Morphology, molecules, and the phylogenetics of cetaceans

Recent phylogenetic analyses of cetacean relationships based on DNA sequence data have challenged the traditional view that baleen whales (Mysticeti) and toothed whales (Odontoceti) are each monophyletic, arguing instead that baleen whales are the sister group of the odontocete family Physeteridae (sperm whales). We reexamined this issue in light of a morphological data set composed of 207 characters and molecular data sets of published 12S, 16S, and cytochrome b mitochondrial DNA sequences. We reach four primary conclusions: (1) Our morphological data set strongly supports the traditional view of odontocete monophyly; (2) the unrooted molecular and morphological trees are very similar, and most of the conflict results from alternative rooting positions; (3) the rooting position of the molecular tree is sensitive to choice of artiodactyl outgroup taxa and the treatment of two small but ambiguously aligned regions of the 12S and 16S sequences, whereas the morphological root is strongly supported; and (4) combined analyses of the morphological and molecular data provide a well-supported phylogenetic estimate consistent with that based on the morphological data alone (and the traditional view of toothed-whale monophyly) but with increased bootstrap support at nearly every node of the tree.

近年来基于DNA序列数据开展的鲸类（Cetacea）系统发育关系研究，对传统认知提出了质疑：传统观点认为须鲸类（Mysticeti）与齿鲸类（Odontoceti）均为单系群，而新研究则提出须鲸类是齿鲸类抹香鲸科（Physeteridae）的姊妹群。本研究依托由207个形态性状组成的数据集，以及已发表的12S、16S核糖体RNA基因与细胞色素b（cytochrome b）线粒体DNA序列分子数据集，重新探讨了这一学术争议。本研究得到四项核心结论：（1）本研究的形态学数据集强烈支持齿鲸类单系群的传统观点；（2）无根分子系统树与形态学系统树的拓扑结构高度相似，绝大多数冲突源自不同的根位置选择；（3）分子树的根位置对所选偶蹄目（Artiodactyla）外类群类群，以及12S与16S序列中两个短小但序列比对存在歧义的区域的处理方式较为敏感，而形态学树的根则得到了强有力的统计支持；（4）联合分析形态学与分子数据得到的系统发育估计结果稳健可靠，与仅基于形态学数据（以及齿鲸类单系群的传统观点）得到的结果一致，且几乎所有树节点的自展支持率（bootstrap support）均有所提升。