Getting a better picture of microbial evolution en route to a network of genomes
Getting a better picture of microbial evolution en route to a network of genomes
复制标题
DOI：
10.1098/rstb.2009.0040
复制
发表时间：
2009-08-12
影响因子：
6.3
通讯作者：
Martin, William
中科院分区：
文献类型：
--
作者：
Dagan, Tal;Martin, William
目前大多数关于进化的思考都是用树的概念来表达的。用具有递归分支的树的概念来表示反复发生的分化事件，是描述多细胞生物（如脊椎动物或陆地植物）进化的一个貌似合理的比喻。但是，如果我们试图把树的比喻强加到整个进化过程中，事情就会严重出错，因为我们越仔细地通过基因和基因组序列比较的镜子来检查微生物基因组，符合分岔树概念的数据量就越少。这主要是因为在微生物中，内共生和横向基因转移是重要的，这两种自然变异机制不同于达尔文所设想的那种自然变异。由于这样的原因，当涉及到讨论所有生物之间的关系时，也就是说，包括微生物和它们的所有基因，而不仅仅是一个或少数几个，许多生物学家现在开始在微生物染色体之间的进化关系的背景下谈论网络，而不是树。但光说还不够。如果我们真的要构建网络而不是树来描述进化过程，它们会是什么样子？在这里，我们考虑内共生和一个涉及181个测序的原核生物的基因组网络的例子，以及它如何与早期细胞进化的一些想法相一致。
Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution.