Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

Special Issue: "Canine Genetics 2"

Wolves were the first animal species to become domesticated by humans, approximately 30,000-50,000 years ago. Human-directed dog breeding over thousands of generations has generated more than 350 recognized breeds displaying surprisingly different phenotypes with respect to morphology, behavior and disease predispositions. The domestication of wolves and the subsequent breeding of dogs can be viewed as one of humankind's oldest and largest genetic experiments and provides us with unique opportunities for research. Dogs have not only become human's best friend but were also described as geneticists' best friend in a past issue of Science. In recognition of the importance of canine genetics, this Special Issue, entitled "Canine Genetics 2", was compiled. It represents a sequel to the former Special Issue "Canine Genetics", which was published in 2019. During the last 15 years, the canine community has heavily relied on a reference genome derived from the female Boxer Tasha. "Canine Genetics 2" includes an article describing a greatly improved version of this important community resource. This Special Issue further contains several reports related to monogenic or complex inherited diseases in dogs. Finally, important aspects of wild canid research, genetic diversity in different populations and canine morphology were investigated.

Multiple Lines of Ecological Evidence Support Ancient Contact Between the African Wild Dog and the Dhole

Genomic tools have greatly enhanced our ability to uncover ancient interspecific gene flow, including cases involving allopatric lineages and/or lineages that have gone extinct. Recently, a genomic analysis revealed the unexpected gene flow between the African wild dog (Lycaon pictus) and the dhole (Cuon alpinus). The two species have currently highly disjunct and patchy distributions in Africa and Asia, respectively, which are remnants of a much wider past distribution. Yet, no reported evidence of their past contact has ever been documented. By hindcasting the past potential distribution of both species during the Last Glacial Maximum and the Last Interglacial, validating paleoclimatic reconstructions with fossil evidence, quantifying the intersection of their bioclimatic niches, and assessing interspecific compatibility, we investigate the location and favorable conditions for such contact and its ecological validity. We were able to identify the Levant region in Eastern Mediterranean during the Last Interglacial as the most suitable spatio-ecological context for the co-occurrence of the two canids, and to provide evidence of a highly significant overlap of the African wild dog niche with the wider niche of the dhole. These results, combined with ecologic traits, including key compatibility features such as cooperative breeding and hunting, provide consistent support for the potential co-occurrence of both canids. We suggest that the ranges of these canids came into contact multiple times during periods resembling the Last Interglacial, eventually facilitating gene flow between the African wild dog and the dhole in their post-divergence history. Our results are highly supportive of the key role of the Levant region in providing connectivity between African and Eurasian faunas and provide further impetus to combine different tools and approaches in advancing the understanding of species evolutionary histories.

Evolutionary history of the extinct Sardinian dhole

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

Eucyon khoikhoi sp. nov. (Carnivora: Canidae) from Langebaanweg ‘E’ Quarry (early Pliocene, South Africa): the most complete African canini from the Mio-Pliocene

A new medium-sized canid, Eucyon khoikhoi sp. nov., is described from the early Pliocene site of Langebaanweg ‘E’ Quarry (South Africa). It possesses a robust dentition with large upper- and lower-second molars, an m1 talonid without a transverse cristid between the entoconid and the hypoconid, and a well-developed hypoconulid shelf. Our cladistic analysis of the earliest better-known African canini, places E. khoikhoi as the most basal taxon of an African clade composed of E. wokari, ?Nyctereutes barryi, ?Schaeffia mohibi and Schaeffia adusta (living side-striped jackal). We suggest an alternative arrangement for the poorly known East African E. intrepidus from the Late Miocene and E. kuta from the Middle Pliocene. Eucyon intrepidus could belong to the same clade as E. khoikhoi, unlike E. kuta, whose dentition suggests a closer relation with the Lupulella group. Thus, these results support the paraphyly of Eucyon, demonstrating the need for an in-depth review of the genus. Eucyon khoikhoi has a body mass comparable to E. kuta and the European E. debonisi and E. monticinensis. We conclude that E. khoikhoi may have had a comparable role in the ecosystem to the extant hypocarnivorous S. adusta.