Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene (nLSU-rDNA) were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used, however, all NJ trees still supported most of the same terminal groupings as MP and ML trees. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, using both parsimony and likelihood tests. Our analyses suggest that weighted parsimony and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife levels or are consistent with morphology-based classification schemes. Analyzes also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several nonmonophyletic groups revealed by these data include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

本研究针对伞菌目（Agaricales）内蘑菇及其近缘类群的系统发育关系，采用核大亚基核糖体DNA序列展开分析。研究对代表伞菌目绝大多数科的154个筛选类群，完成了核编码大亚基RNA基因（nLSU-rDNA）5'端约900个碱基的测序。本研究采用多种系统发育分析方法，包括加权与等权最大简约法（MP）、最大似然法（ML）以及距离法（邻接法NJ）。最大似然分析中用于分支交换的起始树，选自此前生成的最大简约法与邻接法树中最大似然得分最高的那颗。最大简约法与最大似然法得到的系统发育估计结果呈现高度一致性。邻接法树的拓扑结构则随所选用的距离模型存在差异，但所有邻接法树仍支持与最大简约法和最大似然法树多数相同的末端类群聚类。通过最大简约法与似然法检验可知，相较最优的最大简约法和最大似然法树，所有邻接法树的得分均显著偏低。本研究结果表明，加权最大简约法与最大似然法能够最佳推断伞菌目的系统发育关系。自展法与刀切法用于评估系统发育树稳健性时，二者得到的支持度水平相近。系统发育分析揭示了多个伞菌真菌类群，这些类群要么获得中等至高水平的自展或刀切法支持，要么与基于形态学的分类系统一致。分析结果同时支持牛肝菌类与红菇类各自独立的分类地位，二者位于具褶菌类核心类群（即Singer定义的伞菌亚科Agaricineae）的基部。本研究鉴定的单系类群包括：鹅膏科（Amanitaceae）、鬼伞科（Coprinaceae，排除斑褐鬼伞Coprinus comatus与小脆柄菇亚科Panaeolideae）、蘑菇科（Agaricaceae，排除囊皮伞族Cystodermateae）以及部分球盖菇科（Strophariaceae pro parte，包含球盖菇属Stropharia、鳞伞属Pholiota与丝盖伞属Hypholoma）；口蘑属Tricholoma的外生菌根物种（包括同样为菌根营养的白桩菇属Leucopaxillus）；小菇属Mycena与树脂小菇属Resinomycena；白蚁伞属Termitomyces、棒柄伞属Podabrella与离褶伞属Lyophyllum；以及侧耳属Pleurotus与扇菇属Hohenbuehelia。本研究揭示的非单系类群则包括：白蘑科（Tricholomataceae）、丝膜菌科（Cortinariaceae）与蜡伞科（Hygrophoraceae），以及杯伞属Clitocybe、脐菇属Omphalina与小皮伞属Marasmius。本研究为伞菌目未来的分类学研究提供了分析框架，并为大型分子数据集的分析提供了参考建议。