Bioarchaeology Laboratory, Jilin University, Changchun, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Elife. 2022 May 11;11:e73346. doi: 10.7554/eLife.73346.
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 lineage, while the subgenus is another remarkable 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 , a species representative of . We present the first high-quality complete genome of the lineage, which was sequenced to 13.4× 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 phylogenetic tree and found that 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.
马科动物极为丰富的化石记录为宏观进化变化提供了典型范例。马、驴和斑马代表了三个现存的谱系亚属，而 亚属则是另一个在更新世时期从北美洲延伸到埃塞俄比亚的显著谱系。我们对全新世中国北方的 26 个考古样本进行了测序，这些样本在形态学和遗传学上都可以归入 ，这是 的代表种。我们展示了 谱系的第一个高质量完整基因组，其测序深度达到了 13.4×。放射性碳测年表明，尽管末次冰期最大和东亚人类大扩张期间持续出现人口减少，该谱系直到约 3500 年前才灭绝。我们还证实了 的系统发育树，发现它与非马属祖先在 230 万至 270 万年前分化，并且可能在分化后仍然受到二次基因流的影响。我们发现，是较小的遗传多样性而不是增强的近交限制了该物种的生存机会。我们的工作增加了越来越多的文献，这些文献说明了古 DNA 如何为物种灭绝动态和在隐蔽的种群小群体中生存的物种的长期恢复力提供信息。
