Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA.
Syst Biol. 2013 Jan 1;62(1):35-49. doi: 10.1093/sysbio/sys067. Epub 2012 Jul 24.
Large-scale multilocus studies have become common in 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. 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). We used 40 nuclear loci not used in previous studies that investigated the relationship among ratites and tinamous. Our results strongly support the recent molecular studies, revealing that the deepest branch within Palaeognathae separates the ostrich from other members of the clade, rather than the traditional hypothesis that separates the tinamous from the ratites. To ensure these results reflected evolutionary history, we examined potential biases in types of loci used, heterotachy, alignment biases, and discordance between gene trees and the species tree. All analyses consistently supported nonmonophyly of the ratites and no confounding biases were identified. This confirmation that ratites are not monophyletic using independent evidence will hopefully stimulate further comparative research on paleognath development and genetics that might reveal the basis of the morphological convergence in these large, flightless birds.
大规模的多位点研究在分子系统发育学中已变得常见，但当这些研究的结果与有关系统发育的先前信息强烈冲突时，最好的解释方法仍不清楚。这种冲突的一个例子来自平胸类（即南部大陆的大型不能飞行的鸟类，包括鸵鸟、鸸鹋和美洲鸵鸟）。形态数据和许多早期的分子研究强烈支持平胸类的单系性，并且被用作地理隔离生物地理学的范例。然而，最近的研究表明，平胸类不是单系的；相反，飞行的恐鸟在平胸类内部筑巢，而不是在古颚总目鸟类超目中形成它们的姊妹群。大规模的研究可能表现出反映许多因素的偏差，包括用于分析的进化模型拟合的局限性以及序列比对的问题，因此，平胸类不是单系的这一意外结论需要严格评估。一种严格的方法是收集独立的证据（即排除用于产生假设的基因座和/或特征）来检验大规模研究产生的新假设。我们使用了 40 个未在以前研究中用于研究平胸类和恐鸟类关系的核基因座。我们的结果强烈支持最近的分子研究，揭示了古颚总目内部的最深处分支将鸵鸟与该分支的其他成员分开，而不是传统的将恐鸟与平胸类分开的假说。为了确保这些结果反映了进化历史，我们检查了所用基因座类型、异速进化、比对偏差和基因树与种系发生树之间的分歧的潜在偏差。所有分析均一致支持平胸类的非单系性，并未发现混淆偏差。使用独立的证据确认平胸类不是单系的，有望进一步激发对古颚总目的发育和遗传学的比较研究，这可能揭示这些大型、不能飞行的鸟类形态趋同的基础。
