Rediscovery of red wolf ghost alleles in canid population along the American Gulf Coast

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7000 single nucleotide polymorphisms (SNPs) in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges

Population genomic analysis of North American eastern wolves (Canic lycaon) support their conservation priority status

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them

Urban colonization through multiple genetic lenses: The city‐fox phenomenon revisited

Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human‐modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome‐wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC‐linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world

EVOLUTIONARY PROCESSES IN RECENTLY EXPANDED COYOTE (CANIS LATRANS) POPULATIONS: A GENETIC INVESTIGATION OF SUBDIVISION, SELECTION, AND ADMIXTURE EVENTS

Coyotes (Canis latrans), a North American evolved canid, were historically limited to the western half of the continent but have recently undergone a spectacular range expansion. Though range expansions are ubiquitous in nature, with well-described theoretical expectations for reduced diversity, selection for dispersal-related traits, and gene flow with established populations, comparatively few empirical studies have demonstrated these evolutionary processes at the genetic level. Using various molecular approaches, I investigate these processes across two populations of recently expanded coyotes in eastern North America. In chapter one, I demonstrate that population subdivisions correspond to the two known eastern expansion fronts, with an emerging mid-Atlantic contact zone between these two populations. In chapter two, I show that genome-wide diversity is relatively high in both recently expanded populations, which contrasts with the theoretical expectations for populations to bottleneck during range expansion. Further, I identify three genes with known functions in dispersal-related traits that may have been under selection during range expansion in both populations. In chapters three and four, I describe recent and on-going admixture between coyotes and closely related red wolves (C. rufus) on a genome-wide scale. In particular, I characterize a previously unknown admixture zone along the American Gulf Coast, where hybridization among red wolves and encroaching coyotes likely occurred prior to the 1980s, and genetic admixtures still persist today. Overall, these studies highlight how recent advances in genomic sequencing techniques allow complex evolutionary questions to be addressed in wild populations

EVOLUTIONARY PROCESSES IN RECENTLY EXPANDED COYOTE (CANIS LATRANS) POPULATIONS: A GENETIC INVESTIGATION OF SUBDIVISION, SELECTION, AND ADMIXTURE EVENTS

Coyotes (Canis latrans), a North American evolved canid, were historically limited to the western half of the continent but have recently undergone a spectacular range expansion. Though range expansions are ubiquitous in nature, with well-described theoretical expectations for reduced diversity, selection for dispersal-related traits, and gene flow with established populations, comparatively few empirical studies have demonstrated these evolutionary processes at the genetic level. Using various molecular approaches, I investigate these processes across two populations of recently expanded coyotes in eastern North America. In chapter one, I demonstrate that population subdivisions correspond to the two known eastern expansion fronts, with an emerging mid-Atlantic contact zone between these two populations. In chapter two, I show that genome-wide diversity is relatively high in both recently expanded populations, which contrasts with the theoretical expectations for populations to bottleneck during range expansion. Further, I identify three genes with known functions in dispersal-related traits that may have been under selection during range expansion in both populations. In chapters three and four, I describe recent and on-going admixture between coyotes and closely related red wolves (C. rufus) on a genome-wide scale. In particular, I characterize a previously unknown admixture zone along the American Gulf Coast, where hybridization among red wolves and encroaching coyotes likely occurred prior to the 1980s, and genetic admixtures still persist today. Overall, these studies highlight how recent advances in genomic sequencing techniques allow complex evolutionary questions to be addressed in wild populations

High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations

Range expansion is a widespread biological process, with well‐described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome‐wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction‐associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well‐publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts

Swiss fox MHC-linked microsatellite genotypes

This data file contains genotypes for nine microsatellite markers linked to major histocompatibility complex (MHC) genes that were genotyped in 100 red foxes (Vulpes vulpes) sampled in Zurich, Switzerland. Metadata includes sample identification number, sampling location, habitat type, and sex. The five sampling locations span urban (Ueast and Uwest) and rural (Reast, Rwest, and Rnorth) habitats in and around Zurich. Please see the map provided in the inset of Figure 2 to better visualize sampling locations. Missing genotype data is indicated with zeros

A Genome-wide perspective on the persistence of red wolf ancestry in southeastern canids.

The red wolf (Canis rufus), a legally recognized and severely endangered wolf, is known to interbreed with coyotes (C. latrans). Declared extirpated in the wild in 1980, red wolves were reintroduced to North Carolina nearly a decade later. Interbreeding with coyotes was thought to be restricted to a narrow geographic region adjacent to the reintroduced population and largely believed to threaten red wolf recovery. However, red wolf ancestry has recently been discovered in canids along the American Gulf Coast, igniting a broader survey of endangered ancestry in southeastern canid populations. Here, we examine geographic and temporal patterns of genome-wide red wolf ancestry in 260 canids across the southeastern United States at over 164,000 SNP loci. We found that red wolf ancestry was most prevalent in canids sampled from Texas in the mid-1970s, although non-trivial amounts of red wolf ancestry persisted in this region today. Further, red wolf ancestry was also observed in coyotes of North Carolina, despite management efforts to limit the occurrence of hybridization events. Lastly, we found no evidence of substantial red wolf ancestry in southeastern canids outside of these two admixture zones. Overall, this study provides a genome-wide survey of red wolf ancestry in canids across the southeastern United States, which may ultimately inform future red wolf restoration efforts