Confounding factors in the detection of species responses to habitat fragmentation

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat. Fragmentation per se is a landscape-level phenomenon in which species that survive in habitat remnants are confronted with a modified environment of reduced area, increased isolation and novel ecological boundaries. The implications of this for individual organisms are many and varied, because species with differing life history strategies are differentially affected by habitat fragmentation. Here, we review the extensive literature on species responses to habitat fragmentation, and detail the numerous ways in which confounding factors have either masked the detection, or prevented the manifestation, of predicted fragmentation effects.Large numbers of empirical studies continue to document changes in species richness with decreasing habitat area, with positive, negative and no relationships regularly reported. The debate surrounding such widely contrasting results is beginning to be resolved by findings that the expected positive species-area relationship can be masked by matrix-derived spatial subsidies of resources to fragment-dwelling species and by the invasion of matrix-dwelling species into habitat edges. Significant advances have been made recently in our understanding of how species interactions are altered at habitat edges as a result of these changes. Interestingly, changes in biotic and abiotic parameters at edges also make ecological processes more variable than in habitat interiors. Individuals are more likely to encounter habitat edges in fragments with convoluted shapes, leading to increased turnover and variability in population size than in fragments that are compact in shape. Habitat isolation in both space and time disrupts species distribution patterns, with consequent effects on metapopulation dynamics and the genetic structure of fragment-dwelling populations. Again, the matrix habitat is a strong determinant of fragmentation effects within remnants because of its role in regulating dispersal and dispersal-related mortality, the provision of spatial subsidies and the potential mediation of edge-related microclimatic gradients.We show that confounding factors can mask many fragmentation effects. For instance, there are multiple ways in which species traits like trophic level, dispersal ability and degree of habitat specialisation influence species-level responses. The temporal scale of investigation may have a strong influence on the results of a study, with short-term crowding effects eventually giving way to long-term extinction debts. Moreover, many fragmentation effects like changes in genetic, morphological or behavioural traits of species require time to appear. By contrast, synergistic interactions of fragmentation with climate change, human-altered disturbance regimes, species interactions and other drivers of population decline may magnify the impacts of fragmentation. To conclude, we emphasise that anthropogenic fragmentation is a recent phenomenon in evolutionary time and suggest that the final, long-term impacts of habitat fragmentation may not yet have shown themselves.     

Landscape size affects the relative importance of habitat amount,habitat fragmentation,and matrix quality on forest birds

It is important to understand the relative effects of landscape habitat loss, habitat fragmentation, and matrix quality on biodiversity, so that potential management options can be appropriately ranked. However, their effects and relative importance may change with the size of the landscape considered because the multiple (and potentially conflicting) ecological processes that are influenced by landscape structure occur at different spatial scales (e.g. dispersal, predation, foraging). We estimated the relative effects of habitat loss, habitat fragmentation, and matrix quality (measured as the amount of forest, the proportion of forest area contained in large core forests, and the density of roads respectively) on fragmentation‐sensitive forest birds in southern Ontario, Canada using a range of landscape sizes (0.8–310 km²). We used three complementary statistical approaches to estimate relative effects of these correlated landscape factors – 1) multiple regression, 2) information theoretic (AIC) estimates of the most parsimonious model, and 3) multi‐model inference to average effects across all supported models. We controlled for spatial autocorrelation, local habitat, roadside sampling bias, time of day, season, habitat heterogeneity, and the interaction between the effects of habitat amount and fragmentation. We found that relative effects of habitat amount and fragmentation were scale dependent; habitat amount had a consistently positive effect that was consistent over more than two orders of magnitude in landscape area (~1–300 km²). In contrast, the effects of habitat fragmentation depended on the size of the landscape considered. Indeed, for veery Catharus fuscescens, habitat fragmentation had positive effects at one scale and negative effects at another. The effects of matrix quality were generally weak and changed little with scale. For the number of fragmentation sensitive species and the presence of veery, habitat amount was most important in large landscapes and habitat fragmentation in small landscapes but for the presence of ovenbird Seiurus aurocapilla, habitat amount was most important at all scales.     

