Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou

Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)

Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.

Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid

Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.

Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines

Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.

Hide-and-Seek in a Highly Human-Dominated Landscape: Insights into Movement Patterns and Selection of Resting Sites of Rehabilitated Wolves (Canis lupus) in Northern Italy

Assessing the behavioural responses of floating wolves to human presence is crucial for investigating the chance of wolf populations expanding into urbanised landscapes. We studied the movement ecology of three rehabilitated wolves in a highly human-dominated landscape (Po Plain, Italy) to explore wolf's plasticity amid widespread human pressure. To reach this aim, we estimated individual 95% utilisation distributions (UD) after the release and inspected both 95% UDs and net squared displacements to identify individual movement patterns; tested for differences in movement patterns during day and night; and analysed the selection of resting sites during dispersal movement in a highly human-altered environment. Both the 95% UDs and step lengths were smaller for wolves settling in suitable areas than for those settling in more urbanised areas. All wolves exhibited strong temporal segregation with humans during all movement phases, particularly while dispersing across highly urbanised areas. Main roads and proximity to built-up areas were shown to limit wolves' dispersal, whereas small-wooded patches that provide shelter during rest facilitated long-distance movements. This study provides important insights into wolf movement and settling in urban and peri-urban areas, providing critical knowledge to promote human-carnivore coexistence.

Paint it black: first record of melanism in Canada lynx (Lynx canadensis)

Variation in coat colour within mammal species is of enduring interest, likely because of its potential to be either adaptive or maladaptive. Coat colour in the genus Lynx tends to be stable, with little variation within species compared to that of other felids. Canada lynx (Lynx canadensis) have coats that typically are silver grayish in winter and reddish brown in summer with dark spots, and black hairs on the tips of their tails and ears. A rare pallid colourmorph is occasionally observed, suggestive of partial albinism. Here, I report the first record of a melanistic Canada lynx. The individual was photographed during summer in the Yukon (Canada). It had a black coat containing whitish gray guard hairs throughout, as well as whitish gray hairs in the facial ruff and the rostrum and dorsal regions. There are only a small number of records of coat colour polymorphisms in the genus Lynx. The adaptive significance of melanism in lynx is unknown, but the loss of camouflage when hunting during winter is likely maladaptive.

Climatic comparison of the gray wolf (Canis lupus) subspecies in North America using niche-based distribution models and its implications for conservation programs

The gray wolf, Canis lupus, once inhabited much of the northern hemisphere worldwide; however, persecution drove its populations almost to extinction. In North America, diverse conservation programs have been implemented in the last decades to recover its populations in the wild, many of them guided by the historical distribution of the gray wolf subspecies. Over time, several authors have proposed different subspecies classifications. Nevertheless, most of them are mutually inconsistent regarding the number and distribution of subspecies, creating controversy when implementing conservation programs. This study used niche-based distribution models and cluster analysis to explore the bioclimatic profiles of C. lupus across North America and compare them with different subspecies classifications to identify environmental correlatives that support the proposed designations. Our cluster analysis results indicate that the optimal number of climatic groups was five, designated as Northern, Eastern, Western, Coastal, and Southern groups, with transitional overlap boundaries located at their peripheries, indicating climatic gradients between them and supporting the idea of intergrading zones. The geographic ranges of these groups mismatched to a different extent with all subspecies delimitations. In general, the boundaries of putative subspecies did not match the climatic patterns of North America. Our results may contribute to the recovery programs underway for this carnivore by identifying suitable areas for the release of individuals from specific lineages. New approaches to characterizing the intraspecific variation of the gray wolf should include all evidence available, including genetic, morphological, and ecological information.

