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

Abstract

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 13.4× depth-of-coverage. Radiocarbon dating demonstrates that this lineage survived until ~3,500 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.

Subsistence strategies in the Late Neolithic and Bronze Age in Nenjiang River Basin: A zooarchaeological and stable isotope analysis of faunal remains at Honghe site, Northeast China

“…Meanwhile, 44 unknown equine samples from Neolithic remains were sequenced at the ancient DNA laboratory of Jilin University. The result shows 20 samples yielded whole genome data and were identified as E. ovodovi(Cai et al, 2022), which agrees with the morphological data.…”

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)

“…Although we find that hydruntines survived at least two more millennia, our ROH and heterozygosity analyses on the 1 st millennium BCE genome from Çadır Höyük do suggest a dramatic reduction in their effective population size in that period on a par with the critically endangered African wild ass (Moehlman & Kebede, 2014), which would have dramatically increased the risk of extinction (Newman and Pilson,1997). The decline itself could have various non-exclusive causes, including habitat fragmentation as a result of human activity and/or climatic events, or human predation (Bennett et al, 2017;Boulbes & van Asperen, 2019;Cai et al, 2021;Crees and Turvey, 2014;Spassov & Iliev, 2002). It is notable here that the remains of the three individuals studied here were recovered from residential or midden contexts (Archeological Supplement Table 2) and were likely consumed by humans.…”

Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China

“…In addition, many molecular studies verify that the members of “ Mammuthus-Coelodonta faunas” from Northern China are closely related to their Siberian relatives. Recent ancient genetic analyses infer that some extinct or extant species, e.g., Ovodov Horse ( Equus ovodovi ) [ 32 , 33 ], steppe bison [ 24 ], roe deer ( Capreolus spp.) [ 34 ], and red deer ( Cervus elaphus/hanglu/canadensis ) [ 35 ], dispersed between Northern China and Siberia when climate or vegetation changed.…”