Lateral gene transfer as a support for the tree of life
Lateral gene transfer as a support for the tree of life
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DOI：
10.1073/pnas.1116871109
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发表时间：
2012-03-27
影响因子：
11.1
通讯作者：
Daubin, Vincent
中科院分区：
文献类型：
--
作者：
Abby, Sophie S.;Tannier, Eric;Daubin, Vincent
横向基因转移（LGT），即从其他物种获得基因，是一种主要的进化力量。然而，它作为一个适应过程的成功，使生命历史的重建成为一个复杂的难题：如果没有基因在生命进化过程中不受影响，人们如何依靠分子标记来重建物种之间的关系？在此，我们以完全不同的视角审视LGT及其对重建生命历史的影响。而不是试图消除LGT的影响，并忽略了作为一个结果的基因历史的大部分信息，我们使用一个明确的系统发育模型的基因转移，以调和基因的历史与物种树。我们研究了16个细菌和古菌门，代表了分布在336个基因组中的12，000个基因家族的数据集。我们的研究结果表明，在大多数门，LGT提供了丰富的物种多样性的模式上的系统发育信号，这个信号是强大的基因家族的选择研究。我们还发现，LGT带来了一个丰富的信号的根的物种树，这是以前被忽视的位置。我们的研究结果量化了生命之树谱系之间基因转移率的巨大变化，并为“复杂性假说”提供了强有力的支持，该假说指出，其产物参与大分子蛋白质复合物的基因相对耐转移。
Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the reconstruction of the history of life an intricate puzzle: If no gene has remained unaffected during the course of life's evolution, how can one rely on molecular markers to reconstruct the relationships among species? Here, we take a completely different look at LGT and its impact for the reconstruction of the history of life. Rather than trying to remove the effect of LGT in phylogenies, and ignoring as a result most of the information of gene histories, we use an explicit phylogenetic model of gene transfer to reconcile gene histories with the tree of species. We studied 16 bacterial and archaeal phyla, representing a dataset of 12,000 gene families distributed in 336 genomes. Our results show that, in most phyla, LGT provides an abundant phylogenetic signal on the pattern of species diversification and that this signal is robust to the choice of gene families under study. We also find that LGT brings an abundant signal on the location of the root of species trees, which has been previously overlooked. Our results quantify the great variety of gene transfer rates among lineages of the tree of life and provide strong support for the "complexity hypothesis," which states that genes whose products participate to macromolecular protein complexes are relatively resistant to transfer.