Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos
Mikkel-Holger S. Sinding,
Marta M. Ciucani,
Jazmín Ramos-Madrigal,
Alberto Carmagnini,
Jacob Agerbo Rasmussen,
Shaohong Feng,
Guangji Chen,
Filipe G. Vieira,
Valeria Mattiangeli,
Rajinder K. Ganjoo,
Greger Larson,
Thomas Sicheritz-Pontén,
Bent Petersen,
Laurent Frantz,
M. Thomas P. Gilbert,
Daniel G. Bradley
Affiliations
Mikkel-Holger S. Sinding
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland; Corresponding author
Marta M. Ciucani
Globe Institute, University of Copenhagen, Copenhagen, Denmark
Jazmín Ramos-Madrigal
Globe Institute, University of Copenhagen, Copenhagen, Denmark
Alberto Carmagnini
School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
Jacob Agerbo Rasmussen
Globe Institute, University of Copenhagen, Copenhagen, Denmark; Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Shaohong Feng
BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
Guangji Chen
BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China; University of Chinese Academy of Sciences, Beijing, China
Filipe G. Vieira
Globe Institute, University of Copenhagen, Copenhagen, Denmark
Valeria Mattiangeli
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
Rajinder K. Ganjoo
Department of Geology, University of Jammu, Jammu, India
Greger Larson
The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
Thomas Sicheritz-Pontén
Globe Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
Bent Petersen
Globe Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
Laurent Frantz
School of Biological and Chemical Sciences, Queen Mary University of London, London, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
M. Thomas P. Gilbert
Globe Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim, Norway
Daniel G. Bradley
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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.
