Department of Evolutionary Biology, University of Haifa, Haifa, 31905, Israel.
Sci Rep. 2020 Jul 24;10(1):12425. doi: 10.1038/s41598-020-62446-5.
It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material not via vertical descent. Thus, the prevalence of HGT is challenging the meaningfulness of the classical Tree of Life concept. Here we present a comprehensive study of HGT representing the entire prokaryotic world. We mainly rely on a novel analytic approach for analyzing an aggregate of gene histories, by means of the quartet plurality distribution (QPD) that we develop. Through the analysis of real and simulated data, QPD is used to reveal evidence of a barrier against HGT, separating the archaea from the bacteria and making HGT between the two domains, in general, quite rare. In contrast, bacteria's confined HGT is substantially more frequent than archaea's. Our approach also reveals that despite intensive HGT, a strong tree-like signal can be extracted, corroborating several previous works. Thus, QPD, which enables one to analytically combine information from an aggregate of gene trees, can be used for understanding patterns and rates of HGT in prokaryotes, as well as for validating or refuting models of horizontal genetic transfers and evolution in general.
现今已证实，在原核生物中，各种直系同源基因家族表现出相互矛盾的进化历史。导致这种冲突的一个主要因素是水平基因转移（HGT）——即遗传物质并非通过垂直遗传进行传递。因此，HGT 的盛行正挑战着经典生命之树概念的意义。在此，我们对代表整个原核生物世界的 HGT 进行了全面研究。我们主要依赖于一种新颖的分析方法，通过我们开发的四分体多样性分布（QPD）来分析基因史的总和。通过对真实和模拟数据的分析，QPD 被用于揭示存在针对 HGT 的障碍的证据，将古菌与细菌区分开来，并使两者之间的 HGT 变得相当罕见。相比之下，细菌的有限 HGT 比古菌更为常见。我们的方法还表明，尽管存在大量的 HGT，但仍可以提取出强烈的树状信号，这与之前的几项研究结果一致。因此，QPD 可以分析性地结合来自基因树总和的信息，用于理解原核生物中的 HGT 模式和速率，并验证或反驳水平基因转移和进化的模型。
