were more common in covered areas further away from human residents. The detection probability of the yellow mongoose, however, was greater than that of the slender mongoose, and the occupancy probability of the slender mongoose was reduced in the presence of the yellow mongoose. Although both species demonstrated bimodal diurnal peaks in activity, they varied in their active periods, with temporal overlap being greater during colder than warmer months. No complete spatiotemporal overlap (occurrence in the same place at the same time/within a 10-min period) occurred. This may have been as a result of the difference in detection and occupancy probabilities of the two species. Resource availability (food), however, appears to influence the different habitat selection, space use, and activity patterns of yellow and slender mongoose in the study area. Therefore, we conclude that partitioning along the spatial and somewhat on the temporal dimensions aids in the coexistence of these mongoose species in an urban environment.

Ecological traits and the spatial structure of competitive coexistence among carnivores

Competition is a widespread interaction among carnivores, ultimately manifested through one or more dimensions of the species' ecological niche. One of the most explicit manifestations of competitive interactions regards spatial displacement. Its interpretation under a theoretical context provides an important tool to deepen our understanding of biological systems and communities, but also for wildlife management and conservation. We used Bayesian multispecies occupancy models on camera-trapping data from multiple sites in Southwestern Europe (SWE) to investigate competitive interactions within a carnivore guild, and to evaluate how species' ecological traits are shaping coexistence patterns. Seventeen out of 26 pairwise interactions departed from a hypothesis of independent occurrence, with spatial association being twice as frequent as avoidance. Association behaviors were only detected among mesocarnivores, while avoidance mainly involved mesocarnivores avoiding the apex predator (n = 4) and mesocarnivore-only interactions (n = 2). Body mass ratios, defined as the dominant over the subordinate species body mass, revealed an important negative effect ( β ^ = - 0.38 ; C I 95 = - 0.81 t o - 0.06 ) on co-occurrence probability, and support that spatially explicit competitive interactions are mostly expressed by larger species able to dominate over smaller ones, with a threshold in body mass ratios of ~4, above which local-scale intraguild coexistence is unlikely. We found a weak relationship between pairwise trophic niche overlap and the probability of coexistence ( β ^ = - 0.19 ; C I 95 = - 0.58 t o 0.21 ), suggesting that competition for feeding resources may not be a key driver of competition, at least at the scale of our analysis. Despite local-scale avoidance, regional-scale coexistence appears to be maintained by the spatial structuring of the competitive environment. We provide evidence that SWE ecosystems consist of spatially structured competitive environments, and propose that coexistence among near-sized species is likely achieved through the interplay of "facultative" and "behavioral" character displacements. Factors influencing carnivore coexistence likely include context-dependent density and trait-mediated effects, which should be carefully considered for a sound understanding of the mechanisms regulating these communities.

Co-occurrence of bobcats, coyotes, and ocelots in Texas

Interspecific competition among carnivores has been linked to differences in behavior, morphology, and resource use. Insights into these interactions can enhance understanding of local ecological processes that can have impacts on the recovery of endangered species, such as the ocelot (Leopardus pardalis). Ocelots, bobcats (Lynx rufus), and coyotes (Canis latrans) share a small geographic range overlap from South Texas to south-central Mexico but relationships among the three are poorly understood. From May 2011 to March 2018, we conducted a camera trap study to examine co-occurrence patterns among ocelots, bobcats, and coyotes on the East Foundation's El Sauz Ranch in South Texas. We used a novel multiseason extension to multispecies occupancy models with ≥2 interacting species to conduct an exploratory analysis to examine interspecific interactions and examine the potential effects of patch-level and landscape-level metrics relative to the occurrence of these carnivores. We found strong evidence of seasonal mutual coexistence among all three species and observed a species-specific seasonal trend in detection. Seasonal coexistence patterns were also explained by increasing distance from a high-speed roadway. However, these results have important ecological implications for planning ocelot recovery in the rangelands of South Texas. This study suggests a coexistence among ocelots, bobcats, and coyotes under the environmental conditions on the El Sauz Ranch. Further research would provide a better understanding of the ecological mechanisms that facilitate coexistence within this community. As road networks in the region expand over the next few decades, large private working ranches will be needed to provide important habitat for ocelots and other carnivore species.

