Data from: Ratite non-monophyly: independent evidence from 40 novel loci

Large-scale multi-locus studies have become common in the field of molecular phylogenetics, but the best way to interpret these studies when their results strongly conflict with prior information about phylogeny remains unclear. An example of such a conflict is provided by the ratites (the large flightless birds of southern land masses, including ostriches, emus, and rheas). Ratite monophyly is strongly supported by both morphological data and many earlier molecular studies and is used as a textbook example of vicariance biogeography. However, recent studies have indicated that ratites are not monophyletic; instead, the volant tinamous nest inside the ratites rather than forming their sister group within the avian superorder Palaeognathae. Large-scale studies can exhibit biases that reflect a number of factors, including limitations in the fit of the evolutionary models used for analyses and problems with sequence alignment, so the unexpected conclusion that ratites are not monophyletic needs to be rigorously evaluated when considered in light of prior evidence to the contrary. A rigorous approach to testing novel hypotheses generated by large-scale studies is to collect independent evidence (i.e., excluding the loci and/or traits used to generate the hypotheses). This is likely to be particularly important when the novel hypothesis is controversial. Here we used 40 nuclear loci not used in previous studies of the Palaeognathae to investigate the relationship between the ratites and their lesser-known relatives the tinamous. Our results strongly support the recent molecular studies, revealing that the deepest branch within Palaeognathae separates the ostrich from the other members of the clade, rather than the traditional hypothesis that separates the tinamous from the ratites. To ensure these results reflected evolutionary history rather than artifacts, we examined potential biases in types of loci used, heterotachy, alignment biases, and discordance between gene trees and the species tree. All analyses of our data consistently supported non-monophyly of the ratites and no confounding biases could be identified. Given this confirmation that ratites are not monophyletic using independent evidence, we hope that this study stimulates further comparative research focused on paleognath development and genetics that might reveal the basis of the morphological convergence evident in these large, flightless birds.

大规模多位点研究现已在分子系统发育学（molecular phylogenetics）领域中广为应用，但当这类研究的结果与此前已有的系统发育先验信息产生强烈冲突时，其合理的解读路径仍不明确。平胸总目（ratites）——即分布于南半球各大陆的大型无飞鸟类，涵盖鸵鸟、鸸鹋及美洲鸵——便是这类研究冲突的典型实例。平胸总目单系性（monophyly）不仅得到了形态学数据与诸多早期分子研究的强力支持，更被作为隔离分化生物地理学（vicariance biogeography）的教科书级范例。然而近期的研究表明，平胸总目并非单系群；反之，具备飞行能力的䳍形目鸟类（tinamous）嵌套于平胸总目类群内部，而非作为其姊妹群隶属于古颚总目（Palaeognathae）这一鸟类总目。大规模多位点研究可能存在多种偏倚，其成因包括分析所用进化模型（evolutionary models）的适配局限以及序列比对（sequence alignment）相关问题，因此，与既有先验证据相悖的“平胸总目并非单系群”这一意外结论，需要结合原有反面证据开展严格验证。针对大规模研究提出的新假说开展检验的严谨路径，便是收集独立证据——即排除用于生成该假说的基因座与/或性状。当新假说存在争议时，这一路径尤为关键。本研究利用此前古颚总目研究未涉及的40个核基因座（nuclear loci），探究了平胸总目及其鲜为人知的近亲䳍形目鸟类之间的演化关系。我们的研究结果强力支持近期的分子研究结论，揭示出古颚总目内部最深的演化分支将鸵鸟与该演化支的其余类群分离开来，而非传统假说中所主张的将䳍形目鸟类与平胸总目分开。为确保本研究结果反映的是真实演化历史而非实验假象，我们对所用基因座类型的潜在偏倚、进化速率异质性（heterotachy）、比对偏倚以及基因树（gene tree）与物种树（species tree）之间的冲突进行了检验。本研究的所有分析均一致支持平胸总目并非单系群的结论，且未发现任何混淆性偏倚。鉴于利用独立证据证实了平胸总目并非单系群这一结论，我们希望本研究能够推动针对古颚类发育与遗传学的后续比较研究，以期揭示这些大型无飞鸟类所展现出的形态趋同现象背后的机制。