Ancient genomes redate the extinction of Sussemionus , a subgenus of Equus , to late Holocene

Abstract

29 The exceptionally-rich fossil record available for the equid family has provided 30 textbook examples of macroevolutionary changes. Horses, asses and zebras represent 31 three extant subgenus of Equus lineage, while the Sussemionus subgenus is another 32 remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We 33 sequenced 26 archaeological specimens from northern China in Holocene showing 34 morphological features reminiscent of Equus ovodovi, a species representative of 35 Sussemionus, and further confirmed them as this species by genetic analyses. Thus, 36 we present the first high-quality complete genome of the Sussemionus that we 37 sequenced to 12.0× depth-of-coverage and demonstrate that it survived until ~3,500 38 years ago, despite the continued demographic collapse during the Last Glacial 39 Maximum and the great human expansion in East Asia. We also confirmed the Equus 40 phylogenetic tree, and found Sussemionus diverged from the ancestor of non-caballine 41 equids ~2.3-2.7 Million years ago and admixture events could have taken place 42 between them. Our works suggest the small genetic diversity but not the enhanced 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.09.13.460072; this version posted September 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 43 inbreeding mainly limited the chances of survival of the species, and illustrates how 44 ancient DNA can inform on extinction dynamics and the long-term resilience of 45 species surviving in cryptic population pockets. 46 47