Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Syst Biol. 2009 Apr;58(2):224-39. doi: 10.1093/sysbio/syp020. Epub 2009 Jun 4.
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
我们提出了一个包含 6 个基因、420 个物种的最大似然菌物门（真菌中最大的一门）系统发育树。该分析在迄今为止的所有分类学中是最完整的，涵盖了所有 15 个当前界定类别的物种。一些以前无法解决且在真菌分类中没有命名的超级分类群水平节点首次得到解决。基于 6 个基因的系统发育树，我们对所有 6 个基因进行了系统发育信息量分析，并进行了一系列祖先特征状态重建，重点关注子实体形态、子囊开裂以及营养方式和生态进化。逐个基因评估系统发育信息量的结果表明，蛋白质基因（RPB1、RPB2 和 TEF1）的信息量高于核糖体基因，核糖体基因一直是真菌系统学的标准基因。我们对子实体特征的重建与子囊菌中多细胞有性生殖结构的 2 个起源一致，一次在 Pezizomycotina 的共同祖先中，一次在 Neolectomycetes 的共同祖先中。这是首次报道子囊菌子实体的双重起源，突出了评估真菌中形态特征同源性的复杂性。此外，祖先重建支持一个具有暴露子实层（子囊壳）的开放式子实体，作为 Pezizomycotina 的原始形态，具有多个部分（子囊壳）或完全封闭（闭囊壳）的子实体的衍生。子囊开裂在 Pezizomycotina 中最具信息量，大多数超级分类群节点的重建模棱两可。特征状态重建支持陆地腐生生态作为祖先。与以前的研究不同，这些分析支持多个地衣化事件的起源，其中地衣化的丧失不太频繁，仅限于终端、密切相关的物种。
