Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal

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.

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.

Space Use by Woolly Wolf Canis lupus chanco in Gangotri National Park, Western Himalaya, India

The woolly wolf Canis lupus chanco is increasingly being accepted as a unique taxon that needs immediate protection and management; however, information on its ecology remains limited across its range. We used camera trapping data set of 4 years (2015–2019) to investigate seasonal activity patterns and space use and assessed woolly wolf food habits in the Gangotri National Park, western Himalaya, India. We used generalized linear mixed models to assess the distribution of the wolf about prey, seasonal livestock grazing, human presence, habitat, and seasons. We observed a positive association with elevation and a negative response to an increase in ruggedness. The capture of wolves increased in winters, indicating a possible effect of snow on the ranging pattern. Spatial avoidance to anthropogenic pressure was not evident in our study; however, temporal avoidance was observed. The activity pattern of the wolf varied among seasons. Wolves were mostly active in the morning and late evening hours in summer and showed a diurnal activity pattern in winter. A less diverse diet was observed where the mean percentage frequency of occurrence and relative biomass was highest for bharal, followed by livestock. Himalayan marmot Marmota himalayana, birds, and rodents also form minor constituents to the diet. Synthesizing all three factors (space, diet, and activity), it may be stated that the wolf presence in the region is influenced by both wild prey availability and seasonality. Therefore, conservation of woolly wolves would require securing a vast landscape with optimal wild prey.

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.

On the occurrence of the Himalayan Wolf Canis lupus, L. 1758 (Mammalia: Carnivora: Canidae) in the Gaurishankar Conservation Area, Nepal; its existence confirmed through sign and visual evidence in Rolwaling Valley

The Himalayan Wolf Canis lupus L., a top predator of the Third Pole, is proposed to be of a distinct wolf lineage (C. himalayensis) relative to the Holarctic Grey Wolf as described by mtDNA analyses. A biodiversity survey organized by the Gaurishankar Conservation Area Project (GCAP) has captured images of wolves in three different regions, and the study team has observed wolf scats in five additional regions above the tree line in Rolwaling Valley. Further, interviews with local herders provided evidence of wolf depredation of livestock in the area. The Rolwaling Valley in the Gaurishankar Conservation Area was the study area which was divided into 12, 4 x 4 km (16 km2) grid cells, each supplied with one camera trap operated continuously from June to November 2019 (only 6 out of 12 cameras functioned for the duration of our study). Wolf detections were recorded by camera traps from Yalung Pass (4,956 m), Tsho-Rolpa glacial Lake (4,536 m) and the Dudhkunda ridgeline (5,091 m). The photo capture rate index (PCRI) for wolves was 0.71. Our study reports the first photographic evidence of the Himalayan Wolf in the Rolwaling Valley.

Multiple factors influence local perceptions of snow leopards and Himalayan wolves in the central Himalayas, Nepal

An understanding of local perceptions of carnivores is important for conservation and management planning. In the central Himalayas, Nepal, we interviewed 428 individuals from 85 settlements using a semi-structured questionnaire to quantitatively assess local perceptions and tolerance of snow leopards and wolves. We used generalized linear mixed effect models to assess influential factors, and found that tolerance of snow leopards was much higher than of wolves. Interestingly, having experienced livestock losses had a minor impact on perceptions of the carnivores. Occupation of the respondents had a strong effect on perceptions of snow leopards but not of wolves. Literacy and age had weak impacts on snow leopard perceptions, but the interaction among these terms showed a marked effect, that is, being illiterate had a more marked negative impact among older respondents. Among the various factors affecting perceptions of wolves, numbers of livestock owned and gender were the most important predictors. People with larger livestock herds were more negative towards wolves. In terms of gender, males were more positive to wolves than females, but no such pattern was observed for snow leopards. People’s negative perceptions towards wolves were also related to the remoteness of the villages. Factors affecting people’s perceptions could not be generalized for the two species, and thus need to be addressed separately. We suggest future conservation projects and programs should prioritize remote settlements.

Selection and Constraints in the Ecomorphological Adaptive Evolution of the Skull of Living Canidae (Carnivora, Mammalia)

The association between phenotype and ecology is essential for understanding the environmental drivers of morphological evolution. This is a particularly challenging task when dealing with complex traits, such as the skull, where multiple selective pressures are at play and evolution might be constrained by ontogenetic and genetic factors. I integrate morphometric tools, comparative methods, and quantitative genetics to investigate how ontogenetic constraints and selection might have interacted during the evolution of the skull in extant Canidae. The results confirm that the evolution of cranial morphology was largely adaptive and molded by changes in diet composition. While the investigation of the adaptive landscape reveals two main selective lines of least resistance (one associated with size and one associated with functional shape features), rates of evolution along size were higher than those found for shape dimensions, suggesting the influence of constraints on morphological evolution. Structural modeling analyses revealed that size, which is the line of most genetic/phenotypic variation, might have acted as a constraint, negatively impacting dietary evolution. Constraints might have been overcome in the case of selection for the consumption of large prey by associating strong selection along both size and shape directions. The results obtained here show that microevolutionary constraints may have played a role in shaping macroevolutionary patterns of morphological evolution.

