Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics

Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages

Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.

Conservation genomics of wolves: The global impact of RK Wayne's research

RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.

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.

Understanding carnivore interactions in a cold arid trans-Himalayan landscape: What drives co-existence patterns within predator guild along varying resource gradients?

Predators compete for resources aggressively, forming trophic hierarchies that shape the structure of an ecosystem. Competitive interactions between species are modified in the human-altered environment and become particularly important where an introduced predator can have negative effects on native predator and prey species. The trans-Himalayan region of northern India has seen significant development in tourism and associated infrastructure over the last two decades, resulting in many changes to the natural setting of the landscape. While tourism, combined with unmanaged garbage can facilitate red fox (Vulpes vulpes), it also allows free-ranging dogs (Canis lupus familiaris), an introduced mesopredator to thrive, possibly more than the native red fox. We look at the little-known competitive dynamics of these two meso-carnivores, as well as their intra-guild interactions with the region's top carnivores, the snow leopard (Panthera uncia) and the Himalayan wolf (Canis lupus chanco). To study interactions between these four carnivores, we performed multispecies occupancy modeling and analyzed spatiotemporal interactions between these predators using camera trap data. We also collected scat samples to calculate dietary niche overlaps and determine the extent of competition for food resources between these carnivores. The study found that, after controlling for habitat and prey covariates, red fox site use was related positively to snow leopard site use, but negatively to dog and wolf site use. In addition, site use of the dog was associated negatively with top predators, that is, snow leopard and Himalayan wolf, while top predators themselves related negatively in their site use. As anthropogenic impacts increase, we find that these predators coexist in this resource-scarce landscape through dietary or spatiotemporal segregation, implying competition for limited resources. Our research adds to the scant ecological knowledge of the predators in the region and improves our understanding of community dynamics in human-altered ecosystems.

Citizen science facilitates first ever genetic detection of wolf-dog hybridization in Indian savannahs

Human demographic expansion has confined wildlife to fragmented habitats, often in proximity to human-modified landscapes. Such interfaces facilitate increased interactions between feral or domesticated animals and wildlife, posing a high risk to wild species. This is especially relevant for free-ranging dogs (Canis lupus familiaris) and wild canids like gray wolves (Canis lupus) and golden jackals (Canis aureus). Wolf-dog hybridization may lead to a significant reduction of specific adaptations in wolves that could result in the decline of wolf populations. Detection and genetic discrimination of hybrids between dogs and wolves are challenging because of their complex demographic history and close ancestry. Citizen scientists identified two phenotypically different-looking individuals and subsequently collected non-invasive samples that were used by geneticists to test wolf-dog hybridization. Genomic data from shed hair samples of suspected hybrid individuals using double-digest restriction-site-associated DNA (ddRAD) sequencing resulted in 698 single nucleotide polymorphism (SNP) markers. We investigated the genetic origin of these two individuals analyzed with genetically known dogs, wolves, and other canid species including jackals and dholes (Cuon alpinus). Our results provide the first genetic evidence of one F2 hybrid and the other individual could be a complex hybrid between dogs and wolves. Our results re-iterate the power of next-generation sequencing (NGS) for non-invasive samples as an efficient tool for detecting hybrids. Our results suggest the need for more robust monitoring of wolf populations and highlight the tremendous potential for collaborative approaches between citizens and conservation scientists to detect and monitor threats to biodiversity.

The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica)

The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.

Evolutionary legacy of the extirpated red wolf clings to life in gulf-coast canids

Before Europeans colonized North America, a uniquely American wolf roamed the eastern forests of southern Canada to Florida and west to the Great Plains. Known today as "red wolf" (Canis rufus) in the south and "eastern wolf" (Canis lycaon) in the north, evidence suggests that these indigenous forest wolves shared a common evolutionary history until only a few centuries ago when they were extirpated from the intervening majority of their historical range. While the eastern wolf persists today primarily as a small population in Algonquin Provincial Park, Canada, the red wolf was ostensibly driven from its last stronghold in gulf-coastal Louisiana and Texas by 1980. The last-known red wolves were taken captive for propagation and reintroduction. Today, the red wolf exists as ~250 descendants of 12 founders and are distributed among 42 captive breeding facilities and one reintroduced population in coastal North Carolina. As red and eastern wolves declined in the 20th century, coyotes expanded from the west into the eastern forests, replacing them. Along with human persecution, coyote hybridization has been blamed for the late 20th century demise of the red wolf. However, rather than helping to drive the red wolf to extinction, coyote hybridization may have instead helped to preserve it. In this issue of Molecular Ecology, vonHoldt and colleagues provide the most comprehensive description yet of the substantial quantity and distribution of red wolf ancestry sequestered in southeastern coyote populations. They find the highest frequency of red wolf genes in coyotes from the gulf-coastal sites where the last known wild red wolves occurred, but also present evidence for a high prevalence of red wolf genes in coyotes throughout the southeastern expansion zone. Given the significant reduction in genetic diversity in extant red wolves owing to their late 20th century population bottleneck, this coyote-sequestered reservoir of red wolf genes could prove an important resource for red wolf conservation.

