The cryptic African wolf: Canis aureus lupaster is not a golden jackal and is not endemic to Egypt

Multiple Origins and Genomic Basis of Complex Traits in Sighthounds

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.

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.

Ecology, evolution, and conservation of Ethiopia's biodiversity

Ethiopia is home to one of the richest and most unique assemblages of fauna and flora on the African continent. Contained within its borders are two major centers of endemism, the mesic Roof of Africa (also known as the Ethiopian Highlands) and the arid Horn of Africa, resulting from the country's varied topography and consequent geographic isolation. These centers of endemism are crucial to global conservation as evidenced by their classification within the Eastern Afromontane and Horn of Africa biodiversity hotspots, respectively. Ethiopia's diverse ecosystems and the biodiversity they contain are increasingly threatened by climate change and the growing impacts of Africa's second largest human and largest livestock populations. In this paper, we focus on several key areas of recent and ongoing research on Ethiopian biodiversity that have broadened our understanding of nature and its conservation in Africa. Topics explored include the behavioral ecology of Ethiopia's large social mammals, the ecology and conservation of its unique coffee forests, and Ethiopian approaches to community conservation, fortress conservation, and nature-based solutions. We also highlight the increasing prominence of Ethiopian scientists in studies of the country's biodiversity in recent decades. We suggest promising avenues for future research in evolutionary biology, ecology, systematics, and conservation in Ethiopia and discuss how recent and ongoing work in Ethiopia is helping us better understand and conserve nature in the human-dominated landscapes of Africa and other tropical regions today.

From the Balkan towards Western Europe: Range expansion of the golden jackal (Canis aureus)-A climatic niche modeling approach

In recent decades, a rapid range expansion of the golden jackal (Canis aureus) towards Northern and Western Europe has been observed. The golden jackal is a medium-sized canid, with a broad and flexible diet. Almost 200 different parasite species have been reported worldwide from C. aureus, including many parasites that are shared with dogs and cats and parasite species of public health concern. As parasites may follow the range shifts of their host, the range expansion of the golden jackal could be accompanied by changes in the parasite fauna in the new ecosystems. In the new distribution area, the golden jackal could affect ecosystem equilibrium, e.g., through changed competition situations or predation pressure. In a niche modeling approach, we project the future climatic habitat suitability of the golden jackal in Europe in the context of whether climatic changes promote range expansion. We use an ensemble forecast based on six presence-absence algorithms to estimate the climatic suitability of C. aureus for different time periods up to the year 2100 considering different IPCC scenarios on future development. As predictor variables, we used six bioclimatic variables provided by worldclim. Our results clearly indicate that areas with climatic conditions analogous to those of the current core distribution area of the golden jackal in Europe will strongly expand towards the north and the west in future decades. Thus, the observed range expansion may be favored by climate change. The occurrence of stable populations can be expected in Central Europe. With regard to biodiversity and public health concerns, the population and range dynamics of the golden jackal should be surveyed. Correlative niche models provide a useful and frequently applied tool for this purpose. The results can help to make monitoring more efficient by identifying areas with suitable habitat and thus a higher probability of occurrence.

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.

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 canine counts! Significance of a craniodental measure to describe sexual dimorphism in canids: Golden jackals (Canis aureus) and African wolves (Canis lupaster)

Sexual dimorphism is a widespread phenomenon among mammals, including carnivorans. While sexual dimorphism in golden jackals (Canis aureus) has been analysed in the past, in the related and apparently convergent canid, the African wolf (Canis lupaster), it is poorly studied and showed to be relatively small. Previously, sexual size dimorphism (SSD) research in these species was mostly based on skull and body measurements. In our study, we also included dental measurements, namely the diameter of the canine. We used 11 measured sections of 104 adult specimens, comprising 61 golden jackal and 43 African wolf skulls. Data analyses were carried out through logistic regression and conditional inference trees (CIT). To compare the results of SSD to other species, sexual dimorphism indices (SDI) were calculated. Golden jackals and African wolves show significant sexual size dimorphism, both in cranial and dental size. The logistic regression revealed that the mesiodistal diameter of the upper canine is most effective in discerning the sexes. The difference in the calculated SDI of the canine diameter between the sexes amounted to 8.71 in golden jackals and 14.11 in African wolves, respectively—with regional diversity. Thus, the canine diameter is an important measure to investigate SSD as well as an easy tool to apply in the field.

