The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics
The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics
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裸子植物在种子植物中的地位： 克服叶绿体系统发生组学的陷阱
DOI：
10.1093/molbev/msq170
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发表时间：
2010-12-01
影响因子：
10.7
通讯作者：
Hasegawa, Masami
中科院分区：
文献类型：
--
作者：
Zhong, Bojian;Yonezawa, Takahiro;Hasegawa, Masami
买麻藤目的系统位置是种子植物系统学中最有争议的问题之一。为了阐明买麻藤属的位置，一个改进的氨基酸取代矩阵估计的基础上64叶绿体（CP）基因组，并适用于CP基因组数据，包括所有三个谱系的买麻藤属蛋白质的最大似然分析。虽然最初的分析强烈支持姐妹关系买麻藤与柳杉（Cupressophyta或非松科针叶树）（“Gnecup”假说），支持似乎是由长枝吸引（LBA）的文物。事实上，通过去除最有可能与LBA相关的进化最快的蛋白质，支持率急剧下降。此外，另一个分析部分基因组数据与密集的分类单元采样的针叶树显示，在psbC，rp12，和rps7蛋白质，有许多平行的氨基酸之间的谱系导致买麻藤和柳杉，并进一步排除这三个基因，买麻藤与松科的姐妹关系（“买麻藤”假说）成为支持。总体而言，我们的分析表明，LBA和平行替换导致严重偏倚的推断买麻藤类与cp基因组数据的系统发育位置。
The phylogenetic position of Gnetales is one of the most contentious issues in the seed plant systematics. To elucidate the Gnetales position, an improved amino acid substitution matrix was estimated based on 64 chloroplast (cp) genomes and was applied to cp genome data including all three lineages of Gnetales in maximum likelihood analyses of proteins. Although the initial analysis strongly supported the sister relation of Gnetales with Cryptomeria (Cupressophyta or non-Pinaceae conifers) (the "Gnecup" hypothesis), the support seems to be caused by a long-branch attraction (LBA) artifact. Indeed, by removing fastest evolving proteins that are most likely associated with the LBA, the support drastically declined. Furthermore, another analysis of partial genome data with dense taxon sampling of conifers showed that, in psbC, rpl2, and rps7 proteins, there are many parallel amino acid substitutions between the lineages leading to Gnetales and to Cryptomeria, and by further excluding these three genes, the sister relation of Gnetales with Pinaceae (the "Gnepine" hypothesis) became supported. Overall, our analyses indicate that the LBA and parallel substitutions cause a seriously biased inference of phylogenetic position of Gnetales with the cp genome data.