This dataset was used to review and analyze coyote diets across North America in "Coyote diets in North America: geographic and ecological patterns during range expansion" by Jensen et al. in Mammal Review. We only include data from studies that reported data as percent frequency of occurrence and from multiple seasons. We ultimately used 93 of the included studies (294 seasonal records) in our analyses. Methods Literature search In April 2020, we searched Web of Science, Google Scholar, and ProQuest for literature on coyote diets (Appendices S1 and S2). We also searched Google Scholar and ProQuest in Spanish and French (this was not possible on Web of Science), because the coyote’s range extends into Central America and Canada and studies may have been published in those languages (Appendix S2). These searches resulted in ≥ 2066 potentially appropriate results (see Appendix S1 for why ‘≥’). We scanned titles and abstracts for evidence of quantified coyote diet results and downloaded 221 publications for further review. We also used a ‘snowball’ approach to identify additional articles missed during our above searches, wherein we reviewed the literature cited sections of the first 100 of the 221 screened studies (sorted alphabetically). We stopped at 100 because our rate of new article discovery had slowed dramatically by articles 80-100. This snowball search resulted in an additional 29 studies. In total we downloaded 250 studies subject to additional screening through eight criteria designed to standardise our analyses (Appendix S3):

Samples were scat and not intestinal tracts.

Dietary data were assessed using morphometric methods and recorded as the percentage frequency of occurrence (%FO; the number of scat samples found to contain a given prey category divided by the total number of samples). Note that %FO can be > 100% because each scat can contain more than one prey category.

Dietary data were reported by season (i.e., not just an annual average).

Seasonal sample sizes were ≥20.

If sample sizes for each season were not reported, then the total sample size divided by number of seasons was ≥50.

Samples were unique (i.e., we generally used the peer reviewed article if the same results were published in a thesis or dissertation). Authors reported all contents in samples (i.e., we excluded studies that were not comprehensive in their description of diet and only focused on certain food categories). At least four of the six most-consumed food categories (ungulates, lagomorphs, small mammals, vegetation, birds, and invertebrates) were reported.

Data collection We retained 93 studies after implementing our criteria for inclusion, which contained 294 seasonal records. For each study, we recorded the location, the sample size for each season, and the median year it occurred. We recorded the latitude and longitude when provided, but often had to estimate the coordinates by visually selecting a centroid using figures provided by the authors or searching for the study site on Google Maps. Some studies reported data from multiple study sites, in which case we recorded information from each study site separately. We recorded which seasons were reported and, unless specified by the authors, classified spring as March – May, summer as June – August, autumn as September – November and winter as December – February. Some studies only reported a wet and dry season, which we entered as either summer or winter depending on which climate the study took place in (e.g., southern México’s wet season is in summer, while California’s wet season is in winter). We recorded %FO of 12 food categories: 1) small mammals (e.g., small rodents); 2) lagomorphs; 3) wild ungulates (hereafter ‘ungulates’; 4) wild pigs Sus scrofa; 5) livestock (including poultry); 6) carnivora (including opossums Didelphis virginiana, domestic cats Felis catus, and domestic dogs); 7) birds; 8) reptiles and amphibians (hereafter, ‘reptiles’ because amphibians were very rarely reported); 9) invertebrates (e.g., Arthropoda); 10) vegetation (e.g.., fruit); 11) anthropogenic foods; and 12) other foods (e.g., beavers Castor canadensis and fish). For most prey categories we summed %FO values for different species within a single category. However, small prey item values are potentially artificially inflated when using %FO because multiple species can be in a single sample (Reynolds & Aebischer 1991). Therefore, for small mammals, vegetation, and invertebrates we recorded the largest %FO value for a species in those categories (Doherty et al. 2018). For studies that reported grass or pine needles as the highest vegetation %FO (n=5), we chose the next highest %FO value to represent vegetation for that dataset because these items are sometimes inadvertently collected with scat samples. Each of the 12 food categories except wild pigs received a value for each season in a study (i.e., we entered a zero if the category was not reported; Lange et al. 2021). We chose this approach because we assumed that, unless we had reason to believe otherwise (and had excluded the study; see criteria seven and eight above), authors reported coyote diets comprehensively. For wild pigs, we only included studies that reported them (n = 48), given that their range was and is limited to the southern USA and parts of California (Bevins et al. 2014), and so they did not co-occur with coyotes in most of the studies. Therefore, our summary statistics for wild pigs represent their consumption by coyotes where the two species co-occur.