Feeding Patterns of Three Widespread Carnivores—The Wolf, Snow Leopard, and Red Fox—in the Trans-Himalayan Landscape of India

The Trans-Himalayan landscape is an extreme cold desert with limited diversity and a low density of wild prey. The landscape has three widespread carnivores—the wolf Canis lupus chanco, snow leopard Panthera uncia, and red fox Vulpes vulpes—competing for similar prey. We studied predation patterns, dietary competition, and niche segregation of three sympatric carnivores in the Indian Trans-Himalayas. The Himalayan or wooly wolf is one of the oldest lineages and has adapted to extreme cold. We further studied the prey selection of the wolf in the high-altitude environment. We collected 1,600 carnivore scats (wolf = 542, snow leopard = 31, and red fox = 1,027), and additional data on 573 snow leopard scats from literature was used in the analyses. We found that livestock was a major contributor to the wolf (56.46%) and snow leopard diet (30.01%). The wolf consumed blue sheep (8.26%) and ibex (3.13%), whereas the snow leopard subsisted on blue sheep (30.79%) and ibex (17.15%), relatively more frequently. The red fox preyed upon small species like pika and marmots (18.85 %); however, livestock carrions (16.49%), fruits and seeds (15.05%), and human-derived material (11.89%) were also consumed frequently. The dietary niche of three carnivore species highly overlapped (Pianka's index = 0.503, simulated mean = 0.419, p = 0.15) due to livestock. The carnivores segregated their diet in prey items originating from the wild. We tested a relationship between carnivore diet variations and prey/predator functional traits using RLQ ordination. Predator morphology traits like body size, weight, and habitat preference significantly affected the prey selection (p < 0.05). The wolf and snow leopard avoided the competition through habitat selection, while the red fox coexisted by exploiting a broader niche. The wolf showed site-specific variation in prey preferences albeit no prey selection at the landscape level (G2 = 6.79, df = 12, p = 0.87). The wolf preferred wild prey over domestic species at the wild prey rich site. The carnivores in this pastoralist landscape have adapted to exploit livestock resources despite facing persecution. Therefore, managing livestock and simultaneously restoring wild prey is crucial for the conservation of the carnivore guild in the Trans-Himalayan ecosystem.

Tree House Explorer: A Novel Genome Browser for Phylogenomics

Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations (GFF/GTF), recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.

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.

Modeling Potential Impacts of Climate Change on the Distribution of Wooly Wolf (Canis lupus chanco)

The Central Asian wolves form a cohort within the wolf-dog clade known as the wooly wolf (Canis lupus chanco). These wolves are poorly studied and their current extent and distribution remain unknown. Apex predators already existing at higher elevations like wooly wolves can be severely affected by climate change because of the absence of suitable refuge. Concomitantly, in the era of Anthropocene, the change in land use land cover (LULC) is rapidly increasing. Even the most adaptable species occurring in human-dominated landscapes may fail to survive under the combined impact of both climate change and human pressure. We collected 3,776 presence locations of the wooly wolf across its range from published literature and compiled 39 predictor variables for species distribution modeling, which included anthropogenic factors, climatic, vegetation, and topographic features. We predicted the change in their distribution under different anthropogenic factors, climate change, and land-use land-cover change scenarios. Wolf showed affinity toward areas with low to moderately warm temperatures and higher precipitations. It showed negative relationships with forests and farmlands. Our future projections showed an expansion of wolf distribution and habitat suitability under the combined effects of future climate and LULC change. Myanmar and Russia had the introduction of high and medium suitability areas for the wooly wolf in future scenarios. Uzbekistan and Kazakhstan showed the consistent loss in high suitability areas while Mongolia and Bhutan had the largest gain in high suitability areas. The study holds great significance for the protection and management of this species and also provides opportunities to explore the impact on associated species.