The natural history and ecology of melanism in red wolf and coyote populations of the southeastern United States – evidence for Gloger’s rule

Background

Gloger’s rule postulates that animals should be darker colored in warm and humid regions where dense vegetation and dark environments are common. Although rare in Canis populations, melanism in wolves is more common in North America than other regions globally and is believed to follow Gloger’s rule. In the temperate forests of the southeastern United States, historical records of red wolf (Canis rufus) and coyote (Canis latrans) populations document a consistent presence of melanism. Today, the melanistic phenotype is extinct in red wolves while occurring in coyotes and red wolf-coyote hybrids who occupy the red wolf's historical range. To assess if Gloger’s rule could explain the occurrence and maintenance of melanistic phenotypes in Canis taxa, we investigated differences in morphology, habitat selection, and survival associated with pelage color using body measurements, GPS tracking data, and long-term capture-mark-recapture and radio-telemetry data collected on coyotes and hybrids across the southeastern United States.

Results

We found no correlation between morphometrics and pelage color for Canis taxa. However, we observed that melanistic coyotes and hybrids experienced greater annual survival than did their gray conspecifics. Furthermore, we observed that melanistic coyotes maintained larger home ranges and exhibited greater selection for areas with dense canopy cover and wetlands than did gray coyotes.

Conclusions

In the southeastern United States, pelage color influenced habitat selection by coyotes and annual survival of coyotes and hybrids providing evidence that Gloger’s rule is applicable to canids inhabiting regions with dense canopy cover and wetlands. Greater annual survival rates observed in melanistic Canis may be attributed to better concealment in areas with dense canopy cover such as coastal bottomland forests. We suggest that the larger home range sizes of melanistic coyotes may reflect the trade-off of reduced foraging efficiency in lower quality wetland habitat for improved survival. Larger home ranges and differential use of land cover by melanistic coyotes may facilitate weak assortative mating in eastern coyote populations, in which melanistic animals may have lower success of finding compatible mates in comparison to gray conspecifics. We offer that our observations provide a partial explanation for why melanism is relatively low (< 10%) but consistent within coyote populations throughout southeastern parts of their range.

The relevance of genetic structure in ecotype designation and conservation management

The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.

Automated genotyping of microsatellite loci from feces with high throughput sequences

Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.

Fast and flexible estimation of effective migration surfaces

Spatial population genetic data often exhibits ‘isolation-by-distance,’ where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.

A sliver of the past: The decimation of the genetic diversity of the Mexican wolf

The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

Conflicts with Wolves Can Originate from Their Parent Packs

Transmission of experience about prey and habitat supports the survival of next generation of wolves. Thus, the parent pack (PP) can affect whether young migrating wolves (loners) kill farm animals or choose to be in human environments, which generates human-wolf conflicts. Therefore, we researched whether the behavior of loners resembles PP behavior. After being extinct, 22 loners had entered the Netherlands between 2015 and 2019. Among them, 14 could be DNA-identified and linked with their PPs in Germany. Some loners were siblings. We assessed the behavior of each individual and PP through a structured Google search. PP behavior was determined for the loner's rearing period. Similarity between loner and PP behavior was significant (p = 0.022) and applied to 10 of 14 cases: like their PPs, three loners killed sheep and were near humans, five killed sheep and did not approach humans, while two loners were unproblematic, they did not kill sheep, nor were they near humans. Siblings behaved similarly. Thus, sheep killing and proximity to humans may develop during early-life experiences in the PP. However, by negative reinforcement that can be prevented. New methods are suggested to achieve that. As a result, new generations may not be problematic when leaving PPs.

Canada lynx (Lynx canadensis) gene flow across a mountain transition zone in western North America

Mountain ecotones have the potential to cause multiple patterns in divergence, from simple barrier effects to more fundamental ecological divergence. Most work in mountain ecotones in North America has focused on reinforcement between refugial populations, making prediction of how mountains impact species that are not restricted to separate glacial refugia remains difficult. This study focused on the Canada lynx (Lynx canadensis Kerr, 1792), a highly mobile felid considered to be a habitat and dietary specialist. Specifically, we used 14 microsatellite loci and landscape genetic tools to investigate if the Rocky Mountains and associated climatic transitions influence lynx genetic differentiation in western North America. Although lynx exhibited high gene flow across the region, analyses detected structuring of neutral genetic variation across our study area. Gene flow for lynx most strongly related to temperature and elevation compared with other landscape variables (terrain roughness, percent forest cover, and habitat suitability index) and geographic distance alone. Overall, genetic structure in lynx is most consistent with barrier effects created by the Rocky Mountains rather than ecological divergence. Furthermore, warmer temperatures had a measurable impact on gene flow, which suggests connectivity may further decrease in peripheral or fragmented populations as climate warms.

Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros

The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (Monodon monoceros) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyse 121 complete mitochondrial genomes from narwhals sampled across their range and use them in combination with species distribution models to elucidate the influence of past and ongoing climatic shifts on their population structure and demographic history. We find low levels of genetic diversity and limited geographic structuring of genetic clades. We show that narwhals experienced a long-term low effective population size, which increased after the Last Glacial Maximum, when the amount of suitable habitat expanded. Similar post-glacial habitat release has been a key driver of population size expansion of other polar marine predators. Our analyses indicate that habitat availability has been critical to the success of narwhals, raising concerns for their fate in an increasingly warming Arctic.

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R ST and F ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad-scale patterns of genetic structure and closely aligned with the R ST network. The F ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains

Background

The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated.

Methods

In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses.

Results

Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1.

Discussion

In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.

Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves

Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.

Migratory coupling between predators and prey

Animal migrations act to couple ecosystems and are undertaken by some of the world's most endangered taxa. Predators often exploit migrant prey, but the movements taken by these consumers are rarely studied or understood. We define such movements, where migrant prey induce large-scale movements of predators, as migratory coupling. Migratory coupling can have ecological consequences for the participating prey, predators and the communities they traverse across the landscape. We review examples of migratory coupling in the literature and provide hypotheses regarding conditions favourable for their occurrence. We also provide a framework for interactions induced by migratory coupling and demonstrate their potential community-level impacts by examining other forms of spatial shifts in predators. Migratory coupling integrates the fields of landscape, movement, food web and community ecologies, and represents an understudied frontier in ecology.

Cryptic population structure reveals low dispersal in Iberian wolves

Highly mobile mammalian carnivores are expected to have the capability to maintain high levels of gene flow across large geographic scales. Nonetheless, surprising levels of genetic structure have been found in many such populations. We combined genetic and spatial behavioural information from wolves (Canis lupus) in the Iberian Peninsula (Western Europe) during the last two decades to present a particular case of low dispersal levels in a large carnivore population persisting in human-dominated landscapes. We found an exceptionally reticulated pattern of cryptic population structure emerging at two hierarchical levels, in which four or eleven meaningful genetic clusters can be recognized, respectively. These clusters were characterized by moderate-high levels of differentiation (average pairwise F_ST = 0.09–0.19), low levels of admixture and varying degrees of genetic diversity. The number of dispersers identified among the 11 clusters was very low (<4% out of 218 wolves). Spatial information of tracked wolves further confirmed the geographical genetic patterns (only 2 out of 85 collared wolves overlapped with more than one genetic cluster). The high levels of genetic structure in this population may be determined by the recent demographic history of this population, among other factors. The identification of meaningful genetic clusters has implications for the delineation of conservation units and, consequently, on the conservation and management actions for Iberian wolves.