Accounting for the causal basis of collinearity when measuring the effects of habitat loss versus habitat fragmentation

Collinearity among metrics of habitat loss and habitat fragmentation is typically treated as a nuisance in landscape ecology, and it is the norm to use statistical approaches that remove collinear information prior to estimating model parameters. However, collinearity may arise from causal relationships among landscape metrics and may therefore signal the occurrence of indirect effects (where one model predictor influences the response variable by driving changes in another influential predictor). Here we suggest that, far from being merely a statistical nuisance, collinearity may be crucial for accurately quantifying the effects of habitat loss versus habitat fragmentation. We use simulation modelling to create datasets of collinear landscape metrics in which collinearity arose from causal relationships, then test the ability of two statistical approaches to estimate the effects of these metrics on a simulated response variable: 1) multiple regression, which statistically removes collinearity, and was identified in a recent study as the best approach for estimating the effects of collinear landscape metrics (although this study did not account for any indirect effects implied by collinearity among metrics); and 2) path analysis, which accounts for the causal basis of collinearity. In agreement with this previous study, we found that multiple regression gave unbiased estimates of direct effects (effects not mediated by other model predictors). However, it gave biased estimates of total (direct + indirect) effects when indirect effects occurred. In contrast, path analysis reliably identified the causal basis of collinearity and gave unbiased estimates of direct, indirect, and total effects. We suggest that effective research on the impacts of habitat loss versus fragmentation will often require tools that can empirically test whether collinear landscape metrics are causally related, and if so, account for the indirect effects that these causal relationships imply. Path analysis, but not multiple regression, provides such a tool.     

Parallel declines in species and genetic diversity in tropical forest fragments

The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species.     

Characterising extinction debt following habitat fragmentation using neutral theory

Habitat loss leads to species extinctions, both immediately and over the long term as ‘extinction debt’ is repaid. The same quantity of habitat can be lost in different spatial patterns with varying habitat fragmentation. How this translates to species loss remains an open problem requiring an understanding of the interplay between community dynamics and habitat structure across temporal and spatial scales. Here we develop formulas that characterise extinction debt in a spatial neutral model after habitat loss and fragmentation. Central to our formulas are two new metrics, which depend on properties of the taxa and landscape: ‘effective area’, measuring the remaining number of individuals and ‘effective connectivity’, measuring individuals’ ability to disperse through fragmented habitat. This formalises the conventional wisdom that habitat area and habitat connectivity are the two critical requirements for long‐term preservation of biodiversity. Our approach suggests that mechanistic fragmentation metrics help resolve debates about fragmentation and species loss.     

苜蓿草地生境丧失与破碎化对昆虫物种丧失与群落重建的影响

生境破碎化包括生境丧失与破碎化两个相对独立的过程,为探讨这两个过程各自对生物多样性的影响,本文利用苜蓿草地实验模型系统(EMS)构建了36个小区研究不同生境丧失与破碎化对昆虫群落及不同类群的影响,包括18个破碎化小区与18个连续小区,破碎化小区全部采用1 m×1 m(H=1)破碎,连续小区苜蓿连片(H=0),生境丧失采...     

Trophic disruption: a meta‐analysis of how habitat fragmentation affects resource consumption in terrestrial arthropod systems

Habitat fragmentation is a complex process that affects ecological systems in diverse ways, altering everything from population persistence to ecosystem function. Despite widespread recognition that habitat fragmentation can influence food web interactions, consensus on the factors underlying variation in the impacts of fragmentation across systems remains elusive. In this study, we conduct a systematic review and meta‐analysis to quantify the effects of habitat fragmentation and spatial habitat structure on resource consumption in terrestrial arthropod food webs. Across 419 studies, we found a negative overall effect of fragmentation on resource consumption. Variation in effect size was extensive but predictable. Specifically, resource consumption was reduced on small, isolated habitat fragments, higher at patch edges, and neutral with respect to landscape‐scale spatial variables. In general, resource consumption increased in fragmented settings for habitat generalist consumers but decreased for specialist consumers. Our study demonstrates widespread disruption of trophic interactions in fragmented habitats and describes variation among studies that is largely predictable based on the ecological traits of the interacting species. We highlight future prospects for understanding how changes in spatial habitat structure may influence trophic modules and food webs.     