Dominance hierarchy on palm resource partitioning among Neotropical frugivorous mammals

In tropical forests, the diets of many frugivorous mammals overlap, yet how hyper-diverse assemblages of consumers exploit resources and coexist remains poorly understood. We evaluated competitive interactions among three species of terrestrial frugivorous mammals, the ungulate Tayassu pecari (white-lipped peccary), its close relative Pecari tajacu (collared peccary), and a large rodent (Dasyprocta azarae, agouti), in their exploitation strategies of palm resources of different quality. We conducted the study in a large isolated fragment at the tropical Atlantic Forest of Brazil, where these mammal species show high spatial and temporal overlap. We evaluated if body mass and foraging group size define a hierarchy in exploitation of preferentially richer palm resources. We used camera traps and two-species occupancy models to examine patterns of co-occurrence and variable interaction strength between these consumers and three species of palms. Our analyses supported the hypothesis of partial resource overlap but no competition among frugivores, and a body mass dominance hierarchical exploitation of resources. The larger frugivore (white-lipped peccary) dominated patches of the lipid-rich palm Euterpe edulis, where the smallest frugivore (agouti) was absent. Instead, the smallest frugivore concentrated its foraging in areas with the poorest palm resource, Syagrus oleracea. Collared peccaries preferred areas of high abundance of Syagrus romanzoffiana when the other two mammal species were rarely detected or absent, strongly avoided patches of E. edulis, and showed higher average detection probabilities when agoutis were present. Our study highlights the important role of behavioral plasticity in promoting coexistence and indicates that through context-dependent interactions and hierarchical partitioning of resources, consumers can avoid strong competition, even under conditions of high spatial and temporal overlap and high levels of habitat fragmentation and isolation.

Accounting for detection unveils the intricacy of wild boar and rabbit co-occurrence patterns in a Mediterranean landscape

The patterns of species co-occurrence have long served as a primary approach to explore concepts of interspecific interaction. However, the interpretation of such patterns is difficult as they can result from several complex ecological processes, in a scale-dependent manner. Here, we aim to investigate the co-occurrence pattern between European rabbit and wild boar in an estate in Central Portugal, using two-species occupancy modelling. With this framework, we tested species interaction for occupancy and detection, but also the interdependencies between both parameters. According to our results, the wild boar and European rabbit occurred independently in the study area. However, model averaging of the detection parameters revealed a potential positive effect of wild boar’s presence on rabbit’s detection probability. Upon further analysis of the parameter interdependencies, our results suggested that failing to account for a positive effect on rabbit’s detection could lead to potentially biased interpretations of the co-occurrence pattern. Our study, in spite of preliminary, highlights the need to understand these different pathways of species interaction to avoid erroneous inferences.

The rescue effect and inference from isolation-extinction relationships

The rescue effect in metapopulations hypothesises that less isolated patches are unlikely to go extinct because recolonisation may occur between breeding seasons ('recolonisation rescue'), or immigrants may sufficiently bolster population size to prevent extinction altogether ('demographic rescue'). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonisation rescue for metapopulations of black rails (Laterallus jamaicensis) and Virginia rails (Rallus limicola) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonisation rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in non-equilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.

Low-intensity monitoring of small-mammal habitat associations and species interactions in an urban forest-preserve network

Abstract ContextAnthropogenic landscape modification and fragmentation result in loss of species and can alter ecosystem function. Assessment of the ecological value of urban reserve networks requires baseline and continued monitoring. However, depending on the desired indicators and parameters, effective monitoring can involve extensive sampling that is often financially or logistically infeasible. AimsWe employed a low-intensity, mixed-detector survey design to monitor the small-mammal community across a network of 53 fragmented forest preserves (225 sites) in a highly urbanised landscape in the Chicago metropolitan area from August to October, 2009–2012. MethodsWe used a sequential process to fit single-season occupancy and pairwise co-occurrence models for six common small mammal species to evaluate habitat associations and interspecific interactions. Key resultsShrew species and meadow voles occurred more often in open canopy-associated habitats, whereas occupancy was greater for eastern chipmunks, grey squirrels and white-footed mice in closed-canopy habitats. Habitat associations were complicated by negative pairwise interactions, resulting in reduced occurrence of meadow voles when predatory short-tailed shrews were present and lower occupancy rates of white-footed mouse when chipmunk competitors where present. White-footed mice co-occurred with short-tailed shrews, but detection of white-footed mice was lower when either eastern chipmunks or short-tailed shrews were present, suggesting that densities of these species could be inversely related. ConclusionsWe found evidence for both habitat segregation and interspecific interactions among small mammal species, by using low-intensity sampling across the reserve network. Thus, our sampling and analysis approach allowed for adequate assessment of the habitat associations and species interactions within a small-mammal community. ImplicationsOur findings demonstrated the utility of this monitoring strategy and community as bioindicators for urban-reserve networks. The approach described holds promise for efficient monitoring of reserve networks in fragmented landscapes, critical as human population densities and urbanisation increase, and we discuss how adaptive sampling methods could be incorporated to further benefit conservation efforts.

