Data from: Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes

The saola, Pseudoryx nghetinhensis, was unknown to science until its formal description in 1993. This endangered species is a member of the ruminant artiodactyl family Bovidae (cattle, sheep, goats, and antelopes). However, given its puzzling combination of morphological traits, the specific affinities of Pseudoryx within Bovidae are controversial. A preliminary genetic investigation suggested that Pseudoryx should be placed in the subfamily Bovinae (cattle, buffaloes, spiral-horned antelopes, and nilgai), but a recent cladistic analysis of skeletal and dental characters allied Pseudoryx with caprine bovids (sheep, goats, musk oxen, goat antelopes, and Pantholops). The morphological and molecular hypotheses differ in assigning the saola to either of the two most divergent clades of Bovidae. In this report, phylogenetic analyses of DNA sequences from five genes are used to test these alternatives. Protein coding regions, introns, and ribosomal DNAs from the nuclear and mitochondrial genomes discount the hypothesis that Pseudoryx is a close relative of Caprinae. Instead, combined analyses of the DNA data and published morphological evidence place Pseudoryx with Bovini (cattle and buffaloes), a subclade of Bovinae. In separate analysis, the matrix of morphological characters links Pseudoryx with caprine bovids, but in the context of the molecular data, the gross anatomical evidence strongly supports a grouping of Pseudoryx with Bovinae. Surprisingly, the morphological partition provides the most character support in the combined analysis. This striking result is obscured by separate analyses of the individual data sets and the taxonomic congruence approach.

安南锭角羚（Pseudoryx nghetinhensis）直到1993年被正式科学描述之前，一直不为科学界所知。该濒危物种隶属于反刍偶蹄类牛科（Bovidae），涵盖牛、绵羊、山羊与羚羊等类群。然而由于其兼具诸多令人困惑的形态特征，安南锭角羚在牛科内的具体分类亲缘关系一直存在争议。早期一项遗传学预研究提出，应将安南锭角羚归入牛亚科（Bovinae），该类群包含牛、水牛、旋角羚羊及蓝牛羚等物种；但近期一项基于骨骼与牙齿特征的支序分类分析（cladistic analysis）则将安南锭角羚与羊亚科（Caprinae）牛类群归为一类，羊亚科包含绵羊、山羊、麝牛、羊羚及藏羚属（Pantholops）物种。形态学与分子生物学的两类假说，将安南锭角羚分别归入牛科下两个差异最大的演化支（clade）之一，二者分歧显著。本研究通过对5个基因的DNA序列开展系统发育分析（phylogenetic analysis），以检验这两种对立的分类假说。来自核基因组与线粒体基因组的蛋白质编码区、内含子（intron）及核糖体DNA序列数据，均不支持安南锭角羚与羊亚科存在近缘亲缘关系的假说。与之相反，整合DNA序列数据与已发表的形态学证据的联合分析结果显示，安南锭角羚应隶属于牛亚科下的牛族（Bovini）这一演化支，牛族涵盖牛与水牛类群。单独的形态学特征矩阵分析则将安南锭角羚与羊亚科牛类群归为一类，但结合分子数据来看，该大体解剖学证据转而强烈支持安南锭角羚隶属于牛亚科的结论。令人意外的是，在联合分析中，形态学数据分区提供了最高的特征支持度。这一显著结果在单独数据集分析与分类一致性方法（taxonomic congruence approach）的检验中均被掩盖，未能显现。