Landscape genetics and limiting factors

Population connectivity is mediated by the movement of organisms or propagules through landscapes. However, little is known about how variation in the pattern of landscape mosaics affects the detectability of landscape genetic relationships. The goal of this paper is to explore the impacts of limiting factors on landscape genetic processes using simulation modeling. We used spatially explicit, individual-based simulation modeling to quantify the effects of habitat area, fragmentation and the contrast in resistance between habitat and non-habitat on the apparent strength and statistical detectability of landscape genetic relationships. We found that landscape genetic effects are often not detectable when habitat is highly connected. In such situations landscape structure does not limit gene flow. We also found that contrast in resistance values between habitat and non-habitat interacts with habitat extensiveness and fragmentation to affect detectability of landscape genetic relationships. Thus, the influence of landscape features critical to providing connectivity may not be detectable if gene flow is not limited by spatial patterns or resistance contrast of these features. We developed regression equations that reliably predict whether or not isolation by resistance will be detected independently of isolation by distance as a function of habitat fragmentation and contrast in resistance between habitat and non-habitat.     

The Relationship between Habitat Loss and Fragmentation during Urbanization: An Empirical Evaluation from 16 World Cities

Urbanization results in habitat loss and habitat fragmentation concurrently, both influencing biodiversity and ecological processes. To evaluate these impacts, it is important to understand the relationships between habitat loss and habitat fragmentation per se (HLHF) during urbanization. The objectives of this study were two-fold: 1) to quantify the different forms of the HLHF relationship during urbanization using multiple landscape metrics, and 2) to test the validity of the HLHF relations reported in the literature. Our analysis was based on a long-term urbanization dataset (1800–2000) of 16 large cities from around the world. Habitat area was represented as the percentage of non-built-up area in the landscape, while habitat fragmentation was measured using several landscape metrics. Our results show that the relationship between habitat loss and habitat fragmentation during urbanization is commonly monotonic—linear, exponential, or logarithmic, indicating that the degree of habitat fragmentation per se increases with habitat loss in general. We compared our results with 14 hypothesized HLHF relationships based on simulated landscapes found in the literature, and found that four of them were consistent with those of urbanization, whereas the other ten were not. Also, we identified six new HLHF relationships when fragmentation was measured by total core area, normalized total core area, patch density, edge density and landscape shape index, respectively. In addition, our study demonstrated that the “space-for-time” approach, frequently used in ecology and geography, generated specious HLHF relationships, suggesting that this approach is largely inappropriate for analyses of urban landscapes that are highly heterogeneous in space and unusually contingent in dynamics. Our results show both generalities and idiosyncrasies of the HLHF relationship, providing new insights for assessing ecological effects of urbanization.     

Reviewing the potential for including habitat fragmentation to improve life cycle impact assessments for land use impacts on biodiversity

Purpose

The biosphere is progressively subjected to a variety of pressures resulting from anthropogenic activities. Habitat conversion, resulting from anthropogenic land use, is considered the dominant factor driving terrestrial biodiversity loss. Hence, adequate modelling of land use impacts on biodiversity in decision-support tools, like life cycle assessment (LCA), is a priority. State-of-the-art life cycle impact assessment (LCIA) characterisation models for land use impacts on biodiversity translate natural habitat transformation and occupation into biodiversity impacts. However, the currently available models predominantly focus on total habitat loss and ignore the spatial configuration of the landscape. That is, habitat fragmentation effects are ignored in current LCIAs with the exception of one recently developed method.

Methods

Here, we review how habitat fragmentation may affect biodiversity. In addition, we investigate how land use impacts on biodiversity are currently modelled in LCIA and how missing fragmentation impacts can influence the LCIA model results. Finally, we discuss fragmentation literature to evaluate possible methods to include habitat fragmentation into advanced characterisation models.

Results and discussion

We found support in available ecological literature for the notion that habitat fragmentation is a relevant factor when assessing biodiversity loss. Moreover, there are models that capture fragmentation effects on biodiversity that have the potential to be incorporated into current LCIA characterisation models.

Conclusions and recommendations

To enhance the credibility of LCA biodiversity assessments, we suggest that available fragmentation models are adapted, expanded and subsequently incorporated into advanced LCIA characterisation models and promote further efforts to capture the remaining fragmentation effects in LCIA characterisation models.

