Advanced

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

Harder, Christoffer B LU ; Læssøe, Thomas ; Frøslev, Tobias G ; Ekelund, Flemming ; Rosendahl, Søren and Kjøller, Rasmus (2013) In Fungal Biology 117(11-12). p.764-775
Abstract

Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten 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-α (423 bp) and RNA polymerase II (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 had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1... (More)

Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten 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-α (423 bp) and RNA polymerase II (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 had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (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 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (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.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Agaricales/classification, Cluster Analysis, DNA, Fungal/chemistry, DNA, Ribosomal Spacer/chemistry, Genetic Variation, Molecular Sequence Data, Peptide Elongation Factor 1/genetics, Phylogeny, RNA Polymerase II/genetics, Sequence Analysis, DNA
in
Fungal Biology
volume
117
issue
11-12
pages
764 - 775
publisher
Elsevier
external identifiers
  • scopus:84888440901
  • pmid:24295915
ISSN
1878-6146
DOI
10.1016/j.funbio.2013.09.004
language
English
LU publication?
no
additional info
Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
id
65204fa6-aa73-4c72-b49c-d6be40ca03d0
date added to LUP
2020-09-09 11:17:06
date last changed
2020-09-13 07:21:57
@article{65204fa6-aa73-4c72-b49c-d6be40ca03d0,
  abstract     = {<p>Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten 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-α (423 bp) and RNA polymerase II (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 had a low bootstrap (&lt;50) support, and the partition homogeneity incongruence length difference (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 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (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. </p>},
  author       = {Harder, Christoffer B and Læssøe, Thomas and Frøslev, Tobias G and Ekelund, Flemming and Rosendahl, Søren and Kjøller, Rasmus},
  issn         = {1878-6146},
  language     = {eng},
  month        = {12},
  number       = {11-12},
  pages        = {764--775},
  publisher    = {Elsevier},
  series       = {Fungal Biology},
  title        = {A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification},
  url          = {http://dx.doi.org/10.1016/j.funbio.2013.09.004},
  doi          = {10.1016/j.funbio.2013.09.004},
  volume       = {117},
  year         = {2013},
}