Abstract

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.

中文翻译：

---

系统发育数据集中的内源冲突。

摘要

大多数系统发育分析都假定单个进化史是一个基因的基础。但是，生物学过程和错误都会导致基因内冲突。经验数据集中存在这种冲突的程度尚未得到充分记录，但如果普遍存在，则可能对系统发育分析产生深远的影响。我们使用快速简便的方法检查了来自不同分类群的几个大型系统生物学数据集，以识别得到良好支持的基因内冲突。我们发现数据集之间的冲突是高度可变的，所研究基因的从1％到> 92％。我们详细分析了四个示例基因，并在几种情况下分析了模拟数据。我们的结果表明，对齐错误可能是造成冲突的主要原因之一，但其他冲突仍然无法解释，可能代表生物学信号或其他错误。