Ancient genomes reveal an extinct bovine species from mid-latitude Asia

A previously undescribed bovine mitochondrial clade, termed yak X, was recently discovered in Pleistocene Asia.¹ However, the genome-wide relationships of this lineage to other bovines remain unclear. Here, we present 20 Middle and Late Pleistocene yak X nuclear genomes that were recovered from Denisova Cave and other sites in mid-latitude Asia and have a temporal span of over 200,000 years. Phylogenetic and population genomic approaches show that yak X was a separate species that began diverging from extant yaks at least 400,000 years ago. We also document a demographic decline in yak X over the Mid-to-Late Pleistocene, along with potential population turnover accompanied by a decrease in genetic diversity around the Last Interglacial (∼130,000 to ∼115,000 years ago). Unlike divergent hominin lineages within Pleistocene Asia,² we find negligible evidence for gene flow between yak X and other bovine species, including steppe bison (Bison priscus) and aurochs (Bos primigenius), despite their geographic and temporal co-occurrence.¹ Our results show that yak X was a distinct species whose disappearance may have previously gone unrecognized during the Late Quaternary megafaunal extinctions, and highlight the broader Altai-Sayan region as a hotspot of diversity during the Pleistocene.