Kouprey () genomes unveil polytomic origin of wild Asian .

The evolution of the genera and , and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey () and analyzed them alongside other and genomes. We found that possessed genomic signatures characteristic of an independent species closely related to and . We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian -like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.