Characterizing gene tree conflict in plastome-inferred phylogenies
Characterizing gene tree conflict in plastome-inferred phylogenies
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DOI：
10.7717/peerj.7747/supp-9
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发表时间：
2019
期刊：
影响因子：
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通讯作者：
Joseph F. Walker;Nathanael Walker-Hale;Oscar M. Vargas;A. Drew;Larson;Gregory W. Stull
中科院分区：
文献类型：
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作者：
Joseph F. Walker;Nathanael Walker-Hale;Oscar M. Vargas;A. Drew;Larson;Gregory W. Stull
植物间的进化关系主要是通过叶绿体数据推断出来的。到目前为止，还没有一项研究全面研究了基因树冲突的质体。利用被子植物质体的广泛样本，我们描述了质体基因在不同时间尺度上的基因树冲突，并探索了冲突的相关性（例如，进化速度、基因长度、分子类型）。我们发现显著的基因树冲突的背景下，很大程度上没有信息的基因。我们发现比对长度和树长度是一致性的强预测因子，核苷酸优于氨基酸。在最常用的标记中，matK的性能大大优于rbcL；然而，很少使用的基因rpoC2在每次分析中都是表现最好的基因。我们发现rpoC2重构了被子植物的系统发育以及整个连接的编码蛋白质的叶绿体基因。我们的研究结果表明，较长的基因更有利于系统发育重建。通过使用核苷酸减轻一些冲突表明，随机和系统误差可能是大多数观察到的冲突的根源，但鉴于异质重组的记录案例，对质体内生物冲突的进一步研究是有必要的。我们建议研究人员在对系统发育数据进行下游比较分析时，即使使用叶绿体基因组，也应该过滤基因的拓扑一致性。学科进化研究，植物科学
Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes. Subjects Evolutionary Studies, Plant Science