Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4x depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

Automated summary

The rich fossil record of the equid family has provided valuable insights into the macroevolutionary changes in this group. This study analyzed archaeological specimens from Northern China and sequenced the complete genome of Equus ovodovi, a species belonging to the Sussemionus subgenus. The results revealed that this lineage survived until approximately 3500 years ago, despite population collapse during the Last Glacial Maximum and human expansion in East Asia. The study also highlighted the importance of genetic diversity for species' survival.