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Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

机译：整合序列和拓扑结构，可高效，准确地检测水平基因转移

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摘要

One phylogeny-based approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree,and using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fitness of the evolution of the gene sequence data under an optimization criterion, such as maximum parsimony (MP). One major problem with the first approach is that gene tree estimates may have wrong branches, which result in false positive estimates of HGT events, and the second approach is accurate, yet suffers from the computational complexity of searching through the space of possible phylogenetic networks.rnThe contributions of this paper are two-fold. First, we present a measure that computes the support of HGT events inferred from pairs of species and gene trees. The measure uses the bootstrap values of the gene tree branches. Second,we present an integrative method to speed up the approaches for augmenting species trees into phylogenetic networks.rnWe conducted data analysis and performance study of our methods on a data set of 20 genes from the Amborella mitochondrial genome, in which Jeffrey Palmer and his co-workers postulated a massive amount of horizontal gene transfer. As expected, we found that including poorly supported gene tree branches in the analysis results in a high rate of false positive gene transfer events. Further, the bootstrap-based support measure assessed, with high accuracy, the support of the inferred gene transfer events. Further, we obtained very promising results, in terms of both speed and accuracy, when applying our integrative method on these data sets (we are currently studying the performance in extensive simulations).
机译：一种基于系统发育的水平基因转移（HGT）检测方法需要比较基因树和物种树的拓扑，并利用它们的差异来定位HGT事件。另一种方法是基于将树种扩展到系统进化网络中，以在优化标准（例如最大简约性）下提高基因序列数据进化的适应性。第一种方法的一个主要问题是基因树估计可能具有错误的分支，从而导致HGT事件的假阳性估计，而第二种方法是准确的，但仍存在通过可能的系统发生网络空间进行搜索的计算复杂性。 rn本文的贡献有两个方面。首先，我们提出一种措施，用于计算从物种和基因树对中推断出的HGT事件的支持。该度量使用基因树分支的自举值。其次，我们提出了一种综合方法来加快将树种增加到系统进化网络中的方法。我们对来自Amborella线粒体基因组的20个基因的数据集进行了数据分析和性能研究，其中Jeffrey Palmer和他的同事工假设了大量的水平基因转移。如预期的那样，我们发现在分析中包括支持不力的基因树枝会导致假阳性基因转移事件的发生率很高。此外，基于引导程序的支持措施可高精度评估推断的基因转移事件的支持。此外，将集成方法应用到这些数据集时，我们在速度和准确性方面都获得了非常有希望的结果（我们目前正在广泛的模拟中研究性能）。

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  • 来源
    《Comparative Genomics》|2008年|113-127|共15页
  • 会议地点 Paris(FR);Paris(FR)
  • 作者

    Cuong Than; Guohua Jin; Luay Nakhleh;

  • 作者单位

    Department of Computer Science, Rice University, Houston, TX 77005, USA;

    Department of Computer Science, Rice University, Houston, TX 77005, USA;

    Department of Computer Science, Rice University, Houston, TX 77005, USA;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物工程学（生物技术）;
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