     

Diversity and geneflow in a migratory frugivorous fish: implications for Amazonian habitat connectivity

Colossoma macropomum is an ecologically and economically important fish distributed throughout the major tributaries of the Amazon River. C. macropomum require a suite of habitat types for different life stages making them potentially susceptible to the impacts of habitat fragmentation and alteration. As a means of better understanding the potential impacts of development, baseline data on connectivity and patterns of gene flow in species from relatively undisturbed habitat will be of value to monitor potential ecosystem impacts of anthropogenic habitat alteration on native fish communities. We used 13 single sequence repeat markers to determine if fine-scale structuring could be detected at the landscape scale at the Pacaya Samiria National Reserve, Perú. We also applied a model testing approach to evaluate the strength of different migration models, including panmixia, stepping stone and isolation models. Bayesian clustering detected a single genetic grouping across 131 fish. However, a comparison of marginal likelihoods for alternative migration models across PSNR supported a stepping stone model, rather than panmixia (Probability ~1.0). These results demonstrate that even in highly migratory fish with limited genetic structure, the effects of anthropogenic aquatic habitat alterations can be explored using genetic data.     

Fragmentation in eucalypt woodlands promotes nest‐tree occupancy by a despotic species,the noisy miner (Manorina melanocephala)

The effects of habitat fragmentation as a threat to biodiversity are well known; decreased connectivity can potentially influence population processes and dynamics, resulting in smaller, isolated populations that may not function optimally. However, fragmentation may also increase the amount of edge or ecotone habitat available to open country species, benefiting their populations and enabling them to dominate remnant habitats. Noisy miners (Manorina melanocephala) are one such species, occupying eastern‐Australian eucalypt woodlands. They are considered a ‘despotic’ species, in that their presence negatively impacts woodland avifauna biodiversity due to their aggressive exclusion of other taxa from occupied areas. Despite this well‐known impact, little information exists on the patterns of nest‐tree occupancy by noisy miners within eucalypt woodlands. In the current study, we explored the patterns of nest‐tree occupancy by noisy miners across two successive years, aiming to identify preferences for breeding areas relative to vegetation structure. Our results show that both habitat fragmentation and the characteristics of individual eucalypt trees in an area influenced nest‐tree occupancy. Noisy miners constructed nests in trees near the edge of woodland patches more often than expected. Moreover, the nest tree chosen was a eucalypt that was significantly smaller than randomly selected trees from the surrounding area. The results highlight the importance of habitat management measures that may reduce the suitability of woodland patches as nesting sites for this species, in order to mitigate the severe effects of this despotic edge specialist.     

The impact of giant panda foraging on bamboo dynamics in an isolated environment

Wildlife species are threatened by massive habitat destruction worldwide. Habitat fragmentation and isolation spatially constrain animals and in turn cause non-sustainable rates of animal foraging on plant populations. However, little empirical research has been done in large controlled settings to investigate foraging impacts. We conducted an experiment to characterize the impact of panda foraging on the sustainability of its food resource, bamboo, in an enclosed area of natural habitat (approximately 19 ha). We monitored bamboo density, age, and percent cover throughout the enclosure across a 3-year period. We documented marked declines in bamboo density and percent cover as a result of panda foraging, particularly in younger bamboo age classes. We constructed simultaneous autoregressive models to explain bamboo loss to panda foraging and subsequent bamboo recovery as a function of habitat conditions. Areas with high initial bamboo cover not only were prone to high rates of bamboo percent cover loss but also experienced high rates of subsequent bamboo recovery, as bamboo cover loss opened up the understory for new growth. Variograms of ordinary least squares model residuals revealed that the range of spatial autocorrelation in bamboo loss increased over time as available bamboo forage declined. The results have implications for understanding the impact of animal foraging on vegetation and also highlight the importance of preventing further habitat fragmentation and isolation.     