Home range, habitat selection, density, and diet of golden jackals in the Eastern Plains Landscape, Cambodia

We used radiocollars and GPS collars to determine the movements and habitat selection of golden jackals (Canis aureus) in a seasonally dry deciduous forest with no human settlements in eastern Cambodia. We also collected and analyzed 147 scats from jackals to determine their seasonal diet and prey selection. The mean (± SE) annual size of home-range ranges (47.1 ± 2.5 km²; n = 4), which were mutually exclusive between mated pairs, was considerably larger than that previously reported for this species, resulting in an extremely low density (0.01 jackal/km²). The unusually large home ranges and low density probably were due to the harsh dry season when most understory vegetation is burned and nearly all waterholes dry up, thereby causing a large seasonal decline in the availability of small vertebrate prey. Resident groups consisted of an alpha pair, but no betas, and were situated only in areas not occupied by leopards (Panthera pardus) and dholes (Cuon alpinus). Jackals avoided dense forests and streams, and had a strong selection for dirt roads, possibly to avoid larger predators. Overall the jackal diet was diverse, with at least 16 prey items identified, and there was no significant difference in diet composition between the cool-dry and hot-dry seasons. Scat analysis showed that the main food items consumed by jackals were processional termites (Hospitalitermes spp.; 26% biomass consumed), followed by wild pig (Sus scrofa; 20%), muntjac (Muntiacus vaginalis; 20%), and civets (17%). Compared to available biomass, jackals were not random in their consumption of ungulates because muntjac were selectively consumed over larger ungulate species. Dietary overlap with dholes and leopards was relatively low, and consumption patterns indicated jackals were preying on ungulates rather than scavenging from kills of larger carnivores. Our results showed that the jackal is an extremely adaptable and opportunistic species that exhibits unique behaviors to survive in an extreme environment near the edge of its distribution.

Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Background

Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.

Results

Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.

Conclusions

We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07761-5.

Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.

Consequences of the misidentification of museum specimens: the taxonomic status of Canis lupaster soudanicus

Researchers are increasingly using museum collections for taxonomy, systematics, phylogenetics, and faunal analyses, and they assume that taxonomic identifications on museum labels are correct. However, identifications may be incorrect or out of date, which could result in false conclusions from subsequent research. A recent geometric morphometrics analysis of skulls of African canids by Machado and Teta (2020) suggested that Canis lupaster soudanicus is a junior synonym of Lupulella adusta. However, the holotype of soudanicus was not measured and further investigation of the putative soudanicus specimens used in this study showed that these originally were identified as L. adusta. This original identification was confirmed by dental measurements, which also confirm that the holotype of soudanicus is Canis lupaster. Hence, soudanicus should not be synonymized with L. adusta. This example highlights the importance of careful checking of species identifications of museum specimens prior to research and, where possible, including (holo)types of taxa, before making taxonomic changes that could have important consequences for species conservation and management.

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.

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.

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.

Demographic expansion of an African opportunistic carnivore during the Neolithic revolution

The diffusion of Neolithic technology together with the Holocene Climatic Optimum fostered the spread of human settlements and pastoral activities in North Africa, resulting in profound and enduring consequences for the dynamics of species, communities and landscapes. Here, we investigate the demographic history of the African wolf (Canis lupaster), a recently recognized canid species, to understand if demographic trends of this generalist and opportunistic carnivore reflect the increase in food availability that emerged after the arrival of the Neolithic economy in North Africa. We screened nuclear and mitochondrial DNA in samples collected throughout Algeria and Tunisia, and implemented coalescent approaches to estimate the variation of effective population sizes from present to ancestral time. We have found consistent evidence supporting the hypothesis that the African wolf population experienced a meaningful expansion concurring with a period of rapid population expansion of domesticates linked to the advent of agricultural practices.

Foraging ecology of African wolves (Canis lupaster) and its implications for the conservation of Ethiopian wolves (Canis simensis)

African wolves (AWs) are sympatric with endangered Ethiopian wolves (EWs) in parts of their range. Scat analyses have suggested a dietary overlap between AWs and EWs, raising the potential for exploitative competition, and a possible conservation threat to EWs. However, in contrast to that of the well-studied EW, the foraging ecology of AWs remains poorly characterized. Accordingly, we studied the foraging ecology of radio-collared AWs (n = 11 individuals) at two localities with varying levels of anthropogenic disturbance in the Ethiopian Highlands, the Guassa-Menz Community Conservation Area (GMCCA) and Borena-Saynt National Park (BSNP), accumulating 845 h of focal observation across 2952 feeding events. We also monitored rodent abundance and rodent trapping activity by local farmers who experience conflict with AWs. The AW diet consisted largely of rodents (22.0%), insects (24.8%), and goats and sheep (24.3%). Of the total rodents captured by farmers using local traps during peak barley production (July to November) in GMCCA, averaging 24.7 ± 8.5 rodents/hectare/day, 81% (N = 3009) were scavenged by AWs. Further, of all the rodents consumed by AWs, most (74%) were carcasses. These results reveal complex interactions between AWs and local farmers, and highlight the scavenging niche occupied by AWs in anthropogenically altered landscapes in contrast to the active hunting exhibited by EWs in more intact habitats. While AWs cause economic damage to local farmers through livestock predation, they appear to play an important role in scavenging pest rodents among farmlands, a pattern of behaviour which likely mitigates direct and indirect competition with EWs. We suggest two routes to promote the coexistence of AWs and EWs in the Ethiopian highlands: local education efforts highlighting the complex role AWs play in highland ecosystems to reduce their persecution, and enforced protection of intact habitats to preserve habitat preferred by EWs.

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.

