一种检测核苷酸序列重组的两阶段方法
A two-phase approach for detecting recombination in nucleotide sequences
摘要：
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。描述重组事件在分子进化的研究中是重要的，因为对这些事件的推断提供了不同基因序列或基因组之间的系统发育关系的更清晰的画面。然而，检测重组事件可能是一项艰巨的任务，因为不同的重组检测方法的性能可能会有所不同，这取决于重组后发生的进化事件。我们最近评估了重组后事件对重组检测方法的预测准确性的影响，使用模拟的核苷酸序列数据。其他研究支持的主要结论是，在搜索重组事件时，不应依赖于单一方法。在本文中，我们介绍了一个两阶段的战略，应用三个统计措施来检测重组事件的发生，和贝叶斯系统发育的方法在划定断点的核苷酸序列中的事件。我们使用模拟数据来评估这些方法的性能，并证明了这种策略对经验数据的适用性。两阶段策略在应用于大型数据集时被证明是时间有效的，并产生高置信度的结果。
英文摘要：
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.
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