着基因组数据的迅速增加，通过比较基因组学及生物信息学的方法探讨物种适应性进化的遗传基础是目前分子进化的研究热点。张亚平院士课题组针对已公布的海豚基因组，通过与其他近缘物种的基因组进行比较，系统地鉴定出海豚中经历正选择的基因及位点，为理解海豚等鲸目动物的水生适应奠定了基础，同时也为进一步研究这些基因的功能提供了线索。
鲸目动物是哺乳动物中少有的水生物种，它们与现存的偶蹄类大约分化于50个百万年以前。鲸目动物的“二次入水”事件是哺乳动物进化史中一次罕见的生活史转变，它们的生活习性由陆生转变为完全水生。剧烈的环境转变导致它们在生理上及结构上都发生了显着的改变以适应水生生活，例如具有增厚的皮下脂肪层（“鲸油”），长时间潜水及回声定位的能力，同时具有强大的肌肉系统支持水中运动等。尽管人们已经了解到很多生理/形态上的适应性特征，但是这些特征的分子基础并没有得到系统性的解决。基于此，孙艳波博士和周伟平博士等对已公布的海豚基因组进行了系统性的分析。通过构建近缘物种间的高质量序列比对（包括海豚、牛、狗、大熊猫、以及人，共11,838个直系同源基因），在海豚中检测到了368个经历正选择的基因（P < 0.01）。功能聚类分析的结果显示，这些正选择基因显着富集于诸如肌肉收缩、ATP酶、脂肪转运和定位、感知声音、以及糖酵解等功能中。该研究为进一步揭示鲸目动物的进化及其水生适应的分子机制具有重要的参考价值。该研究已在线发表在《Genome Biology and Evolution》杂志。(生物谷Bioon.com)
doi: 10.1093/gbe/evs123
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Genome-Wide Scans for Candidate Genes Involved to the Aquatic Adaptation of Dolphins
Yan-Bo Sun1,3,#, Wei-Ping Zhou1,2,3,#, He-Qun Liu1,3,6, David M. Irwin1,4,5, Yong-Yi Shen1,7,* and Ya-Ping Zhang1,3,*
Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. A total of 3.1% (368) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We re-sequenced some of the positively selected sites (PSSs), within the positively selected genes (PSGs), and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.
