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, 14 (5), e0216883
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Molecular Identification of Late and Terminal Pleistocene Equus Ovodovi From Northeastern China

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Molecular Identification of Late and Terminal Pleistocene Equus Ovodovi From Northeastern China

Jun-Xia Yuan et al. PLoS One.

Abstract

The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Location of sampling sites in this study and fossil findings of E. ovodovi and E. dalianensis.
Sampling site in this study is indicated by a red star; the E. ovodovi specimens in Russia are shown by blue triangles; fossil findings of E. dalianensis according to the literature are shown by green triangles.
Fig 2
Fig 2. Maximum-likelihood phylogenetic tree of complete mitochondrial genomes of equids, rooted using the Hippidion clade as outgroup.
Branch labels show the bootstrap values derived from 1000 replications. Ages of E. ovodovi specimens are indicated following the sample/accession number.
Fig 3
Fig 3. Maximum clade credibility tree of E. ovodovi haplotypes.
Nodes heights are centred on the median posterior age estimate (x-axis) and tips on sample ages. Blue node bars show 95% credibility intervals of the coalescence times. Branch labels show posterior clade probabilities.
Fig 4
Fig 4. Average pairwise mitochondrial distances within non-caballine equid species.

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Grant support

This research was financially supported by the National Natural Science Foundation of China (Nos. 41472014; 41672017) and the “PPP” project jointly funded by China Scholarship Council and DAAD (No. 2016-2041). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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