The impact of soybean expansion on mammal and bird,in the Balsas region,north Brasilian Cerrado

In order to analyse the impact of land use change, it is particularly important to know how organisms use resources distributed across a heterogeneous landscape. The main objective of this study is to analyse the potential impact of land use change on bird and mammal fauna, by using a coupled model approach. The CLUE (Conversion of Land Use and its Effects) model has been applied to obtain the spatial pattern of land use change for a scenario with soybean expansion in the Cerrado of Maranhão State in Brazil. These land use change maps were used as the input for the LEDESS (Landscape Ecological Decision and Evaluation Support System) model to evaluate the impact of habitat fragmentation on mammal and bird species. The scenarios demonstrated that high quality habitat for all studied species will be lost in the future when current trends in agricultural expansion continue, but these changes will have species-specific impacts. The most relevant ecological impact under the explored scenarios was habitat fragmentation expressed by the increase the number of habitat clusters. The coupled model approach of LEDESS and CLUE made it possible to project the spatial impact of soybean expansion on habitat dynamics in the studied region. This model approach can help to design effective ecological infrastructure to facilitate species survival and to implement an effective habitat network in the Balsas region.     

Effects of habitat fragmentation and road density on the distribution pattern of the moor frog Rana arvalis

1. The effects of habitat fragmentation on the distribution pattern of the moor frog Rana arvalis were investigated. Also, the possible isolation effects of the road network were taken into account.
2. Indications were found that habitat fragmentation partly explains the distribution pattern of the moor frog. The statistical models showed a positive effect of pond size (or marsh area) and a negative effect of road density on the probability of occupation of a moorland pond.
3. Because of the strong correlation between habitat quality variables and isolation variables, no unambiguous effects of isolation, described as the amount of suitable terrestrial habitat (moorland) in the surroundings of a moorland pond in a radius of 100–2000 m, could be demonstrated.
4. Spatial differences in road density can play a role in the selection of optimal locations for nature protection areas. The regression model used in this study predicts a reduced occupation probability in 55% of the study area. In the part of the study area adjacent to a motorway, occupation probability is lowered to less than 30%.
5. European studies of habitat fragmentation on amphibian species revealed a mean distance between occupied ponds of <1 km in all studies. This could be a general rule of thumb for persistent amphibian populations. Effects of pond size on the probability of occupation were more variable.
6. When discussing the effects of habitat fragmentation on amphibians and other ground dwelling species, the negative effects of roads are often underestimated.     

Home range size scales to habitat amount and increasing fragmentation in a mobile woodland specialist

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Song parameters of the fuscous honeyeater Lichenostomus fuscus correlate with habitat characteristics in fragmented landscapes

Both avian abundance and species richness decline in response to habitat loss and fragmentation. Studying variation in bird song structure across modified landscapes can provide insights into the effects of habitat alterations on coherence of social interactions within populations. Here, we tested whether fragmentation or change of habitat quality within box‐ironbark forest of central Victoria impacted cultural connectivity and song characteristics in fuscous honeyeater, a declining common Australian bird. First, we tested whether geographic distance and/or spatially‐explicit landscape connectivity models can explain patterns of song similarity across fragmented landscapes. We found no evidence that distance or habitat fragmentation impacts the nature and transmission of fuscous honeyeater song, and concluded that acoustic connectivity at the scale of our study is high. Second, we tested whether variation in habitat quality explains variation in song characteristics. In accordance with acoustic adaptation to habitat structure, birds sang longer songs in sites with more large trees and produced longer common song elements in sites with greater tree height. However, the acoustic adaptation hypothesis cannot explain the finding that in less‐disturbed landscapes with higher tree‐cover birds sang songs (and song elements) with higher maximum frequency and wider frequency bandwidth. We also found that birds sing longer and more variable songs of wider frequency bandwidth in less disturbed sites with a greater number of large mature trees, which may represent better feeding resources. Our study suggests that changes in song structure with habitat degradation could signal disturbed population processess, such as changes in the acoustic communication among resident birds.     

