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首页> 美国卫生研究院文献>PLoS Clinical Trials >Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)
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Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

机译：在没有明显的表型变异的系统发生模式的情况下，在通用水平上的系统发生分类：案例研究在石墨科（子囊菌）

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Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.
机译：分子系统发育通常揭示表型特征所界定的分类单元不是单系的。尽管对表型特征的重新检查通常可以识别出表征进化枝的特征的存在，但是越来越多的研究未能识别出诊断特征，尤其是在缺乏复杂形态的有机体群体中。然后分类学家可以合并这些组，也可以将分类单元拆分为较小的实体。由于二项式命名法的性质，此决定在通用级别上特别重要。在这里，我们提出了一种新方法，可以使用基于形态学的系统进化分箱和多响应置换程序相结合的方法在分类选择之间进行选择，以测试进化枝之间的形态差异。我们举例说明了该方法在部落Thelotremateae中以Chapsa属为重点的情况，Chapsa是一组地衣真菌，其中我们的系统发育估计与传统分类冲突，并且形态和化学特征未显示清晰的系统发育模式。我们生成了线粒体SSU rDNA，核LSU rDNA和蛋白质编码RPB2的75个新DNA序列。该数据集用于使用最大似然法和贝叶斯方法推断系统发育估计。发现Chapsa属是多系的，形成了四个支撑良好的进化枝，其中三个聚集成一个未支撑的进化枝，另一个支撑的进化枝形成了两个支撑的亚进化枝。虽然这些进化枝无法在形态上轻易分离，但合并的分箱/多响应置换程序显示，接受四个进化枝为不同属每个都反映了表型模式，比接受两个属（如果分裂第一进化枝则为五个属）要好得多。 Thelotremateae内的另一种物种Thelotrema petractoides是一种独特的类群，具有类似于裂殖藻的裂殖炭化碳化物，被证明属于Thelotrema之外。因此，在这里描述了新的属天蛾属，十字花科，假单胞菌和假拟青霉菌，并提出了39种新的组合。

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