Phylogeography of the Golden Jackal (Canis aureus) in India

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

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

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.

Morphometric variation in wolves and golden jackal in India (Mammalia, Carnivora)

Species of Canis (Carnivora, Canidae) have similar morphology and distinguishing sympatric species is challenging. We present data on morphometry of skull, body and hair of three wild Canis species that occur in India, which include two wolves (Indian wolf, Canislupuspallipes; and Himalayan wolf, Canishimalayensis) and the golden jackal (Canisaureus). A total of 20 cranial and six body measurements and microscopic characteristics of guard hair were analysed, using multivariate ordination to differentiate between species. Cranial measures of the Himalayan wolves were found to be the largest followed by Indian wolves and golden jackals. However, many measures overlapped amongst the three species. Two Principal Components each, for body measures and cranial measures, explained 86 and 91% of the variation in the data, respectively. These Components discriminated the two wolves from golden jackals, but could not distinguish between wolves. Hair medullary patterns were simple and wide type, whereas hair cuticular patterns showed crenate scale margins, near scale distance and irregular wavey scale patterns for all Canis taxa and were not useful to distinguish species. Data reported in this study further contribute to the existing global data on wild canids for a holistic understanding of the variation within the genus and show that distinguishing between all sympatric species from morphology alone may not be possible.

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.

Cranial variability and differentiation among golden jackals (Canis aureus) in Europe, Asia Minor and Africa

Golden jackal (Canisaureus) expansion in the last decades has triggered research interest in Europe. However, jackal phylogeny and taxonomy are still controversial. Morphometric studies in Europe found differences between Dalmatian and the other European jackals. Recent genetic studies revealed that African and Eurasian golden jackals are distinct species. Moreover, large Canisaureuslupaster may be a cryptic subspecies of the African golden jackal. Although genetic studies suggest changes in Canisaureus taxonomy, morphological and morphometric studies are still needed. The present study proposes the first comprehensive analysis on a wide scale of golden jackal skull morphometry. Extensive morphometric data of jackal skulls from Europe (including a very large Bulgarian sample), Asia Minor, and North Africa were analysed, by applying recently developed statistical tools, to address the following questions: (i) is there geographic variation in skull size and shape among populations from Europe, Anatolia and the Caucasus?, (ii) is the jackal population from the Dalmatian coast different?, and (iii) is there a clear distinction between the Eurasian golden jackal (Canisaureus) and the African wolf (Canislupaster sensu lato), and among populations of African wolves as well? Principal component analysis and linear discriminant analysis were applied on the standardized and log-transformed ratios of the original measurements to clearly separate specimens by shape and size. The results suggest that jackals from Europe, Anatolia and the Caucasus belong to one subspecies: Canisaureusmoreotica (I. Geoffroy Saint-Hilaire, 1835), despite the differences in shape of Dalmatian specimens. The present study confirmed morphometrically that all jackals included so far in the taxon Canisaureus sensu lato may represent three taxa and supports the hypothesis that at least two different taxa (species?) of Canis occur in North Africa, indicating the need for further genetic, morphological, behavioural and ecological research to resolve the taxonomic uncertainty. The results are consistent with recent genetic and morphological studies and give further insights on golden jackal taxonomy. Understanding the species phylogeny and taxonomy is crucial for the conservation and management of the expanding golden jackal population in Europe.

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.

Canis aureus (Carnivore: Canidae)

Canis aureus (Linnaeus, 1758), the golden jackal, is a medium-sized, wide spread, terrestrial carnivore. It is 1 of 7 species found in the genus Canis. It ranges from Africa to Europe, the Middle East, Central Asia, and Southeast Asia. Due to its tolerance of dry habitats and its omnivorous diet, C. aureus can live in a wide variety of habitats. It normally lives in open grassland habitat but also occurs in deserts, woodlands, mangroves, and agricultural and rural habitats in India and Bangladesh. It ranges from sea level in Eritrea to 3,500 m in the Bale Mountains of Ethiopia and 2,000 m in India. C. aureus is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species version 2016.1.

DNA barcoding of three species (Canis aureus, Canis lupus and Vulpes vulpes) of Canidae

Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been used for DNA barcoding and determining the genetic diversity of mammal species. In the current study, our intention was to test the validity of COI barcodes for detecting genetic divergence and to reveal whether or not there is a genetic variation at this marker within canids. Three species (Canis aureus, Canis lupus and Vulpes vulpes) from the family Canidae were selected for DNA barcoding using samples collected from Iran and Turkey. All three species had unique barcoding sequences and none of the sequences were shared among these species. The mean sequence divergences within and among the species were 0.61% and 12.32%, respectively, which fell into the mean divergence ranges found in some mammal groups. The genetic diversity of these three canid species was relatively higher than that found in previously reported studies.