Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer
Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer
复制标题
原绿球藻和聚球藻核心基因一致性的贝叶斯分析及其对水平基因转移的影响
作者：
N. Matzke;P. Shih;C. Kerfeld
人们经常认为，水平基因转移在微生物中是如此普遍，以至于代表垂直遗传模式的系统发育树的概念过于简单，甚至具有误导性。“通用蛋白质”曾被用来推断生物的进化，但被批评为“百分之一的树”。目前，对于那些希望严格评估基于相对少数保守基因的通用蛋白质遗传学如何代表数百个基因的系统发育历史的人来说，几乎没有选择。在这里，我们解决这个问题，提出了一个可视化的方法和贝叶斯框架内的统计测试。我们使用的基因组的海洋蓝藻，一组被认为表现出大量的HGT，作为一个测试案例。我们从28个蓝藻基因组中选取了379个正交基因家族，并估计了树的贝叶斯后验分布-一个“树云”-对于每个家族，以及基于假定的“通用蛋白质”的串联数据集。然后，我们计算各种指标上所有树云内和树云之间的平均距离，并使用非度量多维缩放（NMMDS）可视化这个高维空间。我们表明，树空间是强烈的集群和通用蛋白质树云是统计上显着更接近这个树空间的中心比任何个人的基因树云。我们应用了几种常用的不一致/HGT测试，并表明他们同意HGT在该数据集中很少见，但对哪些基因受到HGT的影响做出了不同的选择。我们的研究结果表明，“百分之一的树”的代表性问题是一个定量的经验问题，系统发育的中心趋势是一个有意义的观察，即使许多个别的基因不同意，由于各种来源的不一致。
It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.
DOI：
10.1073/pnas.0800679105
发表时间：
2008-07-22
影响因子：
11.1
作者：
Dagan, Tal;Artzy-Randrup, Yael;Martin, William
通讯作者：
Martin, William