Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the felsenstein zone
Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the felsenstein zone
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DOI：
10.1093/molbev/msi191
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发表时间：
2005-10-01
影响因子：
10.7
通讯作者：
dePamphilis, CW
中科院分区：
文献类型：
--
作者：
Leebens-Mack, J;Raubeson, LA;dePamphilis, CW
虽然一直强烈支持Amborella和睡莲目（睡莲属）是被子植物发生中从最基部的节分支出来的，但最近这一假设受到了来自Amborella、睡莲属和12种其它陆地植物叶绿体基因组中提取的61个蛋白质编码基因的系统发育分析的挑战.这些特征丰富的分析将以三种禾本科（禾本科）为代表的单子叶植物作为所有其他现存被子植物谱系的姐妹。我们已经从另外六个叶绿体基因组的草图序列中提取了蛋白质编码区，以测试这一令人惊讶的结果是否可能是由于有限的分类单元采样而导致的长分支吸引力的人为产物。新增加的分类群包括三种单子叶植物（菖蒲、丝兰和香蒲）、一种睡莲（睡莲）、一种毛茛科植物（毛茛）和一种裸子植物（银杏）。扩展的DNA和蛋白质数据集的系统发育分析以及显微结构特征（插入缺失）提供了明确的支持Amborella和Nymphaeales作为被子植物系统发育中最基部节点的分支。然而，它们的相对位置被证明取决于分析方法，简约法有利于Amborella作为所有其他被子植物的姐妹，最大似然法（ML）和邻居连接法有利于Amborella +睡莲目分支作为姐妹。ML遗传学支持后一种假设，但前一种假设的可能性没有显著差异。参数引导分析，单基因遗传，估计的分歧日期，和冲突的indel字符都有助于阐明在被子植物进化的最基本的节点的解决冲突的性质。分子测年分析提供了所有现存被子植物的最近共同祖先（MRCA）的中位年龄估计为161 MYA，单子叶植物，木兰科植物和真双子叶植物的MRCA为145 MYA。尽管长序列减少了分支长度和分子测年估计的方差，但改进的分类单元采样对被子植物系统发生的生根的影响以及参数自助分析的结果表明，长分支吸引力可能会误导基因组规模的系统发育分析。
While there has been strong support for Amborella and Nymphaeales ( water lilies) as branching from basal- most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein- coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character- rich analyses placed the monocots, represented by three grasses ( Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein- coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long- branch attraction due to limited taxon sampling. The added taxa include three monocots ( Acorus, Yucca, and Typha), a water lily ( Nuphar), a ranunculid ( Ranunculus), and a gymnosperm ( Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters ( indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal- most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood ( ML) and neighbor- joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single- gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor ( MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long- branch attraction might mislead genome- scale phylogenetic analyses.