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Urbanization has important effects on the distribution and persistence of wildlife communities. Urbanization may alter not just the distributions of individual species, but also co-occurrence patterns and thus the potential for interspecific interactions (e.g., competition, predation) that structure wildlife communities. Little is currently known about how urbanization alters species co-occurrence or how these changes shape urban species assemblages. Using tree squirrels as a model functional group, we quantified how urbanization alters species occurrence and co-occurrence patterns to shape species assemblages, and how these effects vary within and among cities. We constructed a multi-species, multi-season occupancy model to identify relationships between tree squirrel occupancy and co-occurrence and local land and tree canopy cover and examined variation in these relationships within and among nine US cities. Species’ responses to canopy cover were highly variable among, but less variable within cities, suggesting that even common urban wildlife species may respond differently to urban intensity in different landscape contexts. Species co-occurrence was also highly variable among cities and weakly related to canopy cover within a city. These findings provide important evidence that both environmental attributes and species interactions shape urban wildlife communities. Important for management and conservation, they suggest that tree-canopy cover can particularly support forest species co-occurrence and that managing urban forests to provide high canopy cover could contribute to the diversity of urban wildlife communities in forested ecoregions.

1. To realize the potential of citizens to contribute to conservation efforts through the acquisition of data for broad-scale species distribution models, scientists need to understand and minimize the influences of commonly observed sample selection bias on model performance. Yet evaluating these data with independent, planned surveys is rare, even though such evaluation is necessary for understanding and applying data to conservation decisions. 2. We used the state-listed fox squirrel Sciurus niger in Florida, USA, to interpret the performance of models created with opportunistic observations from citizens and professionals by validating models with independent, planned surveys. 3. Data from both citizens and professionals showed sample selection bias with more observations within 50 m of a road. While these groups showed similar sample selection bias in reference to roads, there were clear differences in the spatial coverage of the groups, with citizens observing fox squirrels more frequently in developed areas. 4. Based on predictions at planned field surveys sites, models developed from citizens generally performed similarly to those developed with data collected by professionals. Accounting for potential sample selection bias in models, either through the use of covariates or via aggregating data into home range size grids, provided only slight increases in model performance. 5. Synthesis and applications. Despite sample selection biases, over a broad spatial scale opportunistic citizen data provided reliable predictions and estimates of habitat relationships needed to advance conservation efforts. Our results suggest that the use of professionals may not be needed in volunteer programmes used to determine the distribution of species of conservation interest across broad spatial scales.

The Delmarva fox squirrel (Sciurus niger cinereus) has been listed as endangered by the United States Department of Interior since 1967. A high-priority task for the recovery of this taxon is to determine its current geographic distribution. Toward this end, we have identified a microsatellite locus that unambiguously differentiates Delmarva fox squirrels from eastern gray squirrels (S. carolinensis), which frequently co-occur with Delmarva fox squirrels. Analysis of this marker in noninvasively collected hair samples will allow unequivocal identification of localities occupied by Delmarva fox squirrels with a minimum investment of funds, time, and effort because handling individuals will be unnecessary. This protocol will expedite site review in connection with the Endangered Species Act consultation process.

Squirrels show off multiple landing styles as they speed through the canopy. Squirrels show off multiple landing styles as they speed through the canopy. Squirrels show off multiple landing styles as they speed through the canopy. A fox squirrel jumping across experimental apparatus

Niche partitioning reduces interspecific competition, facilitating coexistence. In urban ecosystems, however, habitat loss reduces species’ ability to spatially partition activity. Temporal partitioning may thus increase in urban areas as species, unable to avoid each other spatially, partition time to avoid competition. In Midwestern US cities, eastern gray squirrels ( Sciurus carolinensis ) and fox squirrels ( S. niger ) co-occur and compete for resources. We identified urban gray and fox squirrel activity patterns and how they vary with season, land cover, and among sites where they do and do not co-occur using camera-trap data. Both species’ activity patterns varied with season and canopy and impervious surface cover. Gray squirrel activity patterns varied in the presence of fox squirrels only in the fall, providing limited support for our temporal partitioning hypothesis. Temporal niche partitioning may thus play a role in supporting these species co-existence when competition is seasonally-elevated (e.g., fall hording), but appears less important in other seasons.

