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...

在分子系统发育学领域，大规模多位点研究已日益普遍，但当研究结果与先前的系统发育信息存在强烈冲突时，如何解读此类研究仍不明确。平胸鸟类（ratites，即南半球陆地上的大型不会飞鸟类，包括鸵鸟、鸸鹋和美洲鸵）便是此类冲突的一个实例。平胸鸟类的单系性（monophyly）得到形态学数据及诸多早期分子研究的有力支持，且被用作隔离生物地理学（vicariance biogeography）的教科书案例。然而，近期研究表明平胸鸟类并非单系类群；相反，会飞的䳍科鸟类（tinamous）嵌套于平胸鸟类类群内部，而非在鸟类超目古颚类（Palaeognathae）中构成其姐妹群。大规模研究可能存在偏差，其反映了多种因素，包括分析所用进化模型的拟合局限性及序列比对问题，因此平胸鸟类非单系性这一出人意料的结论……