Revisiting the Woolly wolf (Canis lupus chanco) phylogeny in Himalaya: Addressing taxonomy, spatial extent and distribution of an ancient lineage in Asia

Of the sub-species of Holarctic wolf, the Woolly wolf (Canis lupus chanco) is uniquely adapted to atmospheric hypoxia and widely distributed across the Himalaya, Qinghai Tibetan Plateau (QTP) and Mongolia. Taxonomic ambiguity still exists for this sub-species because of complex evolutionary history anduse of limited wild samples across its range in Himalaya. We document for the first time population genetic structure and taxonomic affinity of the wolves across western and eastern Himalayan regions from samples collected from the wild (n = 19) using mitochondrial control region (225bp). We found two haplotypes in our data, one widely distributed in the Himalaya that was shared with QTP and the other confined to Himachal Pradesh and Uttarakhand in the western Himalaya, India. After combining our data withpublished sequences (n = 83), we observed 15 haplotypes. Some of these were shared among different locations from India to QTP and a few were private to geographic locations. A phylogenetic tree indicated that Woolly wolves from India, Nepal, QTP and Mongolia are basal to other wolves with shallow divergence (K2P; 0.000-0.044) and high bootstrap values. Demographic analyses based on mismatch distribution and Bayesian skyline plots (BSP) suggested a stable population over a long time (~million years) with signs of recent declines. Regional dominance of private haplotypes across its distribution range may indicate allopatric divergence. This may be due to differences in habitat characteristics, availability of different wild prey species and differential deglaciation within the range of the Woolly wolf during historic time. Presence of basal and shallow divergence within-clade along with unique ecological requirements and adaptation to hypoxia, the Woolly wolf of Himalaya, QTP, and Mongolian regions may be considered as a distinct an Evolutionary Significant Unit (ESU). Identifying management units (MUs) is needed within its distribution range using harmonized multiple genetic data for effective conservation planning.

Morphometric analysis of skull shape reveals unprecedented diversity of African Canidae

We conducted a geometric morphometric analysis to investigate the morphological variation of the golden wolf, Canis lupaster, and to clarify the morphological and taxonomic affinities of different taxa of the genera Canis and Lupulella. We suggest that the variation observed within the complex of Canis lupaster may be incompatible with what would be expected for a single species. We hypothesize that the nominal form C. l. soudanicus is a synonym of Lupulella adusta rather than being part of the golden wolf complex. The subspecies C. l. bea has a generalized jackal morphology (i.e., clusters together with L. mesomelas and C. aureus) and C. l. lupaster occupies an intermediate morphospace position, between jackal-like forms and wolf-like forms. These results contrast with previously published molecular analysis in which mitochondrial data failed to identify differences among golden wolf populations, and nuclear evidence points to the existence of groups that are incompatible with those recovered by morphological analysis. Regarding other jackals, our results depict the absence of morphological overlap between L. m. mesomelas and L. m. schmidti and no differences between putative subspecies of L. adusta. We call attention to the need for more integrative approaches to solve the taxonomic questions in various African Canidae.

mtDNA analysis confirms the endangered Kashmir musk deer extends its range to Nepal

Musk deer Moschus spp. are endemic to the high mountain forests of central Asia. The taxonomic status of musk deer in the central and western Himalayas is poorly understood. We investigated the phylogenetic relationship of musk deer from the central and western Himalayas based on mitochondrial genomic data of Cytochrome b (380 bps) and D-loop (1000 bps). Our results distinguished two divergent lineages using higher bootstrap support (bs) values from the Maximum likelihood and Bayesian posterior probabilities (bpp). Both the Manang and Kaski lineages from central Nepal are confirmed as Himalayan musk deer Moschus leucogaster and represent a species complex widespread throughout the central and eastern Himalayan region. The musk deer Mustang lineage was confirmed as Kashmir musk deer Moschus cupreus and has wide distribution in the western Himalayas (from central Nepal to Afghanistan). Our analysis validates that Kashmir musk deer is a genetically distinct species and it clarifies that Himalayan musk deer and Kashmir musk deer are confirmed instead of Alpine musk deer Moschus chrysogaster which has been previously described from the southern parts of Himalayas of Nepal, India and Pakistan.

