Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
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DOI：
10.1186/1471-2148-4-35
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发表时间：
2004-09-28
影响因子：
3.4
通讯作者：
Palmer JD
中科院分区：
文献类型：
--
作者：
Stefanović S;Rice DW;Palmer JD
大量研究总共使用了约 28 个基因，已达成共识，认为包括安博拉在内的三类植物是所有其他被子植物中最基础的等级。一个主要的例外是 Goremykin 等人最近的研究。 (2003; Mol. Biol. Evol. 20:1499–1505)，他对陆地植物 13 个已测序的叶绿体基因组中的 61 个基因进行分析，几乎总是发现 100% 支持单子叶植物是相对于 Amborella、Calycanthus 和真双子叶植物最深的被子植物。我们假设这种冲突反映了被子植物的根部错误，这是由于分类单元采样不足、系统发育方法不当以及用于代表单子叶植物的草谱系的快速进化而导致的。我们使用两种主要方法来检验这个假设。首先，我们对来自单子叶植物菖蒲的大量叶绿体基因进行了测序，并将这些加上之前测序的菖蒲基因添加到Goremykin等人的研究中。 (2003) 数据集，以探索在其研究中使用的相同分析条件下改变单子叶植物采样的影响。仅用石菖蒲代表单子叶植物，在所有最大似然分析和简约分析以及一些基于距离的分析中都获得了强有力的支持 Amborella 姐妹树。同时具有石菖蒲和草的树要么给出了良好支持的安博雷拉姐妹拓扑，要么给出了极不可能的拓扑，100%支持草姐妹和单子叶植物的并系植物（即，石菖蒲是“双子叶植物”的姐妹，而不是草的姐妹）。其次，我们重新分析了 Goremykin 等人。 (2003) 数据集重点关注旨在解释速率异质性的方法。这些分析支持 Amborella 姐妹假设，引导支持值通常与在不考虑速率异质性的情况下进行的同源分析强烈冲突。此外，我们还进行了一系列有限的分析，其中包括睡莲的叶绿体基因组，其作为基础被子植物的地位最近也受到了挑战。这些分析表明，Amborella（或 Amborella 加睡莲），但不是单子叶植物，是这一有限类群中所有其他被子植物的姐妹群，并且草类姐妹拓扑是一种长分枝吸引伪影，导致被子植物不正确生根。这些结果凸显了特征较多但特征太少的危险，尤其是分子上不同的类群，这种情况长期以来被认为可能产生强烈误导性的分子树。他们还强调使用适当的进化模型在系统发育分析中的重要性。
Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots. We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered monocot sampling under the same analytical conditions used in their study. With Acorus alone representing monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was also, and very recently, challenged. These analyses show that Amborella (or Amborella plus Nymphaea), but not monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
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影响因子：
3
作者：
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通讯作者：
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通讯作者：
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通讯作者：
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