- (1) University of Copenhagen, grid.5254.6, KU
- (2) University of Greenland, grid.449721.d
- (3) University of Oslo, grid.5510.1
- (4) Barcelona Biomedical Research Park, grid.418220.d
- (5) Yunnan University, grid.440773.3
- (6) Kunming Institute of Zoology, grid.419010.d
- (7) Autonomous University of Barcelona, grid.7080.f
- (8) Catalan Institution for Research and Advanced Studies, grid.425902.8
- (9) Centre for Genomic Regulation, grid.11478.3b
- (10) University of California, San Diego, grid.266100.3
- (11) University of Lisbon, grid.9983.b
- (12) Institut des Sciences de l'Evolution de Montpellier, grid.462058.d
- (13) National Zoological Park, grid.467700.2
- (14) Saint Petersburg State University, grid.15447.33
- (15) Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates.
- (16) Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.
- (17) University of Oxford, grid.4991.5
- (18) Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney House, Tubney OX13 5QL, UK; IUCN SSC Canid Specialist Group, Oxford, UK.
- (19) Asian Institute of Medicine, Science and Technology, grid.444449.d
- (20) Technical University of Denmark, grid.5170.3, DTU
- (21) Norwegian University of Science and Technology, grid.5947.f
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.