Data Types and the Phylogeny of Neoaves
Data Types and the Phylogeny of Neoaves
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DOI：
10.3390/birds2010001
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发表时间：
2021-03-01
期刊：
影响因子：
--
通讯作者：
Kimball, Rebecca T.
中科院分区：
文献类型：
--
作者：
Braun, Edward L.;Kimball, Rebecca T.
新鸟雀是现存鸟类中最大的一支，尽管进行了大量的研究，但其进化史仍不清楚。与解决Neoaves早期分支相关的困难可能是由于该组的快速辐射。然而，研究之间的冲突可能会因分析的数据类型而加剧。例如，对编码外显子的分析通常会产生这样的树，即Strisores（夜鹰和盟友）与其余的Neoaves是姐妹，而对非编码数据的分析通常会产生这样的树，其中Mirandornites（火烈鸟和grebes）是其余Neoaves的姐妹。我们对数据类型效应的理解受到了这样一个事实的阻碍，即以前的分析使用了不同的分类群、基因座和非编码数据类型。在这里，我们提供了强有力的佐证的数据类型的影响假设Neoaves的编码和非编码数据来自相同的类群和基因区域的基础上比较树。已知一种简单的分析方法，以尽量减少偏见，由于碱基组成（编码核苷酸嘌呤和嘧啶）导致编码外显子数据与非编码拓扑结构的一致性增加，使用级联分析。这些结果提高了我们对新鸟类系统发育分辨率的理解，并指出了一个挑战--数据类型效应--这可能是鸟类系统发育分析（和许多其他分类群）中的一个重要因素。使用我们的研究结果，我们提供了一个总结性的遗传学，确定了良好的确证关系，并强调了未来的努力应该集中在特定的节点。
The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge-data type effects-that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.