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Citation for Study 14759

Citation title: "A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification".

Study name: "A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification".

This study is part of submission 14759 (Status: Published).

Citation

Harder C.B., & Fr?slev T.G. 2013. A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification. Fungal Biology, 117(11-12): 764-775.

Authors

• Harder C.B. (submitter) +45 31 62 94 16
• Fr?slev T.G.

Abstract

Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested 10 cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-&#945; (423 bp) and RPB1 (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees all had a low bootstrap (<50) support, and the partition homogeneity (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. and our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1, Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity,the overlap was most pronounced for ITS (intraspecific diversity 0-3.5%, interspecific diversity 0.4% to 8.8%). A clustering analysis on tEF separated at a 1.5% level returned all phylogenetic species as OTUs, while ITS at both a 1.5% level and at a 3%-threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single-gene analyses combined with single percentage separation values.

Keywords

Basidiomycete phylogeny; cryptic speciation; DNA barcode; species limits; phylogenetic congruence; Prunulus

External links

• DOI: 10.1016/j.funbio.2013.09.004

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14759
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref22414,
  	 author = {Christoffer Bugge Harder and Tobias Guldberg Fr?slev},
  	 title = {A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification},
  	 year = {2013},
  	 keywords = {Basidiomycete phylogeny; cryptic speciation; DNA barcode; species limits; phylogenetic congruence; Prunulus},
  	 doi = {10.1016/j.funbio.2013.09.004},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Fungal Biology},
  	 volume = {117},
  	 number = {11-12},
  	 pages = {764--775},
  	 abstract = {Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested 10 cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-&#945; (423 bp) and RPB1 (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees all had a low bootstrap (<50) support, and the partition homogeneity (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. and our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1, Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity,the overlap was most pronounced for ITS (intraspecific diversity 0-3.5%, interspecific diversity 0.4% to 8.8%). A clustering analysis on tEF separated at a 1.5% level returned all phylogenetic species as OTUs, while ITS at both a 1.5% level and at a 3%-threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single-gene analyses combined with single percentage separation values.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22414
  AU  - Harder,Christoffer Bugge
  AU  - Fr?slev,Tobias Guldberg
  T1  - A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification
  PY  - 2013
  KW  - Basidiomycete phylogeny; cryptic speciation; DNA barcode; species limits; phylogenetic congruence; Prunulus
  UR  - http://dx.doi.org/10.1016/j.funbio.2013.09.004
  N2  - Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested 10 cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-&#945; (423 bp) and RPB1 (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees all had a low bootstrap (<50) support, and the partition homogeneity (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. and our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1, Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity,the overlap was most pronounced for ITS (intraspecific diversity 0-3.5%, interspecific diversity 0.4% to 8.8%). A clustering analysis on tEF separated at a 1.5% level returned all phylogenetic species as OTUs, while ITS at both a 1.5% level and at a 3%-threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single-gene analyses combined with single percentage separation values.
  L3  - 10.1016/j.funbio.2013.09.004
  JF  - Fungal Biology
  VL  - 117
  IS  - 11-12
  SP  - 764
  EP  - 775
  ER  -