Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci was similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

涵盖绝大多数鸟类多样性的演化支——新鸟类（Neoaves）内部的鸟类演化关系，因众多类群在远古时期发生的快速辐射演化，长期困扰着分类学家。本研究采用全新的系统基因组学方法，通过靶向富集（序列捕获）技术获取鸟类基因组中的超保守元件（UCEs），并结合高通量测序，以解析新鸟类内部的系统发育关系。我们为32种新鸟类以及1个外类群（家鸡）采集了超保守元件基因座的序列数据，并针对缺失数据量不同的数据集开展分析。纳入1541个允许存在缺失数据的基因座的序列比对矩阵，其完整度达87%，由此构建的系统发育树分辨率极高，且贝叶斯树与最大似然（ML）树结果高度一致。尽管对包含416个超保守元件基因座的100%完整矩阵开展分析得到的结果相似，但本次分析中贝叶斯树与ML树的差异更为显著，这表明将基因座数量从416增加至1541，可提升系统发育树的稳定性与分辨率。本研究的新颖发现包括表型差异极大的鸟类类群间存在出人意料的近缘关系：例如鹲科（Phaethontidae）的热带鸟与日鳽科（Eurypygidae）的太阳鹭，以及鸨科（Otididae）的鸨与蕉鹃科（Musophagidae）的蕉鹃。该系统发育树强化了水鸟与陆鸟两大单系演化支的支持证据，同时也为此前研究中存在争议的结论提供了强力支撑，包括鸣禽与鹦鹉的姊妹群关系，以及鹰科和隼科猛禽并非单系群的结论。尽管完全解析新鸟类内部部分深层演化关系仍面临重大挑战，尤其是水鸟与陆鸟之外的类群间的关系，但本研究表明，增加测序数据量将有助于逐步构建分辨率更高的鸟类系统发育树。