Department of Biology, University of California Riverside, Riverside, CA 92521, USA.
Mol Phylogenet Evol. 2009 Dec;53(3):891-906. doi: 10.1016/j.ympev.2009.08.018. Epub 2009 Aug 21.
Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene-Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning approximately 10 million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea.
鲸目动物在适应完全水生的生活方面在哺乳动物中表现出色，但它们的进化史的许多方面仍未得到解决。在这里，我们将来自核基因 RAG1 和 PRM1 的 37 个新序列与该群体的大多数已发表的分子数据（45 个核基因座、转座子、线粒体基因组）合并，并生成了一个由 42,335 个字符组成的超级矩阵。这些数据中的绝大多数从未被合并过。对超级矩阵的基于模型的分析为 87 种鲸目物种产生了一个可靠、一致的进化假说。贝叶斯分析证实了齿鲸（齿鲸）的单系性，稳定了基础齿鲸的关系，并完全解决了须鲸（须鲸）内部以及有问题的多态科海豚科（海洋海豚）的分支事件。仅记录到与最大似然结果相对有限的冲突，并且在简约树中发现的差异得到了非常弱的支持。我们利用贝叶斯超级矩阵树使用松弛时钟方法估计谱系之间的分歧日期。分歧估计显示，在始新世-渐新世边界附近，基础齿鲸谱系的分支迅速，河海豚谱系的古老，拟鲸类的晚中新世辐射，以及大约 1000 万年前开始的海豚科的快速辐射。我们全面的、时间校准的树为鲸目动物的广泛比较研究提供了一个强大的进化工具。