Long-term monitoring of nest boxes and nest logs in a tree-hollow depleted box–ironbark forest in north-eastern Victoria

Forest and woodland areas that have suffered historic degradation of habitat are likely to have reduced populations of tree-hollow dependent wildlife. We investigated the frequency of use of small-entry nest boxes installed 3 m high and vertical nest logs installed 1–3 m high, over 10–30 years in box–ironbark forest in north-east Victoria. Mammals were the dominant users of the nest boxes. Squirrel gliders and sugar gliders collectively used >75% of boxes and brush-tailed phascogales used >30% of boxes. Birds used the nest boxes on just two occasions. Brown treecreepers were the dominant users of the nest logs, with 48 breeding events across 30% of 105 nest logs. Turquoise parrots bred in the logs on five occasions. Gliders used 31% and phascogales 16% of the nest logs. These mammals were directly observed more frequently in the nest boxes than in the nest logs. Our findings show that mammals and birds preferred morphologically different hollows. Further research into the influence of different artificial hollow design elements is required. Nest boxes and nest logs required infrequent maintenance that was easily sustained over time. Our results suggest that tree-hollow dependent wildlife can benefit from restoration of their breeding and shelter sites.

Characterizing species co-occurrence patterns of imperfectly detected stream fishes to inform species reintroduction efforts

Species reintroduction efforts can improve the recovery of imperiled species, but successful implementation of this conservation strategy requires a thorough understanding of the abiotic and biotic factors influencing species viability. Species interactions are especially understudied, in particular by omitting the effect of imperfect detection on negative, neutral, or positive associations within a community. Using repeat surveys from 5 southern Ontario, Canada, Great Lakes tributaries, we quantified species co-occurrence patterns with the eastern sand darter (ESD) (Ammocrypta pellucida), listed as federally threatened, and characterized how imperfect detection during sampling can influence inference regarding these relationships. We used a probabilistic framework that included 3 approaches of increasing complexity: probabilistic co-occurrence analysis ignoring imperfect detection; single-species occupancy models with subsequent co-occurrence analysis; and 2-species occupancy models. We then used our occupancy models to predict suitable sites for potential future reintroduction efforts while considering the influence of negative species interactions. Based on the observed data, ESD showed several positive associations with co-occurring species; however, species associations differed when imperfect detection was considered. Specifically, a negative association between ESD and rosyface shiner (Notropis rubellus) was observed only after accounting for imperfect detection in the Grand River. Alternatively, positive associations in the Grand River between ESD and northern hogsucker (Hypentelium nigricans) and silver shiner (Notropis photogenis) were observed regardless of whether imperfect detection was accounted for. Our models predicted several potential reintroduction sites for ESD in formerly occupied watersheds with high levels of certainty. Overall, our results demonstrate the importance of investigating imperfect detection and species co-occurrence when planning reintroduction efforts.

Soil chemistry, and not short-term (1-2 year) deer exclusion, explains understory plant occupancy in forests affected by acid deposition

The loss of species diversity and plant community structure throughout the temperate deciduous forests of North America have often been attributed to overbrowsing by white-tailed deer (Odocoileus virginanus). Slow species recovery following removal from browsing, or reduction in deer density, has been termed a legacy effect of past deer herbivory. However, vegetation legacy effects have also coincided with changes to soil chemistry throughout the north-eastern USA. In this paper, we assess the viability of soil chemistry (i.e. pH, extractable nutrients and extractable metals) and other factors (topography, light, overstory basal area and location) as alternative explanations for a lack of vegetation recovery. We compared the relative effects of soil chemistry, site conditions and short-term (1-2 year) deer exclusion on single-species occupancy probabilities of 10 plant taxa common to oak-hickory forests in central Pennsylvania. We found detection for all modelled species was constant and high (p ^ > 0.65), and occupancy probability of most taxa was best explained by at least one soil chemistry parameter. Specifically, ericaceous competing vegetation was more likely to occupy acidic (pH < 3.5), base cation-poor (K < 0.20 cmolc kg-1) sites, while deer-preferred plants were less likely to occur when soil manganese exceeded 0.1 cmolc kg-1. Short-term deer exclusion did not explain occupancy of any plant taxon, and site conditions were of nominal importance. This study demonstrates the importance of soil chemistry in shaping plant community composition in the north-central Appalachians, and suggests soil as an alternative, or additional, explanation for deer vegetation legacy effects. We suggest that the reliance on phyto-indicators of deer browsing effects may overestimate the effects of browsing if those species are also limited by unfavourable soil conditions. Future research should consider study designs that address the complexity of deer forest interactions, especially in areas with complex site-vegetation histories.

