Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system
Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system
复制标题
利用分歧时间实现分类等级标准化——重建姬松茸分类系统的案例研究
DOI：
10.1007/s13225-016-0357-x
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发表时间：
2016-05-01
期刊：
影响因子：
20.3
通讯作者：
Moncalvo, Jean-Marc
中科院分区：
文献类型：
--
作者：
Zhao, Rui-Lin;Zhou, Jun-Liang;Moncalvo, Jean-Marc
在林奈分类系统中，分类等级的识别在很大程度上是任意的。一些作者建议使用散度时间作为普遍标准化的标准。松茸菇（Agaricus, Agaricales）是一种具有很高商业价值的蘑菇属。近年来利用ITS序列数据的研究发现了该属内11个新的系统发育谱系，但由于传统分类学中缺乏定义标准，其分类等级尚不确定。在本研究中，我们分析了745份标本（近600份是新收集的）的ITS序列数据，其中86份来自先前识别的亚属和剖面的模式标本。许多单系类群已被确认，但大多数基础关系尚未解决。为了基于LSU， tef-1 α和rpb2序列数据产生多基因系统发育，我们选择了114个已确定的ITS分支的代表。使用BEAST v1.8估计多基因系统发育的分化时间。基于系统发育关系和形态学，我们提出了一种新的蘑菇分类系统，该系统将分化时间作为建立分类等级的标准。我们建议将蘑菇属划分为5个亚属和20个科。假壳虫亚属被大量修正；Agaricus亚属和flavavagaricus亚属的划分范围分别局限于Agaricus和Arvenses剖面；并引入了两个新亚属（Minores和Spissicaules）。伪壳目中保留了Bivelares、Brunneopicti、Chitonioides、Nigrobrunnescentes、Sanguinolenti和Xanthodermatei等组，但后两个组因将Bohusia分节提升到组级而减少，并且在Xanthodermatei组中正式引入一个分支为Hondenses组；介绍了红门、粗门、絮状门和阿莫尼门。节Laeticolores被放置在小的亚属和节Rarolentes和subbrutilescentes被放置在Spissicaules亚属。报道了22个新种，分属不同的科。这项工作表明，ITS数据虽然在较低的分类水平（即物种和物种群的检测）有用，但在推断更深层次的系统发育关系方面价值有限。最后，我们建议建立一个基于分化时间的标准化分类系统，可以使真菌的分类排序更加客观，生物学上更有意义。
The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary. Some authors have proposed the use of divergence time as a universally standardized criterion. Agaricus (Agaricaceae, Agaricales) is a mushroom genus that contains many species of high commercial value. Recent studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus, however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional taxonomy. In this study, we analyzed ITS sequence data from 745 collections (nearly 600 being newly generated) including 86 from type specimens of previously recognized subgenera and sections. Many monophyletic groups were recognized, but most basal relationships were unresolved. One hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU, tef-1 alpha, and rpb2 sequence data. Divergence times within the multi-gene phylogeny were estimated using BEAST v1.8. Based on phylogenetic relationships and with respect to morphology, we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic ranks. We propose to segregate Agaricus into five subgenera and 20 sections. Subgenus Pseudochitonia is substantially emended; circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses, respectively; and two new subgenera (Minores and Spissicaules) are introduced. Within Pseudochitonia, sections Bivelares, Brunneopicti, Chitonioides, Nigrobrunnescentes, Sanguinolenti and Xanthodermatei are maintained, but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses; and sections Rubricosi, Crassispori, Flocculenti, and Amoeni are introduced. Section Laeticolores is placed in the subgenus Minores and sections Rarolentes and Subrutilescentes are placed in the subgenus Spissicaules. Twenty- two new species belonging to various sections are described. This work exemplifies that ITS data, while useful at lower taxonomic levels (i.e., detection of species and species groups), are of limited value for inferring deeper phylogenetic relationships. Finally, we suggest that the establishment of a standardized taxonomic system based on divergence times could result in a more objective, and biologically more meaningful, taxonomic ranking of fungi.