Urbanization and urban sprawl generally degrade and diminish wildlife habitat, threatening to extirpate local populations. However, certain synanthropic species (e.g., coyotes, white‐tailed deer, and squirrels) are able to persist in urban environments and may even occur at greater densities than they do in their natural habitats. Eastern fox squirrels (Sciurus niger) are large tree squirrels that are known to be present in greater densities within urban areas. To determine how landscape characteristics may affect fox squirrel presence, we conducted line‐transect surveys along sidewalks on the Texas A&M University—College Station campus to record presence of fox squirrels and nearest tree species. We calculated Jacobs’ index of selectivity (D) for use of trees by fox squirrels along the transects. Squirrel density was calculated for all transects and modeled using linear regression with environmental (e.g., tree density) and survey (e.g., transect distance) variables. Fox squirrels preferred only a small number of the available tree species, primarily Quercus and Ulmus species. Observed fox squirrel density significantly increased with time of day, temperature, density of oaks (Quercus spp.), and density of all trees, and decreased with distance and area of the transect. These results suggest that even when urban areas contain suitable habitat, use of urban environments by wildlife is still highly selective and dependent on specific habitat requirements. Synanthropic species are able to persist in urban environments and may even occur at greater densities than they do in their natural habitats. To determine how landscape characteristics may affect presence of synanthropic Eastern fox (Sciurus niger) squirrel presence, we conducted line‐transect surveys along sidewalks on the Texas A&M University—College Station campus to record presence of fox squirrels and nearest tree species. Fox squirrels preferred only a small number of the available tree species, primarily Quercus and Ulmus species, and observed fox squirrel density significantly increased with time of day, temperature, and tree and oak density, and decreased with length and area of the transect.

Competition from invasive species is an increasing threat to biodiversity. In Southern California, the western gray squirrel (Sciurus griseus, WGS) is facing competition from the fox squirrel (Sciurus niger, FS), an invasive congener. We used spectral methods to analyze 140 consecutive monthly censuses of WGS and FS within a 11.3 ha section of the California Botanic Garden. Variation in the numbers for both species and their synchrony was distributed across long timescales (>15 months). After filtering out annual changes, concurrent mean monthly temperatures from nearby Ontario Airport yielded a spectrum with a large semi‐annual peak and significant spectral power at long timescales (>28 months). The cospectrum between WGS numbers and temperature revealed a significant negative correlation at long timescales (>35 months). Cospectra also revealed significant negative correlations with temperature at a six‐month timescale for both WGS and FS. Simulations from a model of two competing species indicate that the risk of extinction for the weaker competitor increases quickly as environmental noise shifts from short to long timescales. We analyzed the timescales of fluctuations in detrended mean annual temperatures for the time period 1915–2014 from 1218 locations across the continental USA. In the last two decades, significant shifts from short to long timescales have occurred, from <3 years to 4–6 years. Our results indicate that (i) population fluctuations in co‐occurring native and invasive tree squirrels are synchronous, occur over long timescales, and may be driven by fluctuations in environmental conditions; (ii) long timescale population fluctuations increase the risk of extinction in competing species, especially for the inferior competitor; and (iii) the timescales of interannual environmental fluctuations may be increasing from recent historical values. These results have broad implications for the impact of climate change on the maintenance of biodiversity. This study documents long timescale variation in natural populations of conservation interest, shows that long timescale variation can accelerate the loss of species diversity, and provides evidence that the timescales of environmental fluctuations have increased in recent times. These results have broad implications for the impact of climate change on the maintenance of biodiversity.

Assessing the potential for threatened species to persist and spread within fragmented landscapes requires the identification of core areas that can sustain resident populations and dispersal corridors that can link these core areas with isolated patches of remnant habitat. We developed a set of GIS tools, simulation methods, and network analysis procedures to assess potential landscape connectivity for the Delmarva fox squirrel (DFS; Sciurus higer cinereus), an endangered species inhabiting forested areas on the Delmarva Peninsula, USA. Information on the DFS's life history and dispersal characteristics, together with data on the composition and configuration of land cover on the peninsula, were used as input data for an individual-based model to simulate dispersal patterns of millions of squirrels. Simulation results were then assessed using methods from graph theory, which quantifies habitat attributes associated with local and global connectivity. Several bottlenecks to dispersal were identified that were not apparent from simple distance-based metrics, highlighting specific locations for landscape conservation, restoration, and/or squirrel translocations. Our approach links simulation models, network analysis, and available field data in an efficient and general manner, making these methods useful and appropriate for assessing the movement dynamics of threatened species within landscapes being altered by human and natural disturbances.

Recent advances in optical remote sensing (RS) technology in combination with lightweight Global Positioning System (GPS) tracking devices now make analyzing the multi-scale habitat selection (HS) of small mammals < 2 kg possible. However, there have been relatively few multi-scale HS studies integrating fine-scale RS data with data-rich, GPS-derived movement data from small mammals. This is critical because small mammals commonly select habitat features across multiple scales. To address this gap, we investigated the HS of a small mammal, fox squirrels (Sciurus niger), which are known to cover relatively large areas and select fine-scale environmental features. We specifically asked the following questions: (1) Do next-generation RS variables improve HS models at single spatial scales? (2) Do multi-scale HS models improve upon those at single spatial scales? Using data from 45 individuals, we constructed HS models at three spatial scales: 4 ha (210 m × 210 m), 0.09 ha (30 m × 30 m), and 0.01 ha (10 m × 10 m) using traditional and next-generation RS data. The 4-ha model, using traditional and next-generation RS data, produced the best single-scale model, explaining 58% of the variations in HS. However, the multi-scale model provided the most informative model, explaining 68% of the variations in HS. Our models provide evidence for the value of next-generation RS data when quantifying HS and additional support for the idea of studying HS at multiple spatial scales.

The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.