Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada.
Biol Direct. 2011 Jul 20;6:39; discussion 39. doi: 10.1186/1745-6150-6-39.
We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.
We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.
Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.
我们介绍了几种基于森林和网络的方法来探索微生物进化，并将它们应用于对 30 株大肠杆菌的数千个基因的研究。这个案例研究说明了额外的分析如何为标准的生命之树 (TOL) 方法提供快速的启发式替代方案。
我们使用基因网络来识别具有非典型进化模式的基因，并使用基因组网络来描述大肠杆菌与移动遗传元件之间遗传伙伴关系的进化。我们开发了一种新颖的多色四分体方法来捕捉大肠杆菌内部重组模式，更新氏族工具包，并搜索水平基因转移和致病性对基因进化的影响在两个承载大肠杆菌的大型树木森林中。我们揭示了涉及大肠杆菌的高比率的水平基因转移（研究中的约 40%的树木），并表明大肠杆菌的核心基因和外壳基因都受到非树状进化过程的影响。我们表明，致病性生活方式影响了 30%的基因树的结构，而且致病性菌株比非致病性菌株更有可能相互转移基因。此外，我们提出了五组基因作为致病性的候选移动模块。我们还提供了大肠杆菌和移动遗传元件之间近期水平基因转移的有力证据。
根据生物学家想要解决的进化问题（即模块、遗传伙伴关系、重组、水平基因转移或具有非典型进化模式的基因的识别等），基于森林和网络的方法比重建单个树更可取，因为它们提供了关于基因组进化动态的见解并产生了假设，而不是物种和谱系的相对分支顺序。这种方法的多元化 - 使用树林和网络 - 应该被鼓励用于分析微生物进化中起作用的进化过程。本文经过了以下人员的评审：Ford Doolittle、Tal Pupko、Richard Burian、James McInerney、Didier Raoult 和 Yan Boucher。
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