Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
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DOI：
10.1093/molbev/msr047
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发表时间：
2011-08
影响因子：
10.7
通讯作者：
B. Nabholz;Axel Künstner;Rui Wang;E. Jarvis;H. Ellegren
中科院分区：
文献类型：
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作者：
B. Nabholz;Axel Künstner;Rui Wang;E. Jarvis;H. Ellegren
解决鸟类之间的系统发育关系是系统学中的一个经典问题，特别是当涉及到新鸟类之间的关系时。以前的鸟类系统发育推断仅限于线粒体基因组或少数核基因。在这里，我们应用9种鸟类（几种雀形目，蜂鸟，鸽子，鹦鹉和鸸鹋）的脑深部转录组测序，使用下一代测序技术来了解鸟类转录组进化的特征以及这如何影响系统发育推断，并使用第一代技术将联合收割机与两种鸟类的数据相结合。所述cDNA基因组数据矩阵包括1，995个基因和总共0.77 Mb的外显子序列。首先，我们发现一个意想不到的异质性，在鸟类谱系之间的基础组成的演变。在几个独立的谱系中，第三密码子位置的鸟嘌呤+胞嘧啶（GC）含量显著增加，在雀形目中观察到最强的效果。其次，我们评估GC含量变化对系统发育重建的影响。我们发现重要的拓扑结构之间的不一致，或不考虑GC的变化，每个支持不同的结论，过去的研究，也影响假说的演变特征的声乐学习。第三，我们证明了GC含量的演变和重组率之间的联系，并专注于斑胸草雀血统，发现重组似乎驱动GC含量。虽然我们不能揭示因果关系，但这一观察结果与GC偏倚基因转换模型一致。最后，我们使用这无与伦比的大量鸟类序列数据来研究分子进化的速率，通过化石证据进行校准，并使用短吻鳄转录组测序的数据进行增强。有一个2至3倍的变化，在替代率与雀形目是最迅速的发展和平胸最慢的血统。这项研究说明了下一代测序技术在基因组研究中的潜力，但也说明了使用具有异质碱基组成的全基因组数据时的陷阱。
Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this is particularly so when it comes to understanding the relationships among Neoaves. Previous phylogenetic inference of birds has been limited to mitochondrial genomes or a few nuclear genes. Here, we apply deep brain transcriptome sequencing of nine bird species (several passerines, hummingbirds, dove, parrot, and emu), using next-generation sequencing technology to understand features of transcriptome evolution in birds and how this affects phylogenetic inference, and combine with data from two bird species using first generation technology. The phylogenomic data matrix comprises 1,995 genes and a total of 0.77 Mb of exonic sequence. First, we find an unexpected heterogeneity in the evolution of base composition among avian lineages. There is a pronounced increase in guanine + cytosine (GC) content in the third codon position in several independent lineages, with the strongest effect seen in passerines. Second, we evaluate the effect of GC content variation on phylogenetic reconstruction. We find important inconsistencies between the topologies obtained with or without taking GC variation into account, each supporting different conclusions of past studies and also influencing hypotheses on the evolution of the trait of vocal learning. Third, we demonstrate a link between GC content evolution and recombination rate and, focusing on the zebra finch lineage, find that recombination seems to drive GC content. Although we cannot reveal the causal relationships, this observation is consistent with the model of GC-biased gene conversion. Finally, we use this unparalleled amount of avian sequence data to study the rate of molecular evolution, calibrated by fossil evidence and augmented with data from alligator transcriptome sequencing. There is a 2- to 3-fold variation in substitution rate among lineages with passerines being the most rapidly evolving and ratites the slowest. This study illustrates the potential of next-generation sequencing for phylogenomic studies but also the pitfalls when using genome-wide data with heterogeneous base composition.