Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas
Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas
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走出西藏：现存鼠兔进化史的基因组视角
DOI：
10.1093/molbev/msaa026
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发表时间：
2020
影响因子：
10.7
通讯作者：
Zhang Peng
中科院分区：
文献类型：
--
作者：
Wang XiaoYun;Liang Dan;Jin Wei;Tang MingKun;Shalayiwu;Liu ShaoYing;Zhang Peng
鼠兔广泛分布于北方半球，高度适应寒冷和高山环境。它们是哺乳动物系统学中最复杂和最有问题的类群之一，现存鼠兔的起源和进化历史仍然存在争议。在这项研究中，我们对105个鼠兔样本（29个已命名种和1个推定新种）的全编码序列进行了测序，获得了超过10，000个基因的DNA数据。我们的基因组分析确认了现存鼠兔的四个亚属：异尾鼠兔属、锥尾鼠兔属、鼠兔属和鼠兔属。四个亚属之间的相互关系被强烈解析为（Conothoa，（Alienauroa，（Ochotona，Pika），其中山地群Conothoabe是所有其他鼠兔的姐妹群。我们的分歧时间和系统地理学分析表明，现存鼠兔的最后共同祖先首次出现在中新世中期，即1.14 Ma。与气候、食物供应和传播路径相关的机会的出现，共同促进了鼠兔从青藏高原（QTP）向欧亚大陆和北美其他地区的扩散。我们发现，在鼠兔早期进化中被积极选择的基因大多集中在与耐寒性相关的功能类别中。这些结果表明，QTP可能是作为一个训练场的耐寒性在早期的鼠兔，这给鼠兔一个很大的优势，当气候继续冷却后，中新世中期。我们的研究强调了QTP作为许多冷适应动物起源中心的重要性。
Pikas are widely distributed in the Northern Hemisphere and are highly adapted to cold and alpine environments. They are one of the most complex and problematic groups in mammalian systematics, and the origin and evolutionary history of extant pikas remain controversial. In this study, we sequenced the whole coding sequences of 105 pika samples (29 named species and 1 putative new species) and obtained DNA data for more than 10,000 genes. Our phylogenomic analyses recognized four subgenera of extant pikas:Alienauroa,Conothoa,Ochotona, andPika. The interrelationships between the four subgenera were strongly resolved as (Conothoa, (Alienauroa, (Ochotona,Pika))), with the mountain groupConothoabeing the sister group of all other pikas. Our divergence time and phylogeographic analyses indicated that the last common ancestor of extant pikas first occurred on in the middle Miocene, ∼14 Ma. The emergence of opportunities related to the climate, food supply, and spreading paths in concert promoted the dispersal of pikas from the Qinghai-Tibetan Plateau (QTP) to other parts of Eurasia and North America. We found that the genes that were positively selected in the early evolution of pikas were most concentrated in functional categories related to cold tolerance. These results suggest that the QTP may have served as a training ground for cold tolerance in early pikas, which gives pikas a great advantage when the climate continued to cool after the middle Miocene. Our study highlights the importance of the QTP as a center of origin for many cold-adapted animals.