Department of Geosciences, University of Montana, 32 Campus Drive no. 1296, Missoula, MT 59812-1296, USA.
Archaea. 2012;2012:843539. doi: 10.1155/2012/843539. Epub 2012 Nov 22.
Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral transfer events, or 3.4-4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.
古菌基因组序列的系统发育分析为研究该群体的进化历史提供了窗口，尽管大多数古菌类群缺乏传统的化石记录。在这里，使用定义微生物代谢生态位的关键代谢基因进行了系统发育分析。这些基因通常被认为经历了高频率的水平基因转移。许多基因序列形成的进化枝与使用来自基因组稳定核心的大量基因构建的树相同或相似。令人惊讶的是，这种水平转移事件很容易被识别和量化，在古菌生命领域只发生了相对较少的次数。通过将基因获得事件置于时间框架内，可以定量新代谢基因的获得速率。利用氧气作为末端电子受体的细胞色素氧化酶基因的水平转移率最高（在整个古菌领域，共有 12-14 次水平转移事件，即每十亿年 3.4-4.0 次事件）。参与硫或氮代谢的基因的水平转移率要低得多，大约每十亿年发生一次水平转移事件。这表明关键代谢蛋白的水平转移率是罕见的，而不是猖獗的。
