Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic charact...

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Autores principales:	Sittiporn Parnmen, Robert Lücking, H Thorsten Lumbsch
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7b858eee0e8547518fb42427c1170e89
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spelling	oai:doaj.org-article:7b858eee0e8547518fb42427c1170e892021-11-18T08:05:22ZPhylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).1932-620310.1371/journal.pone.0051392https://doaj.org/article/7b858eee0e8547518fb42427c1170e892012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23251515/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.Sittiporn ParnmenRobert LückingH Thorsten LumbschPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51392 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sittiporn Parnmen Robert Lücking H Thorsten Lumbsch Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
description	Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.
format	article
author	Sittiporn Parnmen Robert Lücking H Thorsten Lumbsch
author_facet	Sittiporn Parnmen Robert Lücking H Thorsten Lumbsch
author_sort	Sittiporn Parnmen
title	Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
title_short	Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
title_full	Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
title_fullStr	Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
title_full_unstemmed	Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
title_sort	phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/7b858eee0e8547518fb42427c1170e89
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Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).

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