Landscape use by two opossums is shaped by habitat preferences rather than by competitive interactions

Given the phylogenetic proximity and similar morphology of opossums (Didelphis spp.), they are good models to study factors that facilitate or impede coexistence of syntopic species and to better understand how landscape changes affect species distributions and habitat use. For this purpose, we used single-species and two-species occupancy models using records of D. albiventris, considered the dominant species, and D. aurita from a camera-trap survey conducted in an agricultural and conservation landscape in the Atlantic Forest of Argentina. We evaluated which factors determined the probability of species occurrence: habitat preferences or interspecific relationships. We also estimated the overlap in daily activity patterns between species, and evaluated changes in D. aurita activity in response to the occupancy probability of D. albiventris. Didelphis aurita had higher occupancy probabilities in the continuous native forest, whereas D. albiventris had higher occupancy probabilities in fragmented forests with less complex and more open vegetation structure, and greater proximity to buildings. Both opossums were almost absent in pine plantations. Results of the co-occurrence models and the overlap in diel activity suggest that D. aurita is not avoiding D. albiventris. Occurrences of these two opossums most probably reflect different adaptations by each species to different habitats, and competitive interactions seem to play a minor role in shaping their current distributions. Didelphis albiventris may be replacing D. aurita mainly as a result of changing environmental conditions, which become unfavorable to the latter but promote the creation of new habitat for the former.

Competition and specialization in an African forest carnivore community

Globally, human activities have led to the impoverishment of species assemblages and the disruption of ecosystem function. Determining whether this poses a threat to future ecosystem stability necessitates a thorough understanding of mechanisms underpinning community assembly and niche selection. Here, we tested for niche segregation within an African small carnivore community in Kibale National Park, Uganda. We used occupancy modeling based on systematic camera trap surveys and fine-scale habitat measures, to identify opposing preferences between closely related species (cats, genets, and mongooses). We modeled diel activity patterns using kernel density functions and calculated the overlap of activity periods between related species. We also used co-occupancy modeling and activity overlap analyses to test whether African golden cats Caracal aurata influenced the smaller carnivores along the spatial and/or temporal axes. There was some evidence that related species segregated habitat and activity patterns. Specialization was particularly strong among forest species. The cats and genets partitioned habitat, while the mongooses partitioned both habitat and activity period. We found little evidence for interference competition between African golden cats and other small carnivores, although weak interference competition was suggested by lower detection probabilities of some species at stations where African golden cats were present. This suggests that community assembly and coexistence in this ecosystem are primarily driven by more complex processes. The studied carnivore community contains several forest specialists, which are typically more prone to localized extinction. Preserving the observed community assemblage will therefore require the maintenance of a large variety of habitats, with a particular focus on those required by the more specialized carnivores.

Spatiotemporal habitat use by a multitrophic Alaska alpine mammal community

Evaluating sympatric habitat use of a mammal community can help determine intra- and inter-guild interactions and identify important habitats, potentially improving the management of these communities with a changing climate. Increasingly variable climatic patterns in Alaska, USA, are raising concerns of mismatched phenologies and altered ecosystem structures. We studied the occupancy of 10 mammal species over 15 months, via camera traps, occupying alpine areas of the Alaska Range in interior Alaska, from 2013 to 2014. We tested hypotheses about how habitat use of these species within and between groups varied by spatial and temporal covariates. Furthermore, we modeled two-species occupancy of brown bears (Ursus arctos Linnaeus, 1758) and gray wolves (Canis lupus Linnaeus, 1758) against different potential prey species. Our results suggest that medium-sized and large herbivore use was positively correlated with fine-scale covariates including rock, forb, and graminoid coverage. Large herbivore habitat use was also correlated with abiotic landscape covariates. Detection probabilities of predators and Dall’s sheep (Ovis dalli dalli Nelson, 1884) was improved by camera traps on wildlife trails. Two-species models suggested co-occurrence of habitat use between brown bear – caribou (Rangifer tarandus (Linnaeus, 1758)) and gray wolf – caribou. Results demonstrate the sympatric habitat use by multiple groups of mammals within Alaskan alpine ecosystems and the importance of incorporating multiple groups and spatial scales when making management decisions.

