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Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system
Zhao, Rui-Lin1; Zhou, Jun-Liang2,3; Chen, Jie4,5; Margaritescu, Simona; Sanchez-Ramirez, Santiago6,7; Hyde, Kevin D.4,5,8; Callac, Philippe9; Parra, Luis A.10; Li, Guo-Jie1; Moncalvo, Jean-Marc6,7
Source PublicationFUNGAL DIVERSITY
AbstractThe 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.
KeywordAgaricaceae Divergence Times Multi-gene Phylogenetics Systematics Taxonomy
Indexed BySCI
WOS Research AreaMycology
WOS SubjectMycology
WOS IDWOS:000379817400002
Citation statistics
Cited Times:46[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Affiliation1.Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing 100101, Peoples R China
2.Beijing Forestry Univ, Inst Microbiol, Beijing 100083, Peoples R China
3.Beijing Forestry Univ, Beijing Key Lab Forest Pest Control, Beijing 100083, Peoples R China
4.Mae Fah Luang Univ, Ctr Excellence Fungal Res, Chiang Rai 57100, Thailand
5.Mae Fah Luang Univ, Sch Sci, Chiang Rai 57100, Thailand
6.Royal Ontario Museum, Dept Nat Hist, Toronto, ON M5S 2C6, Canada
7.Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada
8.Chinese Acad Sci, Key Lab Econ Plants & Biotechnol, Kunming Inst Bot, 132 Lanhei Rd, Kunming 650201, Peoples R China
9.INRA UR1264 Mycol & Securite Aliments, CS 20032, F-33882 Villenave Dornon, France
10.Avda Padre Claret 7,5 G, Burgos 09400, Spain
Recommended Citation
GB/T 7714
Zhao, Rui-Lin,Zhou, Jun-Liang,Chen, Jie,et al. Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system[J]. FUNGAL DIVERSITY,2016,78(1):239-292.
APA Zhao, Rui-Lin.,Zhou, Jun-Liang.,Chen, Jie.,Margaritescu, Simona.,Sanchez-Ramirez, Santiago.,...&Moncalvo, Jean-Marc.(2016).Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system.FUNGAL DIVERSITY,78(1),239-292.
MLA Zhao, Rui-Lin,et al."Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system".FUNGAL DIVERSITY 78.1(2016):239-292.
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