Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
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DOI：
10.1093/molbev/mst116
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发表时间：
2013-09-01
影响因子：
10.7
通讯作者：
Douzery, Emmanuel J. P.
中科院分区：
文献类型：
--
作者：
Romiguier, Jonathan;Ranwez, Vincent;Douzery, Emmanuel J. P.
尽管系统基因组数据集的规模迅速增加，但动物系统发育的许多重要节点仍然没有得到解决。其中，胎盘哺乳动物树的生根仍然是一个有争议的问题。困难之一在于基因之间普遍存在的系统发育冲突，每个基因都在讲述自己的故事，这可能是可靠的，也可能是不可靠的。在这里，我们确定了一个简单的标准，即GC含量，这在很大程度上有助于确定哪些基因树最好地反映了物种树。我们评估了13，111个编码序列比对正确重建胎盘发育的能力。我们发现，GC丰富的基因诱导了大量的基因树之间的冲突，并执行差于AT丰富的基因在检索良好的支持，胎盘树上的共识节点。我们解释这种GC效应主要是由于基因组范围内重组率的变化。事实上，已知重组通过GC偏向的基因转换驱动GC含量进化，并且对于系统发育重建可能是有问题的，例如，在不完整的谱系分选背景下。当我们专注于AT-最丰富的部分的数据集，分辨率水平的胎盘胎生大大增加，并获得了强有力的支持，有利于非洲兽根，即非洲兽作为姐妹集团的所有其他胎盘。我们发现，在哺乳动物中，基因树之间的冲突，到目前为止阻碍了胎盘树的决议，集中在GC丰富的基因组区域。我们认为，GC含量，因为它是一个可靠的指标的长期重组率是一个信息的标准，可以帮助确定最可靠的分子标记的物种树推断。
Despite the rapid increase of size in phylogenomic data sets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable or not. Here, we identified a simple criterion, that is, the GC content, which substantially helps in determining which gene trees best reflect the species tree. We assessed the ability of 13,111 coding sequence alignments to correctly reconstruct the placental phylogeny. We found that GC-rich genes induced a higher amount of conflict among gene trees and performed worse than AT-rich genes in retrieving well-supported, consensual nodes on the placental tree. We interpret this GC effect mainly as a consequence of genome-wide variations in recombination rate. Indeed, recombination is known to drive GC-content evolution through GC-biased gene conversion and might be problematic for phylogenetic reconstruction, for instance, in an incomplete lineage sorting context. When we focused on the AT-richest fraction of the data set, the resolution level of the placental phylogeny was greatly increased, and a strong support was obtained in favor of an Afrotheria rooting, that is, Afrotheria as the sister group of all other placentals. We show that in mammals most conflicts among gene trees, which have so far hampered the resolution of the placental tree, are concentrated in the GC-rich regions of the genome. We argue that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.