Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria.
Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria.
复制标题
DOI：
10.1186/1745-6150-4-35
复制
发表时间：
2009-09-29
期刊：
影响因子：
5.5
通讯作者：
Ochman H
中科院分区：
文献类型：
--
作者：
Kuo CH;Ochman H
由于细菌没有可靠的化石记录，因此要推断其进化历史中事件发生的时间，就需要比较分子序列。这种分子钟的使用是基于这样的假设，即同源基因或位点的替换率在时间上和分类群上是相当恒定的。违反这些条件可能导致错误的推断，并导致估计值相差几个数量级。在这项研究中，我们研究了不同细菌谱系中一组保守基因之间的替换率的一致性，并解决了有关分子测年有效性的问题。通过研究专性内共生体中16 S rRNA基因的进化，这可以通过其宿主的化石记录来校准，我们发现，在一个分支内的速率是一致的，但在不同的细菌谱系中变化很大。全基因组范围内的非同义和同义取代的估计表明，这两个措施是高度可变的，在其整个细菌类群的利率。遗传漂变在决定16 S rRNA基因和非同义位点取代的积累方面发挥着重要作用。此外，基于一组普遍保守的蛋白质编码基因的分歧估计也表现出较低的对应性，那些基于16 S rRNA基因。我们的研究结果证明了基因和细菌分类群之间的广泛替代率。这种高水平的变异警告说，对一个通用的分子钟推断细菌中的分歧时间的假设。然而，通过对同源基因进行相对速率测试，可以推导出可靠的本地时钟，用于校准细菌进化。本文由Adam Eyre-Walker、Simonetta Gribaldo和Tal Pupko（由Dan Graur提名）撰写。
Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating. By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes. Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution. This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur).
登录
查看更多内容
影响因子：
3.9
作者：
Chen, XA;Li, S;Aksoy, S
通讯作者：
Aksoy, S
影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Ostell J;Pruitt KD;Sayers EW
通讯作者：
Sayers EW
影响因子：
3.9
作者：
Bromham, L;Penny, D;Hendy, MD
通讯作者：
Hendy, MD
影响因子：
10.7
作者：
Battistuzzi, Fabia U.;Hedges, S. Blair
通讯作者：
Hedges, S. Blair
影响因子：
3.9
作者：
Lenski, RE;Winkworth, CL;Riley, MA
通讯作者：
Riley, MA