Conservation implications for the Himalayan wolf Canis (lupus) himalayensis based on observations of packs and home sites in Nepal

We provide insights into pack composition and den site parameters of the Himalayan wolf Canis (lupus) himalayensis based on observations of free-ranging wolves in three study areas in Nepal. We combine this with a social survey of the local Buddhist communities regarding human–carnivore conflict, to draw inferences for conservation practice in the Nepalese Himalayas. We recorded eight wolf packs (with an average composition of two adults and three pups), and found five home sites in high-altitude shrubland patches within alpine grasslands at 4,270–4,940 m altitude. There was a spatial–temporal overlap of wolf home sites and livestock herding during spring and summer, which facilitated human–wolf conflict. The litters of three out of five wolf packs found in Dolpa during 2016 were killed by local people in the same year. In Nepal compensation is offered for depredation by snow leopards Panthera uncia, with associated lowering of negative attitudes, but not for depredation by wolves. We recommend the implementation of financial and educational conservation schemes for all conflict-causing carnivores across the Himalayan regions of Nepal.

Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal

Wolves in the Himalayan region form a monophyletic lineage distinct from the present-day Holarctic grey wolf Canis lupus spp. (Linnaeus 1758) found across Eurasia and North America. Here, we analyse phylogenetic relationships and the geographic distribution of mitochondrial DNA haplotypes of the contemporary Himalayan wolf (proposed in previous studies as Canis himalayensis) found in Central Asia. We combine genetic data from a living Himalayan wolf population collected in northwestern Nepal in this study with already published genetic data, and confirm the Himalayan wolf lineage based on mitochondrial genomic data (508 bp cytochrome b and 242 bp D-loop), and X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences. We then compare the genetic profile of the Himalayan wolf lineage found in northwestern Nepal with canid reference sequences from around the globe with maximum likelihood and Bayesian phylogeny building methods to demonstrate that the Himalayan wolf forms a distinct monophyletic clade supported by posterior probabilities/bootstrap for D-loop of greater than 0.92/85 and cytochrome b greater than 0.99/93. The Himalayan wolf shows a unique Y-chromosome (ZFY) haplotype, and shares an X-chromosome haplotype (ZFX) with the newly postulated African wolf. Our results imply that the Himalayan wolf distribution range extends from the Himalayan range north across the Tibetan Plateau up to the Qinghai Lakes region in Qinghai Province in the People's Republic of China. Based on its phylogenetic distinction and its older age of divergence relative to the Holarctic grey wolf, the Himalayan wolf merits formal classification as a distinct taxon of special conservation concern.

Snow Leopard and Himalayan Wolf: Food Habits and Prey Selection in the Central Himalayas, Nepal

Top carnivores play an important role in maintaining energy flow and functioning of the ecosystem, and a clear understanding of their diets and foraging strategies is essential for developing effective conservation strategies. In this paper, we compared diets and prey selection of snow leopards and wolves based on analyses of genotyped scats (snow leopards n = 182, wolves n = 57), collected within 26 sampling grid cells (5×5 km) that were distributed across a vast landscape of ca 5000 km² in the Central Himalayas, Nepal. Within the grid cells, we sampled prey abundances using the double observer method. We found that interspecific differences in diet composition and prey selection reflected their respective habitat preferences, i.e. snow leopards significantly preferred cliff-dwelling wild ungulates (mainly bharal, 57% of identified material in scat samples), whereas wolves preferred typically plain-dwellers (Tibetan gazelle, kiang and argali, 31%). Livestock was consumed less frequently than their proportional availability by both predators (snow leopard = 27%; wolf = 24%), but significant avoidance was only detected among snow leopards. Among livestock species, snow leopards significantly preferred horses and goats, avoided yaks, and used sheep as available. We identified factors influencing diet composition using Generalized Linear Mixed Models. Wolves showed seasonal differences in the occurrence of small mammals/birds, probably due to the winter hibernation of an important prey, marmots. For snow leopard, occurrence of both wild ungulates and livestock in scats depended on sex and latitude. Wild ungulates occurrence increased while livestock decreased from south to north, probably due to a latitudinal gradient in prey availability. Livestock occurred more frequently in scats from male snow leopards (males: 47%, females: 21%), and wild ungulates more frequently in scats from females (males: 48%, females: 70%). The sexual difference agrees with previous telemetry studies on snow leopards and other large carnivores, and may reflect a high-risk high-gain strategy among males.