Habitat and introduced predators influence the occupancy of small threatened macropods in subtropical Australia

Australia has had the highest rate of mammal extinctions in the past two centuries when compared to other continents. Frequently cited threats include habitat loss and fragmentation, changed fire regimes and the impact of introduced predators, namely the red fox (Vulpes vulpes) and the feral cat (Felis catus). Recent studies suggest that Australia's top predator, the dingo (Canis dingo), may have a suppressive effect on fox populations but not on cat populations. The landscape of fear hypothesis proposes that habitat used by prey species comprises high to low risk patches for foraging as determined by the presence and ubiquity of predators within the ecosystem. This results in a landscape of risky versus safe areas for prey species. We investigated the influence of habitat and its interaction with predatory mammals on the occupancy of medium-sized mammals with a focus on threatened macropodid marsupials (the long-nosed potoroo [Potorous tridactylous] and red-legged pademelon [Thylogale stigmatica]). We assumed that differential use of habitats would reflect trade-offs between food and safety. We predicted that medium-sized mammals would prefer habitats for foraging that reduce the risk of predation but that predators would have a positive relationship with medium-sized mammals. We variously used data from 298 camera trap sites across nine conservation reserves in subtropical Australia. Both dingoes and feral cats were broadly distributed, whilst the red fox was rare. Long-nosed potoroos had a strong positive association with dense ground cover, consistent with using habitat complexity to escape predation. Red-legged pademelons showed a preference for open ground cover, consistent with a reliance on rapid bounding to escape predation. Dingoes preferred areas of open ground cover whereas feral cats showed no specific habitat preference. Dingoes were positively associated with long-nosed potoroos whilst feral cats were positively associated with red-legged pademelons. Our study highlights the importance of habitat structure to these threatened mammals and also the need for more detailed study of their interactions with their predators.

Long-Term Data Suggest Potential Interactions of Introduced Walleye and Smallmouth Bass on Native Sauger in Four Missouri River Impoundments

Sauger Sander canadensis, Walleye Sander vitreus, and Smallmouth Bass Micropterus dolomieu, are important sportfish in the four main stem Missouri River reservoirs in South Dakota: Lakes Oahe, Sharpe, Francis Case, and Lewis and Clark. However, native Sauger populations, once assumed to be stable, may be in decline. To identify temporal trends and potential interspecific mechanisms affecting Sauger populations, we examined their long-term abundance trends in standard gillnet surveys and angler catch and harvest trends in long-term creel surveys. We also used a robust design occupancy model to examine changes in within-lake distribution of this species. There are concerns regarding the effects of Walleye and Smallmouth Bass on Sauger, so we also described the population trends of these potential competitors. Standard gillnet surveys indicated declining abundance of both Sauger and Walleye in Lakes Oahe and Sharpe. Sauger abundance has trended down in Lewis and Clark, but upward in Francis Case. Conversely, Walleye abundance trends declined in Francis Case and increased in Lewis and Clark. Occupancy (ψ̂) of Sauger declined in all four reservoirs, indicating a contracting distribution throughout the reservoirs. Walleye occupancy remained ∼1.0. Smallmouth Bass occupancy increased in the three reservoirs with sufficient data for analysis, excluding Lewis and Clark Lake. Smallmouth Bass exhibited steady increases in angler catch and harvest, as well as abundance in long-term gillnet surveys, suggesting expanding and increasing populations. Habitat alteration is hypothesized to be a major driver of the Sauger occupancy and abundance declines. However, Walleye and Smallmouth Bass interactions could also be contributing to observed declines of native Sauger.

This town ain't big enough for both of us…or is it? Spatial co-occurrence between exotic and native species in an urban reserve

Exotic species pose a threat to most ecosystems because of their potential to establish negative interactions with native biota. However, exotic species can also offer resources to native species, especially within highly modified environments such as urban ecosystems. We studied 17 exotic-native pairs of species with the potential to compete with one another, or in which one of the species could offer resources to the other, in an urban ecological reserve located within Mexico City. We used two-species occupancy models to analyze the potential association between the presence of the exotic species and the spatial distribution of the native species, as well as to assess if these species tend to avoid each other (negative spatial interaction) or to co-occur more often than expected under the hypothesis of independent occurrences (positive spatial interaction). Our results revealed few cases in which the exotic species influenced occupancy of the native species, and these spatial interactions were mainly positive, indicated by the fact that the occupancy of the native species was usually higher when the exotic species was also present. Seven of the eight observed non-independent patterns of co-occurrence were evident during the dry months of the year, when resources become scarce for most species. Our results also demonstrate that the observed patterns of species co-occurrence depend on the distance to the nearest urban structure and the amount of herb, shrub, and tree cover, indicating that these habitat features influence whether native species avoid or co-occur with exotic species. Our study represents an important contribution to the understanding of temporal dynamics in the co-occurrence between exotic and native species within urban ecological reserves.

