The net of life: Reconstructing the microbial phylogenetic network
The net of life: Reconstructing the microbial phylogenetic network
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DOI：
10.1101/gr.3666505
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发表时间：
2005-07-01
期刊：
影响因子：
7
通讯作者：
Ouzounis, CA
中科院分区：
文献类型：
--
作者：
Kunin, V;Goldovsky, L;Ouzounis, CA
以前有人建议，微生物物种的系统发育可以更好地描述为一个包含垂直和水平基因转移(HGT)事件的网络。然而，到目前为止，所有的系统发育重建都是微生物树，而不是网络。在这里，我们提出了第一次尝试重建这样一个进化网络，我们称之为“生命网络”。我们使用现有的树重建方法来推断垂直继承，并使用祖先状态推理算法将HGT事件映射到树上。我们还描述了一种加权方案，用于估计生物对之间交换的基因数量。我们证明垂直遗传构成了生命树上基因转移的主体。我们将树节点之间的大部分水平基因流动称为“藤条”，并证明了多个但大多是微小的藤条将树连接在一起。我们的结果强烈表明，HGT网络是一个无标度图，这一发现对基因组进化具有重要意义。我们认为，基因可能会以某些生物体为枢纽，通过HGT网络在微生物物种中极快地传播。
It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life." We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as "vines," and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.