Summary
The evolution of the genera
Bos
and
Bison
, 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 (
Bos sauveli
) and analyzed them alongside other
Bos
and
Bison
genomes. We found that
B. sauveli
possessed genomic signatures characteristic of an independent species closely related to
Bos javanicus
and
Bos gaurus
. 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
Bos
-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the
Bos
complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.