Effect of Landscape Structure on Species Diversity

The effects of habitat fragmentation and their implications for biodiversity is a central issue in conservation biology which still lacks an overall comprehension. There is not yet a clear consensus on how to quantify fragmentation even though it is quite common to couple the effects of habitat loss with habitat fragmentation on biodiversity. Here we address the spatial patterns of species distribution in fragmented landscapes, assuming a neutral community model. To build up the fragmented landscapes, we employ the fractional Brownian motion approach, which in turn permits us to tune the amount of habitat loss and degree of clumping of the landscape independently. The coupling between the neutral community model, here simulated by means of the coalescent method, and fractal neutral landscape models enables us to address how the species–area relationship changes as the spatial patterns of a landscape is varied. The species–area relationship is one of the most fundamental laws in ecology, considered as a central tool in conservation biology, and is used to predict species loss following habitat disturbances. Our simulation results indicate that the level of clumping has a major role in shaping the species–area relationship. For instance, more compact landscapes are more sensitive to the effects of habitat loss and speciation rate. Besides, the level of clumping determines the existence and extension of the power-law regime which is expected to hold at intermediate scales. The distributions of species abundance are strongly influenced by the degree of fragmentation. We also show that the first and second commonest species have approximately self-similar spatial distributions across scales, with the fractal dimensions of the support of the first and second commonest species being very robust to changes in the spatial patterns of the landscape.     

Developing a functional connectivity indicator to detect change in fragmented landscapes

Biodiversity indicators are increasingly used to assess progress towards conservation targets. Particular indicators are required to assess the impacts of habitat fragmentation on landscape connectivity and biodiversity value. This paper recognises that connectivity is best defined by the interaction between species and the landscape in which they occur, and proposes a functional approach to assess connectivity. The approach utilises an incidence function model (IFM) as a spatially explicit method to assess potential species-level connectivity. The standard IFM connectivity measure is modified to account for the influence of the surrounding landscape matrix on edge impacts (through a weighted internal edge buffer) and ecological isolation (through an assessment of least-cost distance to account for landscape permeability). It has been recognised that such patch-based connectivity measures can provide misleading results when used to examine change, as they only focus on between patch movements. As a result, a modified hybrid IFM, based on a combination of patch and cell-based approaches, is developed to account for both within (intra) and between (inter) patch connectivity. The resulting probability of functional connectivity (PFC) indicator was evaluated, alongside a patch-based connectivity measure, through the application to four model landscapes based on changes (2 negative and 2 positive) to a control landscape. The four model landscapes illustrate the impact of landscape change on habitat area, edge impacts and matrix permeability. The proposed PFC indicator successfully discriminated between the two negative and the two positive changes to the control landscape, whereas, the patch-based connectivity measure detected change successfully within three of the four landscapes. The PFC indicator predicted a decrease in intra and inter-patch connectivity following habitat loss and fragmentation (negative change 1), whereas patch-based connectivity measures indicate an increase in connectivity between fragmented patches. The proposed PFC indicator offers the opportunity to take the necessary species-based perspective to examine functional connectivity, incorporating habitat preference, dispersal probability, edge impacts and ecological isolation/permeability. The urgency to assess changes in connectivity and support conservation policy means that there is little time to wait for more complete data. We believe the proposed approach provides a robust balance between the data required and the biologically meaningful indicator produced.     

Investigating the distribution of prairie dogs in an urban landscape

Habitat fragmentation is a prevalent threat to biological diversity, and urbanization is a primary agent of fragmentation and a leading cause of species endangerment. Landscape biogeographic and local habitat characteristics can be important determinants of the distribution of species in habitat patches in urban landscapes. However, the specifics of which characteristics are most critical to maintaining biological diversity are not fully known for prairie ecosystems, especially in fragmented urban habitat. This study focuses on black-tailed prairie dogs along an urban gradient in Denver, CO. Prairie dogs have declined precipitously throughout the region and are an essential part of the prairie ecosystem, making them excellent study subjects. We identified a series of habitat fragments along a gradient of urbanization in the fully urbanized areas and south suburbs of Denver, CO, both containing and not containing prairie dogs. Local characteristics, including fragment slope and vegetative cover, and landscape characteristics, including fragment size, age and connectivity, were measured on each fragment. We used likelihood-based methods to explore which variables most accurately predicted prairie dog occurrence within our study area. Multiple factors influenced the distribution of prairie dogs in urban settings, with colony connectivity the strongest predictor of occupancy. Large and recently isolated fragments near other prairie dog colonies, flat areas and those with high graminoid cover were most likely to support prairie dog populations. Our study provides the first attempt to model prairie dog occurrence in highly fragmented urban habitat and has important implications for the management and conservation of prairie dogs.