High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

中文翻译：

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真菌的高级分类和进化生态分析的工具

高通量测序研究产生了大量的分类学数据。由于排列问题和缺乏系统发育主干，因此很难检验回收的分类单元和物种假说的进化生态学假设。我们提出了更新的门类和类级别的真菌分类，以解释单亲和发散时间，这样主要分类学等级就可以提供更多信息。根据系统发育和发散时间的估计，我们将门类排序为鸭嘴菌，Basidiobolomycota，Calcarisporiellomycota，Glomeromycota，Entomophthomyomycota，Entorrhizomycota，Kickxellomycota，Monoblepharomycota，Mortierellomycota和Olpidiomycota。我们接受9个附属王国来容纳这18个门。我们认为核王国（门核科和Font科）是真菌的姐妹群体。我们还介绍了一个perl脚本和一个newick格式的分类主干，用于使用此分类系统或任何其他分类系统将“物种假说”分配给分层的分类学框架。我们提供了一个基于全球土壤真菌数据集测试进化生态学假设的示例。