Intragenic Conflict in Phylogenomic Data Sets
Intragenic Conflict in Phylogenomic Data Sets
复制标题
系统基因组数据集中的基因内冲突
DOI：
10.1093/molbev/msaa170
复制
发表时间：
2020
影响因子：
10.7
通讯作者：
Stephen A Smith, Nathanael Walker-Hale
中科院分区：
文献类型：
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作者：
Stephen A Smith, Nathanael Walker-Hale
大多数系统发育分析都假设一个基因有一个单一的进化史。然而，生物过程和错误都可能导致内部冲突。这种冲突在经验数据集中存在的程度没有很好的记录，但如果常见，可能对系统发育分析产生深远的影响。我们检查了几个大型系统基因组数据集从不同的分类群使用一个快速和简单的方法来确定有充分支持的基因内冲突。我们发现数据集之间的冲突是高度可变的，在被调查的基因中，从1%到bb0.92%不等。我们详细分析了四个典型基因，并分析了几种情况下的模拟数据。我们的研究结果表明，对齐误差可能是冲突的一个主要来源，但其他冲突仍然无法解释，可能代表生物信号或其他错误。无论是作为数据分析管道的一部分还是探索生物学过程，基因内系统发育信号的分析应该变得普遍。
Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.