Implementation of an occupancy-based monitoring protocol for a widespread and cryptic species, the New England cottontail (Sylvilagus transitionalis)

Context Designing effective long-term monitoring strategies is essential for managing wildlife populations. Implementing a cost-effective, practical monitoring program is especially challenging for widespread but locally rare species. Early successional habitat preferred by the New England cottontail (NEC) has become increasingly rare and fragmented, resulting in substantial declines from their peak distribution in the mid-1900s. The introduction of a possible competitor species, the eastern cottontail (EC), may also have played a role. Uncertainty surrounding how these factors have contributed to NEC declines has complicated management and necessitated development of an appropriate monitoring framework to understand possible drivers of distribution and dynamics. Aims Because estimating species abundance is costly, we designed presence–absence surveys to estimate species distributions, test assumptions about competitive interactions, and improve understanding of demographic processes for eastern cottontails (EC) and New England cottontails (NEC). The survey protocol aimed to balance long-term management objectives with practical considerations associated with monitoring a widespread but uncommon species. Modelling data arising from these observations allow for estimation of covariate relationships between species status and environmental conditions including habitat and competition. The framework also allows inference about species status at unsurveyed locations. Methods We designed a monitoring protocol to collect data across six north-eastern USA states and, using data collected from the first year of monitoring, fit a suite of single-season occupancy models to assess how abiotic and biotic factors influence NEC occurrence, correcting for imperfect detectability. Key results Models did not provide substantial support for competitive interactions between EC and NEC. NEC occurrence patterns appear to be influenced by several remotely sensed habitat covariates (land-cover classes), a habitat-suitability index, and, to a lesser degree, plot-level habitat covariates (understorey density and canopy cover). Conclusions We recommend continuing presence–absence monitoring and the development of dynamic occupancy models to provide further evidence regarding hypotheses of competitive interactions and habitat influences on the underlying dynamics of NEC occupancy. Implications State and federal agencies responsible for conserving this and other threatened species can engage with researchers in thoughtful discussions, based on management objectives, regarding appropriate monitoring design to ensure that the allocation of monitoring efforts provides useful inference on population drivers to inform management intervention.

Environmental gradients in old-growth Appalachian forest predict fine-scale distribution, co-occurrence, and density of woodland salamanders

Woodland salamanders are among the most abundant vertebrate animals in temperate deciduous forests of eastern North America. Because of their abundance, woodland salamanders are responsible for the transformation of nutrients and translocation of energy between highly disparate levels of trophic organization: detrital food webs and high-order predators. However, the spatial extent of woodland salamanders' role in the ecosystem is likely contingent upon the distribution of their biomass throughout the forest. We sought to determine if natural environmental gradients influence the fine-scale distribution and density of Southern Ravine Salamanders (Plethodon richmondi) and Cumberland Plateau Salamanders (P. kentucki). We addressed this objective by constructing occupancy, co-occurrence, and abundance models from temporally replicated surveys within an old-growth forest in the Cumberland Plateau region of Kentucky. We found that Plethodon richmondi had a more restricted fine-scale distribution than P. kentucki (mean occupancy probability [ψ ¯ ^ ] = 0.737) and exhibited variable density, from <250 to >1000 individuals per hectare, associated with increased soil moisture and reduced solar exposure due to slope face. While more ubiquitously distributed (ψ ¯ ^  = 0.95), P. kentucki density varied from <400 to >1,000 individuals per hectare and was inversely related to increased solar exposure from canopy disturbance and landscape convexity. Our data suggest co-occurrence patterns of P. richmondi and P. kentucki are influenced primarily by abiotic conditions within the forest, and that populations likely occur independently and without evidence of biotic interaction. Given the critical role that woodland salamanders play in the maintenance of forest health, regions that support large populations of woodland salamanders, such as those highlighted in this study-mesic forest stands on north-to-east facing slopes with dense canopy and abundant natural cover, may provide enhanced ecosystem services and support the stability of the total forest.