Disentangling genetic structure for genetic monitoring of complex populations

Genetic monitoring estimates temporal changes in population parameters from molecular marker information. Most populations are complex in structure and change through time by expanding or contracting their geographic range, becoming fragmented or coalescing, or increasing or decreasing density. Traditional approaches to genetic monitoring rely on quantifying temporal shifts of specific population metrics-heterozygosity, numbers of alleles, effective population size-or measures of geographic differentiation such as FST. However, the accuracy and precision of the results can be heavily influenced by the type of genetic marker used and how closely they adhere to analytical assumptions. Care must be taken to ensure that inferences reflect actual population processes rather than changing molecular techniques or incorrect assumptions of an underlying model of population structure. In many species of conservation concern, true population structure is unknown, or structure might shift over time. In these cases, metrics based on inappropriate assumptions of population structure may not provide quality information regarding the monitored population. Thus, we need an inference model that decouples the complex elements that define population structure from estimation of population parameters of interest and reveals, rather than assumes, fine details of population structure. Encompassing a broad range of possible population structures would enable comparable inferences across biological systems, even in the face of range expansion or contraction, fragmentation, or changes in density. Currently, the best candidate is the spatial Λ-Fleming-Viot (SLFV) model, a spatially explicit individually based coalescent model that allows independent inference of two of the most important elements of population structure: local population density and local dispersal. We support increased use of the SLFV model for genetic monitoring by highlighting its benefits over traditional approaches. We also discuss necessary future directions for model development to support large genomic datasets informing real-world management and conservation issues.

Panmixia and Limited Interspecific Introgression in Coyotes (Canis latrans) from West Virginia and Virginia, USA

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 with 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 2 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 with 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.

Pathology, clinical signs, and tissue distribution of Toxoplasma gondii in experimentally infected reindeer (Rangifer tarandus)

Toxoplasma gondii is a zoonotic parasite found in vertebrates worldwide for which felids serve as definitive hosts. Despite low densities of felids in northern Canada, Inuit people in some regions show unexpectedly high levels of exposure, possibly through handling and consumption of Arctic wildlife. Free-ranging caribou (Rangifer tarandus) are widely harvested for food across the Canadian North, show evidence of seroexposure to T. gondii, and are currently declining in numbers throughout the Arctic. We experimentally infected three captive reindeer (conspecific with caribou) with 1000, 5000 or 10,000 oocysts of T. gondii via stomach intubation to assess clinical signs of infection, pathology, and tissue distribution. An unexposed reindeer served as a negative control. Signs of stress, aggression, and depression were noted for the first two weeks following infection. By 4 weeks post infection, all infected reindeer were positive on a modified agglutination test at the highest titer tested (1:200) for antibodies to T. gondii. At 20 weeks post infection, no gross abnormalities were observed on necropsy. Following histopathology and immunohistochemistry, tissue cysts were visualized in the reindeer given the highest and lowest dose of oocysts. Focal pleuritis and alveolitis were associated with respiratory problems in reindeer given the middle dose. DNA of T. gondii was detected following traditional DNA extraction and conventional PCR on 25 mg samples from 17/33 muscles and organs, and by magnetic capture DNA extraction from 100 g samples from all 26 tissues examined. This research demonstrated that reindeer/caribou can serve as intermediate hosts for T. gondii, and that the parasite may be associated with health effects in wildlife. The presence of T. gondii in all tissues tested, many of which are commonly consumed raw, smoked, or dried in northern communities, suggests that caribou may serve as a source of human exposure to T. gondii.

Temporal and geographic patterns of kinship structure in common dolphins (Delphinus delphis) suggest site fidelity and female-biased long-distance dispersal

ABSTRACT

Social structure plays a crucial role in determining a species' dispersal patterns and genetic structure. Cetaceans show a diversity of social and mating systems, but their effects on dispersal and genetic structure are not well known, in part because of technical difficulties in obtaining robust observational data. Here, we combine genetic profiling and GIS analysis to identify patterns of kin distribution over time and space, to infer mating structure and dispersal patterns in short-beaked common dolphins (Delphinus delphis). This species is highly social, and exhibits weak spatial genetic structure in the Northeast Atlantic and Mediterranean Sea, thought to result from fluid social structure and low levels of site fidelity. We found that although sampled groups were not composed of closely related individuals, close kin were frequently found in the same geographic location over several years. Our results suggest that common dolphin exhibits some level of site fidelity, which could be explained by foraging for temporally varying prey resource in areas familiar to individuals. Dispersal from natal area likely involves long-distance movements of females, as males are found more frequently than females in the same locations as their close kin. Long-distance dispersal may explain the near panmixia observed in this species. By analysing individuals sampled in the same geographic location over multiple years, we avoid caveats associated with divergence-based methods of inferring sex-biased dispersal. We thus provide a unique perspective on this species' social structure and dispersal behaviour, and how it relates to the observed low levels of population genetic structure in European waters.

