Data from: The position of Cetacea within Mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also, that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate amounts to 89% of the ingroup. Addition of data from recently described cetacean astragali attributed to cetaceans does not overturn artiodactyl monophyly.

对于研究鲸目（Cetacea，包含鲸、海豚和鼠海豚）这一演化支从完全陆生转向完全水生生活所伴随的生物形态与功能转变的进化生物学家而言，明确鲸目在哺乳纲（Mammalia）中的系统发育位置具有核心重要性。基于分子数据的系统发育分析与基于形态学数据的系统发育分析均将鲸目置于有蹄类（Ungulates）之中，但二者在其他方面存在冲突。形态学家认为鲸目与已灭绝的陆生有蹄类类群中兽类（mesonychians）亲缘关系最近，但对于奇蹄目（Perissodactyla，奇数趾有蹄类）还是偶蹄目（Artiodactyla，偶数趾有蹄类）是现存与鲸目亲缘关系最近的演化支，学界长期存在分歧，且一直认为这两个目均为单系群（monophyletic）。
与此形成鲜明对比的是，绝大多数基于分子数据的系统发育分析不仅表明偶蹄类是现存与鲸目亲缘关系最近的类群，还指出偶蹄目为并系群（paraphyletic）——除非鲸目嵌入偶蹄目内部，且通常作为河马科（Hippopotamidae）的姊妹群（sister group）。
本研究对10个现存类群与30个灭绝类群的123个形态学性状开展最大简约法（maximum parsimony）分析，以此检验关于鲸目姊妹群关系的多项假说所对应的形态学证据。我们主张将部分多状态性状（multistate characters）设置为有序性状，因为该处理方式可纳入关于层级式形态转变的相关信息。无论多状态性状设置为有序还是无序，在所有最简约树中，偶蹄目均为鲸目现存的姊妹类群。当部分多状态性状设置为有序时，灭绝演化支中兽类（Mesonychia，包含中兽科Mesonychidae + 近河狸兽科Hapalodectidae）为鲸目的姊妹类群，且偶蹄目为单系群。
若将所有化石类群从分析中移除，则偶蹄目为并系群，鲸目嵌入偶蹄目内部，这表明在有蹄类演化支的系统发育分析中纳入中兽类与其他灭绝基干类群（stem taxa），对于恢复偶蹄目的单系性至关重要。仅依靠分子数据得到的系统发育树可能存在分支结果不一致的风险，原因在于无法采样灭绝演化支——保守估计该类群占内类群（ingroup）的89%。新增近期报道的归属鲸类的距骨（astragalus，复数astragali）相关数据，并未推翻偶蹄目的单系性。