Hofstetter Valérie, Miadlikowska Jolanta, Kauff Frank, Lutzoni François
Department of Biology, Duke University, Durham, NC 27708-0338, USA.
Mol Phylogenet Evol. 2007 Jul;44(1):412-26. doi: 10.1016/j.ympev.2006.10.016. Epub 2006 Oct 25.
The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.
基于对茶渍纲（子囊菌门）地衣形成真菌的最大似然法自展分析，我们研究了两个蛋白质编码基因（RPB1和RPB2）以及三个核糖体RNA编码基因（nucSSU、nucLSU和mitSSU）单独及各种组合所提供的分辨率和统计支持。我们的结果表明，用于地衣形成子囊菌分子系统学的最佳位点（单个和组合）是蛋白质编码基因（RPB1和RPB2）。RPB1和RPB2基因在系统发育上比核糖体基因座的所有双位点和三位点组合更有效。这两个位点的每个的第三密码子位置提供了支持茶渍纲内系统发育关系的最多特征。在本研究中使用的三个核糖体基因座中，mitSSU与RPB1和RPB2组合时对系统发育分析的贡献最大。除mitSSU外，核糖体基因最难恢复，因为它们通常含有许多内含子，导致PCR偏向于众多无内含子的共提取污染真菌（主要是子囊菌门中的座囊菌纲、座囊菌目和粪壳菌纲，以及担子菌门的成员），这些真菌栖息在地衣叶状体中。与现有系统发育相比，对82个茶渍纲成员的五个位点组合数据集进行的最大似然分析提供了一个分辨率良好且支持度良好的树状图。我们确认了茶渍纲中三个公认亚纲的单系性，即粉衣菌亚纲、星裂盘菌亚纲和茶渍亚纲；后者首次被界定为单系，排除了脐衣科和标鳞衣属。蜡盘菌属（以前在蜡盘菌科，目前是茶渍科的成员）代表了茶渍纲内的第一次进化分支，早于粉衣菌亚纲的分化。本研究为指导未来地衣形成及相关子囊菌多基因座系统发育研究的位点选择提供了必要的基础。
