A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
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DOI：
10.1371/journal.pone.0054848
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Brumfield RT
中科院分区：
文献类型：
--
作者：
McCormack JE;Harvey MG;Faircloth BC;Crawford NG;Glenn TC;Brumfield RT
Neoaves（包含绝大多数鸟类多样性的分支）中鸟类之间的进化关系，由于众多谱系的古老而快速的辐射而让系统学家感到烦恼。我们应用了一种新的系统发育学方法，利用鸟类基因组中超保守元件 (UCE) 的目标富集（序列捕获）和高通量测序来解决 Neoaves 中的关系。我们从 Neoaves 的 32 个成员和一个外群（鸡）的 UCE 位点收集了序列数据，并分析了缺失数据量不同的数据集。允许缺失数据的 1,541 个基因座的比对完成度为 87%，并产生了高度解析的系统发育，贝叶斯树和最大似然 (ML) 树之间具有广泛的一致性。尽管 416 个 UCE 位点的 100% 完整矩阵的结果相似，但在该分析中贝叶斯树和 ML 树的差异更大，这表明从 416 个位点增加到 1,541 个位点会导致树的稳定性和分辨率提高。我们研究的新结果包括表型不同的鸟类家族之间令人惊讶的密切关系，例如热带鸟（Phaethontidae）和日鹬（Eurypygidae）以及鸨（Otididae）和斑鸠（Musophagidae）之间的关系。这种系统发育支持了对单系水鸟和陆地鸟类进化支的支持，也有力地支持了先前研究中存在争议的结果，包括雀形目和鹦鹉之间的姐妹关系以及鹰和猎鹰家族中猛禽的非单系关系。尽管要完全解决新鸟的一些深层关系，特别是水鸟和陆鸟以外的谱系之间的关系，仍然存在重大挑战，但这项研究表明，更多的数据将产生日益清晰的鸟类系统发育。
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 were 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.
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影响因子：
5.4
作者：
Brown JW;Rest JS;García-Moreno J;Sorenson MD;Mindell DP
通讯作者：
Mindell DP
影响因子：
4.1
作者：
Gibb, Gillian C.;Penny, David
通讯作者：
Penny, David
影响因子：
2.6
作者：
Glenn, Travis C.;French, Jeffrey O.;Sawyer, Roger H.
通讯作者：
Sawyer, Roger H.
DOI：
10.1073/pnas.0607004104
发表时间：
2007-04-03
影响因子：
11.1
作者：
Edwards, Scott V.;Liu, Liang;Pearl, Dennis K.
通讯作者：
Pearl, Dennis K.
影响因子：
3.5
作者：
Chojnowski, Jena L.;Kimball, Rebecca T.;Braun, Edward L.
通讯作者：
Braun, Edward L.