Our sequence data provided 26 mitochondrial genomes and 3 complete nuclear genomes for Equus (Sussemionus) ovodovi.

The Equus (Sussemionus) subgenus represents one equine lineage that has become recently extinct. Its latest known representative was found in the fossil record of Siberia and dated to ~12,700 years ago, but its extinction dynamics remains poorly known. We sequenced the first genome of the extinct E. (Sussemionus) ovodovi species and generated genome-scale data for 25 additional specimens. We found that the demographic collapse started prior to, but continued during the great human expansion and the Last Glacial Maximum. The species, however, survived in Northeast China until at least 3,400 years ago, despite populations of extremely small sizes. Our study illustrates how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.