Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation
Lin Zeng, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室，云南 昆明650223, 中国, Hequn Liu, Xiaolong Tu, Changmian Ji, Xiao Gou, Ali Esmailizadeh, Sheng Wang, Mingshan Wang, Mingcheng Wang, Xiaolong Li, Hadi Charati, Adeniyi C. Adeola, R. A. M. Adedokun, Olatunbosun Oladipo, Sunday Charles Olaogun, Oscar J. Sanke, Mangbon Godwin F., Sheila C. Ommeh, Bernard Agwanda, Jacqueline Kasiiti Lichoti, Jianlin Han, Hongkun Zheng, Changfa Wang, Ya‐Ping Zhang, Laurent Frantz, Dong‐Dong Wu, 中国热带农业科学院热带生物技术研究所 海南省南繁生物安全与分子育种重点实验室，海南 海口 571101, 中国, 云南农业大学动物科学技术学院，云南 昆明650201, 中国, 中国科学院大学，昆明生命科学学院, 云南 昆明650204, 中国, 中国科学院中非联合研究中心, 云南 昆明650223, 中国, 中国科学院动物进化与遗传前沿交叉卓越创新中心, 云南 昆明650223, 中国, 中国科学院三江源国家公园研究院, 青海 西宁 810008, 中国, 安诺优达基因科技(北京)有限公司, 北京 100176, 中国, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室, 云南省畜禽分子生物学重点实验室, 中国西南野生生物种质资源库, 云南 昆明650223, 中国, Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria, Division of Veterinary Office, Serti 663101, Nigeria, 山东省农业科学院奶牛研究中心马属动物研究室, 山东 济南 250131, 中国, 聊城大学聊城毛驴高效繁育与生态饲养研究院, 山东 聊城 252059, 中国, 中国农业科学院-国际家畜研究所畜禽牧草遗传资源联合实验室, 北京 100193, 中国, 百迈客生物科技, 北京101300, 中国, Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria, Division of Veterinary Office, Serti 663101, Nigeria
Abstract
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a <i>de novo</i> genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the <i>EPAS1</i> locus in kiangs. In Tibetan donkeys, however, another gene, i.e., <i>EGLN1</i>, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.