Population genomics of grey wolves and wolf-like canids in North America

Late Pleistocene onset of mutualistic human/canid (Canis spp.) relationships in subarctic Alaska

Large canids (wolves, dogs, and coyote) and people form a close relationship in northern (subarctic and arctic) socioecological systems. Here, we document the antiquity of this bond and the multiple ways it manifested in interior Alaska, a region key to understanding the peopling of the Americas and early northern lifeways. We compile original and existing genomic, isotopic, and osteological canid data from archaeological, paleontological, and modern sites. Results show that in contrast to canids recovered in non-anthropic contexts, canids recovered in association with human occupations are markedly diverse. They include multiple species and intraspecific lineages, morphological variation, and diets ranging from terrestrial to marine. This variation is expressed along both geographic and temporal gradients, starting in the terminal Pleistocene with canids showing high marine dietary estimates. This paper provides evidence of the multiple ecological relationships between canids and people in the north-from predation, probable commensalism, and taming, to domestication-and of their early onset.

A map of canine sequence variation relative to a Greenland wolf outgroup

For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.

Estimation of spatial demographic maps from polymorphism data using a neural network

A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity-by-descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN.

Estimation of spatial demographic maps from polymorphism data using a neural network

A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity by descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology, and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN .

Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.

Population genomics of the muskox' resilience in the near absence of genetic variation

Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.

Genomic insights into the conservation of wild and domestic animal diversity: A review

Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.

Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization

Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.

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.

From high masked to high realized genetic load in inbred Scandinavian wolves

When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.

Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast

Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.

An assessment of mercury and its dietary drivers in fur of Arctic wolves from Greenland and High Arctic Canada

Mercury has become a ubiquitous hazardous element even ending up in pristine areas such as the Arctic, where it biomagnifies and leaves especially top predators vulnerable to potential health effects. Here we investigate total mercury (THg) concentrations and dietary proxies for trophic position and habitat foraging (δ¹⁵N and δ¹³C, respectively) in fur of 30 Arctic wolves collected during 1869-1998 in the Canadian High Arctic and Greenland. Fur THg concentrations (mean ± SD) of 1.46 ± 1.39 μg g ^-1 dry weight are within the range of earlier reported values for other Arctic terrestrial species. Based on putative thresholds for Hg-mediated toxic health effects, the studied Arctic wolves have most likely not been at compromised health. Dietary proxies show high dietary plasticity among Arctic wolves deriving nutrition from both marine and terrestrial food sources at various trophic positions. Variability in THg concentrations seem to be related to the wolves' trophic position rather than to different carbon sources or regional differences (East Greenland, the Foxe Basin and Baffin Bay area, respectively). Although the present study remains limited due to the scarce, yet unique historic study material and small sample size, it provides novel information on temporal and spatial variation in Hg pollution of remote Arctic species.

From STRs to SNPs via ddRAD-seq: Geographic assignment of confiscated tortoises at reduced costs

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

Demography and evolutionary history of grey wolf populations around the Bering Strait

Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived^1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.

The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves

Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.

The Australian dingo is an early offshoot of modern breed dogs

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.¹ Although dogs of variable size are found in the archeological record,^2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.⁵ Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.^6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.⁸ The identification of a functional mutation associated with IGF1 has thus far proven elusive.^6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Maybe So, Maybe Not: Canis lepophagus at Hagerman Fossil Beds National Monument, Idaho, USA

A canid dentary is described from the Pliocene Glenns Ferry Formation at Hagerman Fossil Beds National Monument, south-central Idaho, USA. The specimen possesses traits in alliance with and measurements falling within or exceeding those of Canis lepophagus. The dentary, along with a tarsal IV (cuboid) and an exploded canine come from the base of the fossiliferous Sahara complex within the monument. Improved geochronologic control provided by new tephrochronologic mapping by the U.S. Geological Survey-National Park Service Hagerman Paleontology, Environments, and Tephrochronology Project supports an interpolated age of approximately 3.9 Ma, placing it in the early Blancan North American Land Mammal Age. It is conservatively referred to herein as Canis aff. C. lepophagus with the caveat that it is an early and robust example of that species. A smaller canid, initially assigned to Canis lepophagus and then to Canis ferox, is also known from Hagerman. Most specimens of Canis ferox, including the holotype, were recently reassigned to Eucyon ferox, but specimens from the Hagerman and Rexroad faunas were left as Canis sp. and possibly attributed to C. lepophagus. We agree that these smaller canids belong in Canis and not Eucyon but reject placing them within C. lepophagus; we refer to them here as Hagerman-Rexroad Canis. This study confirms the presence of two approximately coyote-sized canids at Hagerman and adds to the growing list of carnivorans now known from these fossil beds.

The genome sequence of the grey wolf, Canis lupus Linnaeus 1758

We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.

Evolutionary history of the extinct Sardinian dhole

The Sardinian dhole (Cynotherium sardous)¹ was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene.^2-5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor.^3,6-9 Morphometric analyses^3,6,8-12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca-21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids-probably a result of the long-term isolation-that could have contributed to the subsequent extinction of the Sardinian dhole.