SIGNIFICANCE STATEMENT

Movement patterns and social interactions are aspects of wild animal's behaviour important for understanding their ecology. However, tracking these behaviours directly can be very challenging in wide-ranging species such as whales and dolphins. In this study, we used genetic information to detect how patterns of kin associations change in space and time, to infer aspects of movement and social structure. We identified previously unknown site fidelity, and suggested that dispersal usually involves females, travelling long distances from the natal area. Our data analysis strategy overcomes known limitations of previously used genetic inference methods, and provides a new approach to identify differences in dispersal between the sexes, which contribute to better understanding of the species' behaviour and ecology. In this case, we suggest that females are more likely to disperse than males, a pattern unusual amongst mammals.

Howl variation across Himalayan, North African, Indian, and Holarctic wolf clades: tracing divergence in the world's oldest wolf lineages using acoustics

Vocal divergence within species often corresponds to morphological, environmental, and genetic differences between populations. Wolf howls are long-range signals that encode individual, group, and subspecies differences, yet the factors that may drive this variation are poorly understood. Furthermore, the taxonomic division within the Canis genus remains contended and additional data are required to clarify the position of the Himalayan, North African, and Indian wolves within Canis lupus. We recorded 451 howls from the 3 most basal wolf lineages-Himalayan C. lupus chanco-Himalayan haplotype, North African C. lupus lupaster, and Indian C. lupus pallipes wolves-and present a howl acoustic description within each clade. With an additional 619 howls from 7 Holarctic subspecies, we used a random forest classifier and principal component analysis on 9 acoustic parameters to assess whether Himalayan, North African, and Indian wolf howls exhibit acoustic differences compared to each other and Holarctic wolf howls. Generally, both the North African and Indian wolf howls exhibited high mean fundamental frequency (F0) and short duration compared to the Holarctic clade. In contrast, the Himalayan wolf howls typically had lower mean F0, unmodulated frequencies, and short howls compared to Holarctic wolf howls. The Himalayan and North African wolves had the most acoustically distinct howls and differed significantly from each other and to the Holarctic wolves. Along with the influence of body size and environmental differences, these results suggest that genetic divergence and/or geographic distance may play an important role in understanding howl variation across subspecies.

Environmental and anthropogenic drivers of connectivity patterns: A basis for prioritizing conservation efforts for threatened populations

Ecosystem fragmentation and habitat loss have been the focus of landscape management due to restrictions on contemporary connectivity and dispersal of populations. Here, we used an individual approach to determine the drivers of genetic differentiation in caribou of the Canadian Rockies. We modelled the effects of isolation by distance, landscape resistance and predation risk and evaluated the consequences of individual migratory behaviour (seasonally migratory vs. sedentary) on gene flow in this threatened species. We applied distance-based and reciprocal causal modelling approaches, testing alternative hypotheses on the effects of geographic, topographic, environmental and local population-specific variables on genetic differentiation and relatedness among individuals. Overall, gene flow was restricted to neighbouring local populations, with spatial coordinates, local population size, groups and elevation explaining connectivity among individuals. Landscape resistance, geographic distances and predation risk were correlated with genetic distances, with correlations threefold higher for sedentary than for migratory caribou. As local caribou populations are increasingly isolated, our results indicate the need to address genetic connectivity, especially for populations with individuals displaying different migratory behaviours, whilst maintaining quality habitat both within and across the ranges of threatened populations.