The geographic distribution of coyotes (Canis latrans) has dramatically expanded since 1900, spreading across much of North America in a period when most other mammal species have been declining. Although this considerable expansion has been well documented at the state/provincial scale, continent-wide descriptions of coyote spread have portrayed conflicting distributions for coyotes prior to the 1900s, with popularly referenced anecdotal accounts showing them restricted to the great plains, and more obscure, but data-rich accounts suggesting they ranged across the arid west. To provide a scientifically credible map of the coyote’s historical range (10,000 – 300 BP) and describe their range expansion from 1900 to 2016, we synthesized archaeological and fossil records, museum specimens, peer-reviewed reports, and records from wildlife management agencies. Museum specimens confirm that coyotes have been present in the arid west and California throughout the Holocene, well before European colonization. Their range in the late 1800s was undistinguishable from earlier periods, and matched the distribution of non-forest habitat in the region. Coyote expansion began around 1900 as they moved north into taiga forests, east into deciduous forests, west into costal temperate rain forests, and south into tropical rainforests. Forest fragmentation and the extirpation of larger predators probably enabled these expansions. In addition, hybridization with wolves (C. lupus, C. lycaon, and/or C. rufus) and/or domestic dogs has been documented in the east, and suspected in the south. Our detailed account of the original range of coyotes and their subsequent expansion provides the core description of a large scale ecological experiment that can help us better understand the predator-prey interactions, as well as evolution through hybridization.

Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.

The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci. These genotypes were compared to those from other canid populations to evaluate the extent of genetic introgression. We conducted spatial clustering analyses and spatial autocorrelation to assess genetic structure among sampled coyotes. Coyotes across the two states had high genetic diversity, and we found no evidence of genetic structure. Six to sixteen percent of individuals displayed some evidence of genetic introgression from other species depending on the method and criteria used, but the population possessed predominantly coyote ancestry. Our findings suggested introgression from other canid populations has played less of a role in shaping the genetic character of coyotes in these states compared to populations closer to the Canadian border. Coyotes appear to display a panmictic population structure despite high habitat heterogeneity and heavy human influence in the spatial environment, underscoring the adaptability of the species.

This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83392 Carnivores are among the most conspicuous, charismatic and economically important mammals in shortgrass steppe, yet relatively is little is known about their populations or of the ecological factors that determine their distribution and abundance, in part because densities tend to be low. Mammalian carnivores represent the top predators in grassland food webs, consuming rodents, rabbits, young ungulates and other small vertebrates. In addition, shortgrass steppe is the primary habitat of the swift fox (Vulpes velox), a species of special conservation concern throughout most of its range. Fox populations are thought to be limited by predation from coyotes (Canis latrans), the most common carnivore in these grasslands and a species of interest, both for its ecological roles and well as a target species for human exploitation, ie hunting and predator control. In 1994, we implemented a low-intensity sampling scheme to monitor long-term changes in relative abundance of mammalian carnivores and help us examine interactions between these predators and their small mammal prey, including rodents and rabbits. We estimated relative abundance of carnivores using scat surveys along a fixed route. Four times each year (January, April, July, October), we drove a 32-km route consisting of pasture two-track and gravel roads on the CPER. We first drove the route to remove all scats (‘PRE-census’); we then returned ~14 d later and counted the number of scats deposited on the route (‘CENSUS’). We recorded the species that deposited the scat and estimated the scat age based on external appearance (4 categories). Beginning in 1997, we recorded the vegetation (habitat) type and topographic position of all scat locations to describe habitat use. Latrines are indicated by locations containing multiple scats. We used the ‘CENSUS’ data to calculate a scat index, defined as the number of scats deposited per km of road per night. The scat index can be used to estimate population density using equations for coyotes (Knowlton 1982) and swift foxes (Schauster et al. 2002) that described the rate of scat deposition from surveys where density was known. To estimate density and compare trends among seasons and years, we omitted scats collected along the 8.3 km of the route that occurred on gravel county roads. These roads are graded sporadically, sometimes between pre-census and census surveys, which tended to remove scats. (NOTE: these observations are NOT omitted in the dataset). Resources in this dataset:Resource Title: Website Pointer to html file. File Name: Web Page, url: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-sgs&identifier=135 Webpage with information and links to data files for download

