Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years

Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years Full article

Journal

Genome Biology and Evolution
ISSN: 1759-6653

Output data

Year: 2025, Volume: 17, Number: 11, Pages: 1-12 Pages count : 12 DOI: 10.1093/gbe/evaf206

Tags

ancient DNA, bovine, yak, Denisova Cave, Altai, Siberia.

Authors

Gilardet Alexandre ^1,2 , Oppenheimer Jonas ³ , Sinding Mikkel-Holger S. ⁴ , Lord Edana ^1,2 , Chacón-Duque J.Camilo ^1,2 , Oteo-García Gonzalo ^1,5 , Xenikoudakis Georgios ^1,5 , Kosintsev Pavel ^6,7 , Southon John ⁸ , Vasiliev Sergey K. ⁹ , Shunkov Michael V. ⁹ , Kozlikin Maxim B. ⁹ , Douka Katerina ¹⁰ , Shapiro Beth ³ , Heintzman Peter D. ^1,11 , Dalén Love ^1,2,12

Affiliations

1	Centre for Palaeogenetics, Stockholm 10691, Sweden
2	Department of Zoology, Stockholm University, Stockholm 10691, Sweden
3	Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
4	Department of Biology, The University of Copenhagen, Copenhagen 2100, Denmark
5	Department of Archaeology and Classical Studies, Stockholm University, Stockholm 11418, Sweden
6	Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
7	Department of History, Ural Federal University, Yekaterinburg, Russia
8	Department of Earth System Science, University of California, Irvine, CA, USA
9	Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
10	Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
11	Department of Geological Sciences, Stockholm University, Stockholm 10691, Sweden
12	Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden

Funding (1)

24-18-00069

Bovines have a complex poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.

Gilardet A. , Oppenheimer J. , Sinding M-H.S. , Lord E. , Chacón-Duque J.C. , Oteo-García G. , Xenikoudakis G. , Kosintsev P. , Southon J. , Vasiliev S.K. , Shunkov M.V. , Kozlikin M.B. , Douka K. , Shapiro B. , Heintzman P.D. , Dalén L.
Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years
Genome Biology and Evolution. 2025. V.17. N11. P.1-12. DOI: 10.1093/gbe/evaf206 WOS Scopus

Web of science:	WOS:001617837900001
Scopus:	2-s2.0-105022272215

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