Competition between sympatric wolf taxa: an example involving African and Ethiopian wolves

Carnivore populations are declining globally due to range contraction, persecution and prey depletion. One consequence of these patterns is increased range and niche overlap with other carnivores, and thus an elevated potential for competitive exclusion. Here, we document competition between an endangered canid, the Ethiopian wolf (EW), and the newly discovered African wolf (AW) in central Ethiopia. The diet of the ecological specialist EW was dominated by rodents, whereas the AW consumed a more diverse diet also including insects and non-rodent mammals. EWs used predominantly intact habitat, whereas AWs used mostly areas disturbed by humans and their livestock. We observed 82 encounters between the two species, of which 94% were agonistic. The outcomes of agonistic encounters followed a territory-specific dominance pattern, with EWs dominating in intact habitat and AWs in human-disturbed areas. For AWs, the likelihood of winning encounters also increased with group size. Rodent species consumed by EWs were also available in the human-disturbed areas, suggesting that these areas could be suitable habitat for EWs if AWs were not present. Increasing human encroachment not only affects the prey base of EWs, but also may impact their survival by intensifying competition with sympatric AWs.

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.

The geographical distribution of grey wolves (Canis lupus) in China: a systematic review

The grey wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, and its distribution and ecology in Europe and North America are largely well described. However, the distribution of grey wolf in southern China is still highly controversial. Several well-known western literatures stated that there are no grey wolves in southern China, while the presence of grey wolf across China has been indicated in A Guide to the Mammals of China, published by Princeton University Press. It is essential to solve this discrepancy since dogs may have originated from grey wolfs in southern China. Therefore, we systematically investigated Chinese literatures about wild animal surveys and identified more than 100 articles and books that included information of the distribution of grey wolves in China. We also surveyed the collections of three Chinese natural museums and found 26 grey wolf skins specimens collected across China. Moreover, we investigated the fossil records of wolf in China and identified 25 archaeological sites with wolf remains including south China. In conclusion, with the comprehensive summary of Chinese literatures, museum specimens and fossil records, we demonstrate that grey wolves does distribute across all parts of the Chinese mainland, including the most southern parts of China.

A synoptic overview of golden jackal parasites reveals high diversity of species

The golden jackal (Canis aureus) is a species under significant and fast geographic expansion. Various parasites are known from golden jackals across their geographic range, and certain groups can be spread during their expansion, increasing the risk of cross-infection with other carnivores or even humans. The current list of the golden jackal parasites includes 194 species and was compiled on the basis of an extensive literature search published from historical times until April 2017, and is shown herein in synoptic tables followed by critical comments of the various findings. This large variety of parasites is related to the extensive geographic range, territorial mobility and a very unselective diet. The vast majority of these parasites are shared with domestic dogs or cats. The zoonotic potential is the most important aspect of species reported in the golden jackal, some of them, such as Echinococcus spp., hookworms, Toxocara spp., or Trichinella spp., having a great public health impact. Our review brings overwhelming evidence on the importance of Canis aureus as a wild reservoir of human and animal parasites.

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.

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

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

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.

First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers

Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linked Zfy intron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal-domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at the K locus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.

A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus

In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states.

Phylogeography of the Golden Jackal (Canis aureus) in India

The golden jackal (Canis aureus) is one of the most common and widely distributed carnivores in India but phylogeographic studies on the species have been limited across its range. Recent studies have observed absence of mitochondrial (mt) DNA diversity in European populations while some North African populations of golden jackal were found to carry gray wolf (Canis lupus lupaster) mtDNA lineages. In the present study, we sequenced 440 basepairs (bp) of control region (CR) and 412 bp of cytochrome b (cyt b) gene of mtDNA from 62 golden jackals sampled from India (n = 55), Israel (n = 2) and Bulgaria (n = 5), to obtain a total of eighteen haplotypes, comprising sixteen from India and one each from Israel and Bulgaria. Except for three previously described haplotypes represented by one cyt b and one CR haplotype both from India, and one CR haplotype from Bulgaria, all haplotypes identified in this study are new. Genetic diversity was high in golden jackals compared to that reported for other canids in India. Unlike the paraphyletic status of African conspecifics with the gray wolf, the Indian (and other Eurasian) golden jackal clustered in a distinct but shallow monophyletic clade, displaying no evidence of admixture with sympatric and related gray wolf and domestic dog clades in the region. Phylogeographic analyses indicated no clear pattern of genetic structuring of the golden jackal haplotypes and the median joining network revealed a star-shaped polytomy indicative of recent expansion of the species from India. Indian haplotypes were observed to be interior and thus ancestral compared to haplotypes from Europe and Israel, which were peripheral and hence more derived. Molecular tests for demographic expansion confirmed a recent event of expansion of golden jackals in the Indian subcontinent, which can be traced back ~ 37,000 years ago during the late Pleistocene. Our results suggest that golden jackals have had a potentially longer evolutionary history in India than in other parts of the world, although further sampling from Africa, the Middle East and south-east Asia is needed to test this hypothesis.

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.