A performance study of the impact of recombination on species tree analysis
A performance study of the impact of recombination on species tree analysis
复制标题
重组对物种树分析影响的性能研究
作者：
Zhiwei Wang;Kevin J. Liu
背景从基因组序列数据重建物种遗传的最广泛使用的最先进的方法假设采样位点是相同的和独立的分布。原则上，基因座之间的自由重组和缺乏基因座内重组是满足该假设所必需的。很少有研究量化重组对物种树推断方法的实际影响，甚至更少的研究为此目的使用基因组序列数据。一个突出的例外是拉尼尔和诺尔斯2012年的研究。该研究的一个主要发现是，假设基因座之间的自由重组，物种树推断方法对基因座内重组相对稳健。后一种假设意味着，关于重组的影响，物种树analysis.ResultsThe本研究的目标是进一步研究这个开放的问题没有完全解决的开放问题。使用模拟的基础上的多物种合并与重组模型以及经验数据集，我们比较了常见的基于流水线的技术推断物种的遗传。模拟条件包括一系列数据集大小和重组率的几种选择，这些重组率要么在基因座之间是均匀的，要么包含重组热点。我们发现，明确利用推断的重组断点来描绘无重组间隔的管道与广泛使用的基于连锁不平衡衰变预处理序列的替代方案相比，具有更高的准确性。此外，使用一个相对简单的方法重组断点推理不降低下游物种树推理的准确性相比，更准确的alternatives.ConclusionsOur的研究结果澄清了重组后，目前的基因组管道物种树推理的影响。利用推断的重组断点来密集地对基因组序列中的基因座进行采样的基于流水线的方法可以容忍基因座内重组和违反基因座之间自由重组的假设。
BackgroundThe most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed. In principle, free recombination between loci and a lack of intra-locus recombination are necessary to satisfy this assumption. Few studies have quantified the practical impact of recombination on species tree inference methods, and even fewer have used genomic sequence data for this purpose. One prominent exception is the 2012 study of Lanier and Knowles. A main finding from the study was that species tree inference methods are relatively robust to intra-locus recombination, assuming free recombination between loci. The latter assumption means that the open question regarding the impact of recombination on species tree analysis is not fully resolved.ResultsThe goal of this study is to further investigate this open question. Using simulations based upon the multi-species coalescent-with-recombination model as well as empirical datasets, we compared common pipeline-based techniques for inferring species phylogenies. The simulation conditions included a range of dataset sizes and several choices for recombination rate which was either uniform across loci or incorporated recombination hotspots. We found that pipelines which explicitly utilize inferred recombination breakpoints to delineate recombination-free intervals result in greater accuracy compared to widely used alternatives that preprocess sequences based upon linkage disequilibrium decay. Furthermore, the use of a relatively simple approach for recombination breakpoint inference does not degrade the accuracy of downstream species tree inference compared to more accurate alternatives.ConclusionsOur findings clarify the impact of recombination upon current phylogenomic pipelines for species tree inference. Pipeline-based approaches which utilize inferred recombination breakpoints to densely sample loci across genomic sequences can tolerate intra-locus recombination and violations of the assumption of free recombination between loci.
影响因子：
4.5
作者：
Staubach F;Lorenc A;Messer PW;Tang K;Petrov DA;Tautz D
通讯作者：
Tautz D