Data from: A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

近年来的研究已报道了鲸类（cetaceans）中与其水生适应能力相关的多种分子适应性事件，但现有相关研究均未纳入河马（hippopotamus）类群，这使得我们无法厘清鲸类的分子适应性演化是发生在其与半水生姊妹类群分化之前还是之后。本研究获取了河马与座头鲸的全新转录组数据，并结合已公开的其他8种鲸类的转录组数据开展联合分析。我们共鉴定出超过11000个同源基因（orthologous genes），构建了覆盖23种哺乳动物的全基因组范围数据集，包含6845个编码DNA序列（coding DNA sequences）——据我们所知，这是目前为止规模最大的鲸类系统基因组学数据集。我们在河马与鲸类共同祖先所在的演化支上鉴定出9个受到正选择（positive selection）的基因；相较于河马支系的64个受正选择基因，鲸类支系中共发现461个受正选择的基因。功能注释（functional annotation）分析显示，这些适应性基因涉及脂质代谢、缺氧耐受、肌肉与大脑功能等多种生物学过程。结合蛋白质-蛋白质相互作用（protein–protein interactions）数据，我们发现鲸类中与神经和肌肉系统相关的基因产物存在聚集现象。本研究未发现两类群共享祖先适应性的有力证据，现存鲸类的绝大多数分子适应性演化事件均发生在其与河马科（hippopotamids）分化之后。