Merckx Vincent, Bakker Freek T, Huysmans Suzy, Smets Erik
Laboratory of Plant Systematics, K.U.Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium.
National Herbarium of the Netherlands, Wageningen University Branch, Gen. Foulkesweg 37, 6703 BL Wageningen, The Netherlands.
Cladistics. 2009 Feb;25(1):64-77. doi: 10.1111/j.1096-0031.2008.00241.x.
Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford-Olsen-Waddell-Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.
由于形态简化以及缺乏可扩增的质体基因，异养植物光合近缘种的鉴定存在问题。尽管核基因和线粒体基因序列可能提供了受欢迎的系统发育标记替代来源，但这些基因中存在的速率异质性可能会在系统发育分析中引入偏差/系统误差。我们基于核18S rDNA和线粒体atpA DNA序列数据，以及使用简约法、似然法和贝叶斯推断方法，研究了水玉簪科的系统发育位置。这些基因在近缘类群之间进化速率的显著差异导致了相互矛盾的结果：虽然对18S rDNA和合并数据的简约分析强烈支持水玉簪科的单系性，但贝叶斯推断，无论有无宽松分子钟，以及斯沃福德 - 奥尔森 - 瓦德尔 - 希利斯（SOWH）检验都明确拒绝了这一假设。我们表明，数据中的速率异质性在简约分析中导致了长枝吸引假象。然而，使用基于模型的推断方法，水玉簪科是否为单系性的问题仍然难以捉摸。一方面，最大似然非参数自展法和参数假设检验未能支持并系的水玉簪科，另一方面，贝叶斯推断方法（无论有无宽松分子钟）都显著拒绝了单系的水玉簪科。这些结果表明，充分的抽样、使用速率均匀的数据以及应用不同的推断方法是构建菌根异养植物系统发育假说的重要因素。© 威利·亨尼希协会2009年。
