A Bayesian Method for Analyzing Lateral Gene Transfer
A Bayesian Method for Analyzing Lateral Gene Transfer
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DOI：
10.1093/sysbio/syu007
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发表时间：
2014-05-01
影响因子：
6.5
通讯作者：
Lagergren, Jens
中科院分区：
文献类型：
--
作者：
Sjostrand, Joel;Tofigh, Ali;Lagergren, Jens
横向基因转移（Lateral gene transfer， LGT）是指在属于同一或不同物种的两个非垂直相关个体之间转移DNA的过程，它被认为是原核生物进化的重要力量，并对真核生物的进化产生了越来越多的影响。LGT因其在细菌中转移致病元素和抗生素抗性以及将转基因作物的农药抗性转移到其他植物中的潜力而引起了公众的广泛关注。从更广泛的角度来看，越来越多的研究强调了LGT在使生物体占据新的生态位或适应环境变化方面的作用。LGT对标准的基于树的进化概念提出的挑战也在争论中。然而，由于缺乏计算工具，LGT的研究受到严重限制。目前可用的最好的LGT算法是基于简约性的系统发育方法，它需要一个预先计算的基因树，并且不能在有时差异很大的最简约的解决方案之间进行选择。此外，在许多研究中，应用了简单的启发式方法，只能处理假定的同源物，而完全忽略了基因复制（GDs）。因此，在特定基因家族中提出的LGT，以及一般的LGT率，仍然存在争议。我们提出了一种基于贝叶斯马尔可夫链蒙特卡罗的方法，该方法集成了GD，基因丢失，LGT和序列进化，并将该方法应用于两组细菌的全基因组分析：Mollicutes和Cyanobacteria。分析表明，虽然远缘种间的LGT率较高，但近缘种间的LGT和重复的净组合率平均较高。我们还表明，在基因树推断中忽略可调和性的常见做法高估了LGT和重复事件的数量。[贝叶斯;基因重复;基因损失;水平基因转移；横向基因转移；密度;系统发生学。]。
Lateral gene transfer (LGT)uwhich transfers DNA between two non-vertically related individuals belonging to the same or different speciesuis recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events. [Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.].