Analysis of Acorus calamus chloroplast genome and its phylogenetic implications
Analysis of Acorus calamus chloroplast genome and its phylogenetic implications
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DOI：
10.1093/molbev/msi173
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发表时间：
2005-09-01
影响因子：
10.7
通讯作者：
Hellwig, FH
中科院分区：
文献类型：
--
作者：
Goremykin, VV;Holland, B;Hellwig, FH
确定被子植物主要品系之间的系统发育关系是一个长期存在的问题，但这些品系的亲缘关系的不确定性仍然存在。虽然许多研究表明ANITA（Amborella-Nymphaeates-Illiciales-Trimeniales-Aristolochiales）等级在被子植物中是基础的，但对完整叶绿体基因组序列的研究也提出了另一种树，其中导致禾本科植物的线在被子植物中首先分支。为了改进现有叶绿体基因组数据中的分类单元采样，我们对单子叶植物菖蒲的叶绿体基因组进行了测序。我们产生了一个串联的比对（89,436个位置的15个分类群），包括几乎所有的序列可用于种子植物内的生殖重建。数据仍然包含支持ANITA基础和草基础的假设。使用模拟，我们可以表明，是ANITA基础假设真的，简约（和距离为基础的方法与许多模型）预计将无法恢复it. The不言自明的解释，这种失败似乎是一个长枝吸引力（LBA）之间的进化枝的草和外组。然而，这个LBA不能解释使用最大似然（ML）方法恢复的树拓扑结构和使用简约和基于距离的方法恢复的拓扑结构之间的差异时，草被删除。此外，最大简约法和距离法都不能一致地恢复ML树，根据模拟，当删除外组（Pinus）时，它们会被期望恢复ML树，这表明生成树不正确或最佳对称模型被错误指定（或两者兼而有之）。我们证明了ML下恢复的树对模型规范非常敏感，并且最好的对称模型被错误指定。因此，我们仍然不可知论之间的系统发育关系基础被子植物谱系。
Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenefic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeates-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.