Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes
Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes
复制标题
DOI：
10.1016/j.gene.2007.11.016
复制
发表时间：
2008-02-01
期刊：
影响因子：
3.5
通讯作者：
Braun, Edward L.
中科院分区：
文献类型：
--
作者：
Chojnowski, Jena L.;Kimball, Rebecca T.;Braun, Edward L.
Neoaves是最多样化的主要鸟类分支，包含近似95%的鸟类物种，它经历了一个古老但快速的多样化，使得分支基础的关系难以解决。事实上，Neoaves被认为是一个“硬”多分割，不能用任何数量的数据来解决。然而，这一结论是基于缓慢进化的编码序列和核糖体RNA，最近一些使用更快速进化的内含子序列的研究表明，在Neoaves的基础上有一些解决方案。为了进一步研究内含子和外显子在遗传学中的应用，我们对两个未连接的网格蛋白重链基因（CLTC和CLTCL 1）的部分进行了测序。基于单个分区（即内含子和外显子）的系统发育树，组合数据集和使用Robinson-Foulds距离（拓扑差异的度量）的已发表的同源性比较显示出比预期的更多的相似性，这表明Neoaves的基础上有结构。我们发现，内含子提供了更多的信息网站，受到较少的同质性，并提供了更好的支持，广为接受的分支，这表明内含子的进化更适合于确定密集的分支事件，如基地的Neoaves。此外，系统发育能力分析表明，现有的鸟类分子数据集不太可能提供足够的系统发育信息，以解决在新鸟类的基础上的关系，特别是当外显子或其他缓慢演变的地区。虽然无法使用现有数据明确建立Neoaves中的订单之间的关系，但Neoaves的基础似乎并不代表硬多分割。我们的分析表明，大型内含子数据集有最好的潜力，以解决鸟类之间的关系，并表明其他系统发育问题的内含子数据的效用应进行检查。(C)2007 Elsevier B. V.保留所有权利。
Neoaves is the most diverse major avian clade, containing similar to 95% of avian species, and it underwent an ancient but rapid diversification that has made resolution of relationships at the base of the clade difficult. in fact, Neoaves has been suggested to be a "hard" polytomy that cannot be resolved with any amount of data. However, this conclusion was based on slowly evolving coding sequences and ribosomal RNAs and some recent studies using more rapidly evolving intron sequences have suggested some resolution at the base of Neoaves. To further examine the utility of introns and exons for phylogenetics, we sequenced parts of two unlinked clathrin heavy chain genes (CLTC and CLTCL1). Comparisons of phylogenetic trees based upon individual partitions (i.e. introns and exons), the combined dataset, and published phylogenies using Robinson-Foulds distances (a metric of topological differences) revealed more similarity than expected by chance, suggesting there is structure at the base of Neoaves. We found that introns provided more informative sites, were subject to less homoplasy, and provided better support for well-accepted clades, suggesting that intron evolution is better suited to determining closely-spaced branching events like the base of Neoaves. Furthermore, phylogenetic power analyses indicated that existing molecular datasets for birds are unlikely to provide sufficient phylogenetic information to resolve relationships at the base of Neoaves, especially when comprised of exon or other slowly evolving regions. Although relationships among the orders in Neoaves cannot be definitively established using available data, the base of Neoaves does not appear to represent a hard polytomy. Our analyses suggest that large intron datasets have the best potential to resolve relationships among avian orders and indicate that the utility of intron data for other phylogenetic questions should be examined. (C) 2007 Elsevier B.V. All rights reserved.