Abstract The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]

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使用目标序列捕获对鲸类生命之树进行系统发育解析

摘要 鲸目动物的进化，从早期过渡到水生生活方式到随后的多样化，一直是众多研究的主题。然而，尽管鲸类家族之间的高层关系已经基本确定，但这些群体内系统学的几个方面仍未解决。有问题的进化枝包括海洋海豚（37 种），它们经历了最近的快速辐射，以及喙鲸（22 种），它们尚未使用核位点进行详细研究。高通量测序与针对特定基因组序列的技术的结合应用提供了一种强大的方法，可以快速生成大量用于系统发育研究的直系同源序列数据。为了阐明鲸目动物内的系统发育关系，我们将序列捕获与 Illumina 测序相结合，为 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \ 生成数据usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document} 3200 个蛋白质编码基因，用于 68 种鲸类动物及其近亲，包括侏儒河马。通过组合来自 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{ 的数据\oddsidemargin}{-69pt} \begin{document} }{}$>$\end{document} 38,000 个外显子，现有序列来自 11 种鲸类和 7 个外群分类群，我们为鲸类动物制作了第一个综合比较基因组数据集，涵盖 6,527,596 个对齐的碱基对 (bp) 和 89 个分类群。以最大似然和贝叶斯推理重建的系统发育树，以及对单个基因树的合并分析，产生了大部分一致且支持良好的树。我们的结果完全解决了喙鲸之间的关系以及海洋海豚之间有争议的关系，尤其是有问题的海豚科。我们使用 MCMCTree 对物种发散时间进行贝叶斯估计，并将我们的完整数据集与类时钟基因的子集进行比较。使用完整数据集的分析始终显示出比减少的数据集更小的发散时间差异。此外，新化石的整合（例如，Mystacodon selenensis) 表明冠鲸科的分化早于晚始新世之前，冠海豚科的分化早在中中新世。[鲸类；系统基因组学；海豚科; 紫蛉科; 海豚；鲸鱼。]