Interface of Human/Wildlife Interactions: An Example of a Bold Coyote (Canis latrans) in Atlanta, GA, USA

There is arguably no other North American species that better illustrates the complexities of the human-wildlife interface than the coyote. In this study, a melanistic coyote in metropolitan Atlanta, Georgia was exhibiting unusually bold behaviors that included encounters with humans, domestic dogs, and attempts to enter homes. After tracking this coyote (nicknamed Carmine) across a highly urbanized landscape with participatory science, including at least 80 publicly reported sightings, he was captured and relocated to a wildlife sanctuary. Genome-wide analyses revealed 92.8% coyote ancestry, 1.7% gray wolf ancestry, and 5.5% domestic dog ancestry. The dog alleles in Carmine’s genome were estimated to have been acquired by his ancestors 14–29 years ago. Despite his bold behavior, Carmine did not carry any mutations known to shape hypersociability in canines. He did, however, carry a single copy of the dominant mutation responsible for his melanistic coat color. This detailed study of Carmine dispels common assumptions about the reticent coyote personality and the origins of behavior. His unusual bold behavior created a higher level of human-coyote interaction. He now serves as a public ambassador for human-wildlife coexistence, urging the global community to reconsider mythologies about wildlife and promote coexistence with them in landscapes significantly altered by human activity in our rapidly changing world.

Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification

Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred in the Early Pliocene (∼ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred during the Early Pleistocene (∼1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ∼0.66 and ∼0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Unveiling the Fecal Microbiota in Two Captive Mexican Wolf (Canis lupus baileyi) Populations Receiving Different Type of Diets

Simple Summary

The Mexican wolf (Canis lupus baileyi) is an endangered canine. Both Mexico and the United States are currently collaborating to reproduce and reintroduce individuals to their original habitats. However, keeping these wolves in captivity represents a great commitment to meet their basic needs. Diet is a determining factor that is closely related to health and reproductive fitness. The type of diet that is fed to canines in captivity must provide the required nutrients for their development and welfare. The study of the fecal microbiota is a non-invasive way to establish the abundance and diversity of bacterial communities to determine if they are in a healthy condition. We analyzed data from two captive populations of Mexican wolves (i.e., northern and central Mexico) receiving different type of diets (Michilia population: mainly kibble vs. Ocotal population: mainly raw meat). The operational taxonomic units (OTUs) in Michilia resulted in 204 genera and 316 species, while in Ocotal there were 232 genera and 379 species. In the Michilia, dominance of bacteria that degrade carbohydrates was observed (related to kibble diet). In contrast, the Ocotal microbiota was dominated by protein-degrading bacteria (related to raw meat diet). The main outcomes generated in this study should help to enhance the welfare of the captive Mexican wolves to increase its numbers.

Abstract

The Mexican wolf (Canis lupus baileyi) was once distributed in southern United States and northern Mexico. It is an endangered subspecies detached from the gray wolf, and likely exemplifies one of the original migration waves of C. lupus into the new world. This is a canine whose individuals survive in specialized facilities, zoos, and museums as part of captive-breeding programs. In order to contribute to the improvement of the management of this species and favor its long-term conservation in Mexico, we aimed to evaluate the diversity and abundance of the fecal bacterial microbiota in two populations exposed to different types of diet: (1) Michilia (23° N, 104° W); kibble daily and raw meat sporadically, and (2) Ocotal (19° N, 99° W); raw meat daily and live animals periodically. Next generation sequencing (V3-V4 16S rRNA gene) by Illumina was implemented. The operational taxonomic units (OTUs) in Michilia resulted in 9 phyla, 19 classes, 34 orders, 61 families, 204 genera, and 316 species, while in Ocotal there were 12 phyla, 24 classes, 37 orders, 69 families, 232 genera, and 379 species. Higher estimated Chao1 richness, Shannon diversity, and core microbiota were observed in Ocotal. Differences (p < 0.05) between populations occurred according to the Bray–Curtis beta diversity index. In the Michilia, dominance of bacteria that degrade carbohydrates (Firmicutes, Lachnospiraceae, Blautia, Clostrodium, Eisenbergiella, Romboutsia, and Ruminococcus) was observed; they are abundant in kibble diets. In contrast, the Ocotal microbiota was dominated by protein-degrading bacteria (Fusobacteria, Fusobacteriaceae, and Fusobacteria), indicating a possible positive relation with a raw meat diet. The information generated in this study is fundamental to support the implementation of better management plans in the two populations considered here, as well as in different facilities of southern United States and Mexico, where this subspecies is kept in captivity for conservation purposes.

Considering Pleistocene North American wolves and coyotes in the eastern Canis origin story

The evolutionary origins and hybridization patterns of Canis species in North America have been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes are most often partitioned into a 2-species model that assigns all ancestry to gray wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored potential Pleistocene era progenitors and opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to: (a) identify potential Pleistocene progenitors to southern North American gray wolves and eastern wolves; and (b) illuminate opportunities for ancient hybridization events. Specifically, we propose that Beringian gray wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) are likely progenitors to Mexican and Plains gray wolves and eastern wolves, respectively, and may represent a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.

Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote

The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.

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.

Updating the Bibliography of Interbreeding among Canis in North America

This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.

Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in N_e between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.

Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.

Population genomics for wildlife conservation and management

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

Origins and genetic legacy of prehistoric dogs

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

Illuminating the mysteries of wolf history

One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

see also the Perspective by Rena M. Schweizer and Robert K. Wayne.

Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage

The evolutionary relationships between extinct and extant lineages provide important insight into species' response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period's profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves' evolutionary history, and could have facilitated their adaptation to environmental change.

Complete mitochondrial genome of the Greenland wolf, Canis lupus orion

The Greenland wolf, Canis lupus orion as s subspecies of the gray wolf, is native to Greenland. Here, we assembled a complete 16,650 bp genome for the C. l. orion mitochondrion by employing Illumina HiSeq platform. The complete mitochondrial genome contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. Overall DNA sequence of the C. l. orion mitochondrion was identical to that of gray wolf C. l. lupus, although slight difference was observed in their control regions. The genomic structure of C. l. orion mitochondrion was conserved with the gene arrangements of mitogenomes published in Canidae, and phylogenetic analysis confirmed the sister relationship among Canis sp. This information will provide essential molecular reference to elucidate biogeography, phylogenetic distance, and evolutionary history in gray wolves.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.