Ecological theory posits that the strength of interspecific interactions is fundamentally underpinned by the population sizes of the involved species. Nonetheless, contemporary approaches for modelling species interactions predominantly centre around occupancy states. Here, we use simulations to illuminate the inadequacies of modelling species interactions solely as a function of occupancy, as is common practice in ecology. We demonstrate erroneous inference into species interactions due to bias in parameter estimates when considering species occupancy alone. To address this critical issue, we propose, develop, and demonstrate an occupancy-abundance model designed explicitly for modelling abundance-mediated species interactions involving two or more species. When modelling interactions as a function of abundance rather than occupancy, we uncover previously unidentified interactions. Through an empirical case study and comprehensive simulations, we demonstrate the importance of accountin..., In the case study using empirical data, we examine the intraguild interactions between three carnivores, a top mesopredator in the system, the coyote, an intermediate mesopredator, the fisher, and a small carnivore, the American marten. There is a long history of examining intraguild interactions between fisher and marten through harvest (e.g., Hardy, 1907; Krohn, Zielinski, & Boone, 1997). Recent harvest-based evidence was used to infer negative interactions between all three species, with fishers being limited through intraguild killing by coyotes, and martens being limited by both fisher and coyotes (Jensen & Humphries, 2019). Nonetheless, the three species co-occur over much of the marten’s limited range in New York State and recent analysis using Rota et al. (2016) co-occurrence models was inconsistent with previous hypotheses. This analysis found fisher occupancy was higher conditional on coyote presence, and marten occurred independently from both other species (Twining e..., , # Abundance-mediated species interactions

Summary

These are MCMC samplers, data simulators, and processing and run scripts for a occupancy-abundance model for abundance-mediated species interactions with a full example case study. This model framework models detection/non-detection data to estimated occupancy, abundance, and interactions between the species of interest. This model enables the user to apply summarized detection/non-detection data collected over repeat surveys to model interactions as a function of abundance. These samplers are presented in Twining et al. 2024, and are based on adaptations of the Waddle et al. (2010) formulation for modelling species interactions within an occupancy model, but instead of modelling the state model of a subordinate species a function of the occupancy states, it is modelled as a function of abundance (N). We provide a range of MCMC samplers for different ecological scenarios between two or more sp...

Understanding the ecological roles of species that influence ecosystem processes is a central goal of ecology and conservation biology. Eastern coyotes (Canis latrans) have ascended to the role of apex predator across much of eastern North America since the extirpation of wolves (Canis spp.) and there has been considerable confusion regarding their ability to prey on ungulates and their ecological niche relative to wolves. Eastern wolves (C. lycaon) are thought to have been the historical top predator in eastern deciduous forests and have previously been characterized as deer specialists that are inefficient predators of moose because of their smaller size relative to gray wolves (C. lupus). We investigated intrinsic and extrinsic influences on per capita kill rates of white-tailed deer (Odocoileus virginianus) and moose (Alces alces) during winter by sympatric packs of eastern coyotes, eastern wolves, and admixed canids in Ontario, Canada to clarify the predatory ability and ecological roles of the different canid top predators of eastern North America. Eastern coyote ancestry within packs negatively influenced per capita total ungulate (deer and moose combined) and moose kill rates. Furthermore, canids in packs dominated by eastern coyote ancestry consumed significantly less ungulate biomass and more anthropogenic food than packs dominated by wolf ancestry. Similar to gray wolves in previous studies, eastern wolves preyed on deer where they were available. However, in areas were deer were scarce, eastern wolves killed moose at rates similar to those previously documented for gray wolves at comparable moose densities across North America. Eastern coyotes are effective deer predators, but their dietary flexibility and low kill rates on moose suggest they have not replaced the ecological role of wolves in eastern North America.

Coyotes (Canis latrans) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (Lynx rufus) and gray foxes (Urocyon cinereoargenteus) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (Odocoileus virginianus) and wild turkeys (Meleagris gallopavo). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020-2021. We collected 180 scat samples along 295.9 kilometers (71.1 – 122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcodin..., , , # Data from: Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis

Data includes DNA metabarcoding diet analysis from coyotes, bobcats, and gray foxes sampled at three sites in South Carolina during MayJune 2020-2021. We identified consensus predator species via DNA metabarcoding and mtDNA. We consolidated data into 8 categories of diet for frequency of occurrence analysis.

Description of the Data and file structure

Data in file "Youngmann et al_2023_data_PLOSONE.csv" includes DNA metabarcoding sequence ID (Jvid), scat identification (SampleID), Year, Site, Latitude, Longitude, DNA metabarcoding predator species id (Ac12S), mitochondrial DNA predator species id (mtDNA), consensus predator species id (Consensus), and 8 categories of prey (Deer, Wild turkey, Rabbit, Squirrel, Small mammal, Avian, Herpetofauna, Other). The "Jvid" DNA metabarcoding sequence ID column is cross-referenced with the sample IDs i...

1. Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics.
2. In the present study, we assessed spatial variation in diet characteristics, gut microbiome, and the association between these two ecological traits across populations of coyotes (Canis latrans). We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations.
3. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values.
4. Though consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with gray wolves (Canis lupus).
5. The gut microbial community exhibited marked spatial variation across populations with the lowest OTU diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13C and microbial community attributes. However, positive associations between δ15N and specific microbial genera increased as coyotes ascended trophic levels.
6. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology, and alterations in behavior. 05-May-2020

MetaData_Quality_VCFThis file contains 1) metadata that describes each sample used, 2) quality scores from sequencing on Illumina platform, and 3) an initial VCF file with individual genotypes compiled from the raw sequencing data (refer to methods in publication for a description of genotypes used to generate the PCA in the manuscript).Eastern Wolf Raw DataThis file contains raw Illumina sequence data for the Eastern Wolves (Canis lycaon). Please check the metadata to confirm and cross-reference sample IDs.EasternWolfRawData.zipEastern Coyote Raw DataThis file contains raw Illumina sequence data for the Eastern Coyotes (Canis latrans var.). Please check the metadata to confirm and cross-reference sample IDs.EasternCoyoteRawData.zipGreat Lakes Boreal Wolf Raw DataThis file contains raw Illumina sequence data for the Great Lakes Boeal Wolves (Canis lupus var). Please check the metadata to confirm and cross-reference sample IDs.GreatLakesBorealWolfRawData.zipGrey Wolf Raw DataThis file contains raw Illumina sequence data for the Grey Wolves (Canis lupus) and Dog (Canis lupus familiaris). Please check the metadata to confirm and cross-reference sample IDs.GreyWolfDogRawData.zipWestern Coyote Raw DataThis file contains raw Illumina sequence data for the Western Coyotes (Canis latrans). Please check the metadata to confirm and cross-reference sample IDs.WesternCoyoteRawData.zip Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.

Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.

The nesting population of greater sandhill cranes on Malheur National Wildlife Refuge, Oregon has declined from 236 pairs in 1971 to 181 pairs in 1986. Nesting studies conducted from 1966 to 1987 have repeatedly demonstrated that the primary limiting factor for cranes nesting on Malheur Refuge is the predation of eggs by ravens, raccoons, and coyotes, and the predations on prefledged chicks by coyotes. On 21 January 1986, Malheur Refuge staff assisted by U.S. Department of Agriculture Animal and Plant Health Inspection Service) employees began controlling predators on approximately 27,000 acres (14%) of Malheur Refuge. Recruitment of crane chicks in the predator control area (14.9%) was the highest ever recorded on the refuge. Because of the highly successful results recorded in 1986, the predator control area was expanded in 1987 to include approximately 46% (85,000 acres) of the refuge. In 1987, 460 coyotes were removed by the following methods: aerial gunning(80%), calling and shooting (8%), trapping and snares (7%), and denning (6%). An estimated 124 ravens were removed using 124 dozen chicken eggs injected with DRC-1339 and an additional 13 ravens were shot. Sixteen raccoons were taken by the following methods: snare 3, shooting 3, live trap 3, and leg hold trap 7. Overall crane production was 43 chicks, less than the 50 recorded last year but above the average annual production of 31. Recruitment was 10.6%, significantly higher than average (6.6%) but less than the record of 14.9% recorded in last year's predator control area. Additional nesting studies of ducks showed a similar pattern i.e., nesting success was well above long term averages but below the high levels recorded last year. The one notable exception was Canada geese which had the highest nesting success ever recorded on the refuge. The primary factors believed responsible for the diminished results in 1987 were: 1) much drier conditions in 1987 which reduced nesting habitat for cranes and attracted more coyotes to the refuge from adjacent arid areas, 2) slightly higher coyote populations county-wide, 3) less intense predator control efforts per acre in 1987 versus 1986, and 4) cool, wet weather in June that most likely increased chick mortality. The objectives of the 1987 effort were to have a nesting success of 75%, fledging success 25%, and recruitment 15%. The actual outcome was 57%, 17.1%, and 10.6% respectively. All of these outcomes were well above long-term averages but below objective levels. Based on these results, the 1987 season was judged a limited success. In comparing 1987 results with long term averages for nesting success and chick mortality the data suggests that a minimum of 17-18 chicks (same as last year) reached flight stage that would not have survived without predator control this year. It is recommended that control efforts for 1988 be held the same as 1987 with an increased effort to be given to all control efforts, particularly during April-flay.