Detecting recombination in evolving nucleotide sequences.
Detecting recombination in evolving nucleotide sequences.
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DOI：
10.1186/1471-2105-7-412
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发表时间：
2006-09-18
影响因子：
3
通讯作者：
Ragan MA
中科院分区：
文献类型：
--
作者：
Chan CX;Beiko RG;Ragan MA
遗传重组可以在一组同源基因内产生异质的系统发育历史。这些重组事件可能被随后的残基取代所掩盖，从而使其检测复杂化。虽然有许多算法用于识别重组事件，但关于后续置换对可用重组检测方法的准确性的影响知之甚少。我们评估了随后的取代对检测模拟重组事件的影响，在一个同质进化模型下，四个核苷酸序列的集合。每个位点的后续取代的量、序列的先前进化历史以及重组事件的互易性或非互易性都影响所检查的重组检测程序的准确性。基于贝叶斯遗传学的方法在检测重组事件的证据和识别重组断点方面表现出很高的准确性。与我们测试的其他方法相比，这些方法对参数设置不太敏感，因此更容易以一致的方式应用于各种数据集。重组后取代倾向于降低重组检测程序的预测准确性。检测重组区域的最佳方法不一定是鉴定重组断裂点最准确的方法。对于涉及高度发散序列或大数据集的困难检测问题，可以连续运行不同类型的方法以提高效率，并且可能比单独使用的任何单一方法产生更好的预测准确性。
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions, which consequently complicate their detection. While there are many algorithms for the identification of recombination events, little is known about the effects of subsequent substitutions on the accuracy of available recombination-detection approaches. We assessed the effect of subsequent substitutions on the detection of simulated recombination events within sets of four nucleotide sequences under a homogeneous evolutionary model. The amount of subsequent substitutions per site, prior evolutionary history of the sequences, and reciprocality or non-reciprocality of the recombination event all affected the accuracy of the recombination-detecting programs examined. Bayesian phylogenetic-based approaches showed high accuracy in detecting evidence of recombination event and in identifying recombination breakpoints. These approaches were less sensitive to parameter settings than other methods we tested, making them easier to apply to various data sets in a consistent manner. Post-recombination substitutions tend to diminish the predictive accuracy of recombination-detecting programs. The best method for detecting recombined regions is not necessarily the most accurate in identifying recombination breakpoints. For difficult detection problems involving highly divergent sequences or large data sets, different types of approach can be run in succession to increase efficiency, and can potentially yield better predictive accuracy than any single method used in isolation.
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影响因子：
10.7
作者：
Jakobsen, IB;Wilson, SR;Easteal, S
通讯作者：
Easteal, S
影响因子：
10.7
作者：
Bryant, D;Moulton, V
通讯作者：
Moulton, V
影响因子：
30.8
作者：
Jeffreys, AJ;May, CA
通讯作者：
May, CA
DOI：
10.1073/pnas.0600744103
发表时间：
2006-03-21
影响因子：
11.1
作者：
Inagaki, Y;Susko, E;Roger, AJ
通讯作者：
Roger, AJ
影响因子：
2.5
作者：
CONOVER, WJ;JOHNSON, ME;JOHNSON, MM
通讯作者：
JOHNSON, MM