Selection in the evolution of gene duplications.
Selection in the evolution of gene duplications.
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DOI：
10.1186/gb-2002-3-2-research0008
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发表时间：
2002
期刊：
影响因子：
12.3
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Kondrashov FA;Rogozin IB;Wolf YI;Koonin EV
基因复制在新生物功能的进化中起着重要作用。理论研究通常假设复制本身是选择性中性的，并且在复制之后，其中一个基因拷贝从纯化（稳定）选择中解脱出来，这为新功能的进化创造了潜力。为了寻找复制后加速进化的系统证据，我们使用了来自26种细菌、6种古细菌和7种真核生物基因组的数据，比较了不同物种中作用于最近复制的基因（类似基因）和类似分化的、未复制的同源基因的选择模式和强度。我们发现，在大多数近亲对中，非同义与同义替换的比率(Kn/Ks) <<1，而且近亲通常以相似的速度进化，没有明显的不对称，这表明由复制产生的两个近亲都受到净化选择的影响。然而，这种选择要比净化选择弱得多，而净化选择影响的是与所分析的相似物分化程度相同的非重复同源物。大多数最近复制的基因似乎与各种形式的环境反应有关；特别是，它们中的许多编码膜和分泌蛋白。这一分析结果表明，最近重复的同源物比具有相同发散水平和相似功能的同源物进化得更快，但显然没有经历中性进化阶段。我们假设，在进化谱系中持续存在的基因复制从其起源时起就是有益的，这主要是由于响应可变环境条件的蛋白质剂量效应；一旦达到更高的分化水平，重复很可能在其进化的后期阶段产生新的功能。
Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.
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DOI：
10.1073/pnas.91.8.2950
发表时间：
1994-04-12
影响因子：
11.1
作者：
CLARK, AG
通讯作者：
CLARK, AG
影响因子：
2.9
作者：
JONES, DT;TAYLOR, WR;THORTON, JM
通讯作者：
THORTON, JM
影响因子：
3.1
作者：
Bridges, CB
通讯作者：
Bridges, CB
DOI：
10.1073/pnas.76.1.396
发表时间：
1979-01-01
影响因子：
11.1
作者：
CROW, JF;KIMURA, M
通讯作者：
KIMURA, M
影响因子：
5.8
作者：
Danecek, Petr;Auton, Adam;Durbin, Richard
通讯作者：
Durbin, Richard