Comparative Ecological Perspectives of Two Ancient Lineages of Gray Wolves: Woolly Wolf (Canis lupus chanco) and Indian Wolf (Canis lupus pallipes)

Geographical isolation can often lead to speciation, and two disconnected populations of the same species living in drastically different bioclimatic regions provide an opportunity to understand the process of speciation. The Woolly wolf is found in the cold-arid, Trans-Himalayan landscape, while the Indian wolf inhabits the semi-arid grasslands of Central India. Both the lineages of wolves from India have generated scientific debate on their taxonomic status in recent years. In this study, we collected data and reviewed published literature to document the ecological and behavioral differences between the Woolly wolf and the Indian wolf. Most studies have used genetic data; hence we discuss variation in spatial ecology, habitat preferences, vocalization, diet diversity and cranial measurements of these two subspecies. The spatial ecology of two lineages was compared from the data on three Woolly and ten Indian wolves tagged with GPS collars. The telemetry data shows that there has been no difference in the day-night movement of Woolly wolves, whereas Indian wolves show significant high displacement during the night. The BBMM method indicated that Woolly wolf home ranges were three times larger than the Indian wolf. The Woolly wolf diet is comprised of 20 different types of food items, whereas the Indian wolf diet consists of 17 types. The Woolly and Indian wolf largely depend upon domestic prey base, i.e., 48.44 and 40.34%, respectively. We found no differences in the howling parameters of these subspecies. Moreover, the Woolly wolf skull was significantly longer and broader than the Indian wolf. Wolves of India are ancient and diverged from the main clade about 200,000–1,000,000 years ago. Their genetic and ecological evolution in different bioclimatic zones has resulted in considerable differences as distinct subspecies. The present study is a step in understanding ecological differences between two important, genetically unique subspecies of wolves.

Distribution, Status, and Conservation of the Indian Peninsular Wolf

An understanding of the distribution range and status of a species is paramount for its conservation. We used photo captures from 26,838 camera traps deployed over 121,337 km2 along with data from radio-telemetry, published, and authenticated wolf sightings to infer wolf locations. A total of 3,324 presence locations were obtained and after accounting for spatial redundancy 574 locations were used for modeling in maximum entropy framework (MaxEnt) with ecologically relevant covariates to infer potentially occupied habitats. Relationships of wolf occurrence with eco-geographical variables were interpreted based on response curves. Wolves avoided dense wet forests, human disturbances beyond a threshold, arid deserts, and areas with high top-carnivore density, but occurred in semi-arid scrub, grassland, open forests systems with moderate winter temperatures. The potential habitat that can support wolf occupancy was 364,425 km2 with the largest wolf habitat available in western India (Saurashtra-Kachchh-Thar landscape 102,837 km2). Wolf habitats across all landscapes were connected with no barriers to dispersal. Breeding packs likely occurred in ≈89,000 km2. Using an average territory size of 188 (SE 23) km2, India could potentially hold 423–540 wolf packs. With an average adult pack size of 3 (SE 0.24), and a wolf density < 1 per 100 km2 in occupied but non-breeding habitats, a wolf population of 3,170 (SE range 2,568–3,847) adults was estimated. The states of Madhya Pradesh, Rajasthan, Gujarat, and Maharashtra were major strongholds for the species. Within forested landscapes, wolves tended to avoid top-carnivores but were more sympatric with leopards and dhole compared to tigers and lions. This ancient wolf lineage is threatened by habitat loss to development, hybridization with dogs, fast-traffic roads, diseases, and severe persecution by pastoralists. Their status is as precarious as that of the tiger, yet focused conservation efforts are lacking. Breeding habitat patches within each landscape identified in this study should be made safe from human persecution and free of feral dogs so as to permit packs to breed and successfully recruit individuals to ensure wolf persistence in the larger landscape for the long term.

Disentangling the admixed trails of grey wolf evolution

The predominant phylogenetic patterns within a genome do not always reflect correctly the history of evolutionary divergence and speciation, and the true phylogenetic signal tends to be concentrated within low-recombination regions of the genome. In this issue of Molecular Ecology, Hennelly et al. show that this is also the case for intraspecific relationships that are characterized by considerable gene flow between lineages. The study reconstructs the phylogenetic relationships of Indian and Tibetan wolves with other grey wolf (Canis lupus) populations worldwide, and demonstrates that these two populations represent phylogenetically distinct lineages. This inference was supported by using low-recombination regions of autosomal chromosomes and the X chromosome, which proved to be essential for correct inference of the lineage splitting order. Their study illustrates the power of analytical approaches that implement knowledge of genome evolution patterns to reconstruct complex intraspecific evolutionary relationships. The study also provides a compelling example of the application of modern phylogenomic approaches in the identification of evolutionarily significant units for the purpose of species conservation.