New insights on the history of canids in Oceania based on mitochondrial and nuclear data

How and when dingoes arrived in Oceania poses a fascinating question for scientists with interest in the historical movements of humans and dogs. The dingo holds a unique position as top terrestrial predator of Australia and exists in a wild state. In the first geographical survey of genetic diversity in the dingo using whole mitochondrial genomes, we analysed 16,428 bp in 25 individuals from five separate populations. We also investigated 13 nuclear loci to compare with the mitochondrial population history patterns. Phylogenetic analyses based upon mitochondrial DNA and nuclear DNA support the hypothesis that there are at least two distinct populations of dingo, one of which occurs in the northwest and the other in the southeast of the continent. Conservative molecular dating based upon mitochondrial DNA suggest that the lineages split approximately 8300 years before present, likely outside Australia but within Oceania. The close relationship between dingoes and New Guinea Singing Dogs suggests that plausibly dingoes spread into Australia via the land bridge between Papua New Guinea and Australia although seafaring introductions cannot be rejected. The geographical distribution of these divergent lineages suggests there were multiple independent dingo immigrations. Importantly, the observation of multiple dingo populations suggests the need for revision of existing conservation and management programs that treat dingoes as a single homogeneous population.

Intestinal parasites of gray wolves (Canis lupus) in northern and western Canada

Gray wolves (Canis lupus L., 1758) are mobile opportunistic predators that can be infected by a wide range of parasites, with many acquired via predator–prey relationships. Historically, many of these parasites were identified only to genus or family, but genetic tools now enable identification of parasite fauna to species and beyond. We examined 191 intestines from wolves harvested for other purposes from regions in the Northwest Territories, British Columbia, Saskatchewan, and Manitoba. Adult helminths were collected from intestinal contents for morphological and molecular identification, and for a subset of wolves, fecal samples were also analyzed to detect helminth eggs and protozoan (oo)cysts. Using both detection methods, we found that 83% of 191 intestines contained one or more parasite species, including cestodes (Taenia spp., Echinococcus spp., and Diphyllobothrium sp.), nematodes (Uncinaria stenocephala Railliet, 1884, Trichuris spp., Physaloptera spp., and Toxascaris leonina (von Linstow, 1902)), a trematode (Alaria sp.), and protozoa (Sarcocystis spp., Giardia sp., and Cryptosporidium spp.). Molecular characterization identified one species of Diphyllobothrium (Diphyllobothrium latum (L., 1758) Cobbold, 1858), three species of Taenia (Taenia krabbei Moniez, 1879, Taenia hydatigena Pallas, 1766, and Taenia multiceps Leske, 1786), and two Giardia duodenalis (Davaine) Deschiens, 1921 assemblages (B and C). These results demonstrate the diverse diet of wolves and illustrate the possibility of parasite spillover among wildlife, domestic animals, and people.

Variation in the intensity and prevalence of macroparasites in migratory caribou: a quasi-circumpolar study

Comparative studies across time and geographical regions are useful to improve our understanding of the health of wildlife populations. Our goal was to study parasitism in migratory caribou (Rangifer tarandus (L., 1758)) of North America and Greenland. A total of 1507 caribou were sampled across 12 herds to assess seven of their main helminth and arthropod macroparasites between 1978 and 2010. We sought to determine which factors such as sex, age class, herd size, and season best explained the prevalence and intensity of those parasites. Intensity of warble fly (Hypoderma tarandi (L., 1758)) larvae increased with age for males, whereas the opposite was observed in females. Prevalence of giant liver flukes (Fascioloides magna (Bassi, 1875) Ward, 1917), tapeworm Taenia hydatigena Pallas, 1766, and nose bot fly (Cephenemyia trompe (Modeer, 1786)) larvae was higher in adults than in calves. Prevalence of F. magna and T. hydatigena was higher at high herd size than at lower herd size. Greenland herds had the lowest prevalence of T. hydatigena and of the tapeworm Taenia krabbei Moniez, 1879, a higher intensity of H. tarandi, and a higher prevalence of C. trompe than the other herds. Of the herds from Quebec and Labrador, the Rivière-George herd had a higher prevalence of F. magna than the Rivière-aux-Feuilles herd. Our research provides the first comparative survey of these parasites of caribou across a broad spatial–temporal range.

Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (H_D  = 0.904 ± 0.011 and H_D  = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (F_ST  = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.