Deep phylogenetic incongruence in the angiosperm clade Rosidae.
Deep phylogenetic incongruence in the angiosperm clade Rosidae.
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DOI：
10.1016/j.ympev.2014.11.003
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发表时间：
2015-02
影响因子：
4.1
通讯作者：
Miao-miao Sun;D. Soltis;D. Soltis;P. Soltis;P. Soltis;Xinyu Zhu;J. Burleigh;Zhiduan Chen
中科院分区：
文献类型：
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作者：
Miao-miao Sun;D. Soltis;D. Soltis;P. Soltis;P. Soltis;Xinyu Zhu;J. Burleigh;Zhiduan Chen
对大型数据集的分析可以帮助解决生命树中的困难节点，并揭示复杂的进化历史。卫矛目-草酸目-锦葵目（COM）分支在蔷薇科中的位置仍然是被子植物中最令人困惑的系统发育问题之一，以前的分析将其与Fabidae或Malvidae一起放置。为了阐明COM的位置，我们组装了叶绿体，线粒体和核序列的多基因矩阵，以及大的单拷贝和多拷贝核基因数据集。多基因数据集的分析表明叶绿体和核和线粒体数据集之间的冲突，结果是强大的各种字符编码和数据排除处理。单拷贝和多拷贝核基因座的分析表明，大多数基因座支持锦葵科的COM定位，支持蚕豆科的COM的基因座较少，而在蚕豆科和锦葵科的进化枝之外，几乎没有基因座支持COM。虽然不完整的谱系排序和古老的渐渗杂交仍然是合理的解释之间的冲突位点，更完整的采样是必要的，以充分评估这些假设。我们的研究结果强调了基因组数据集在揭示深层不一致性和复杂的进化模式方面的重要性。
Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal complex evolutionary histories. The placement of the Celastrales–Oxalidales–Malpighiales (COM) clade withinRosidaeremains one of the most confounding phylogenetic questions in angiosperms, with previous analyses placing it with eitherFabidaeorMalvidae. To elucidate the position of COM, we assembled multi-gene matrices of chloroplast, mitochondrial, and nuclear sequences, as well as large single- and multi-copy nuclear gene data sets. Analyses of multi-gene data sets demonstrate conflict between the chloroplast and both nuclear and mitochondrial data sets, and the results are robust to various character-coding and data-exclusion treatments. Analyses of single- and multi-copy nuclear loci indicate that most loci support the placement of COM withMalvidae, fewer loci support COM withFabidae, and almost no loci support COM outside a clade ofFabidaeandMalvidae. Although incomplete lineage sorting and ancient introgressive hybridization remain as plausible explanations for the conflict among loci, more complete sampling is necessary to evaluate these hypotheses fully. Our results emphasize the importance of genomic data sets for revealing deep incongruence and complex patterns of evolution.