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.

中南大羚（saola），学名Pseudoryx nghetinhensis，直至1993年正式被科学记述前从未为学界所知。这一濒危物种隶属于反刍偶蹄类的牛科（Bovidae，涵盖牛、绵羊、山羊与羚羊），然而因其兼具诸多令人困惑的形态特征，该属在牛科内的具体分类亲缘关系始终存在争议。一项初步遗传学研究曾提出，应将中南大羚归入牛亚科（Bovinae，包含牛、水牛、旋角羚羊及蓝牛羚）；但近期一项基于骨骼与牙齿特征的分支分类分析（cladistic analysis）则将其与羊亚科类群（caprine bovids，涵盖绵羊、山羊、麝牛、山羊羚羊以及藏羚羊Pantholops）归为一类。形态学与分子学假说的分歧点在于，将中南大羚划归牛科两个分化程度最高的支系之一。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、内含子及核糖体DNA序列，均否定了“中南大羚与羊亚科（Caprinae）为近亲”的假说。与之相反，对DNA数据与已发表形态学证据的联合分析显示，中南大羚应归入牛亚科下的牛族（Bovini，包含牛与水牛）这一亚支。单独分析时，形态学特征矩阵将中南大羚与羊亚科类群关联起来；但结合分子数据来看，大体解剖学证据则强力支持中南大羚归入牛亚科的结论。令人意外的是，在联合分析中，形态学数据分区（morphological partition）提供了最高的特征支持度，这一引人注目的结果在单独分析各数据集以及采用分类群一致性方法（taxonomic congruence approach）时会被掩盖。