TY - JOUR
T1 - A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification
AU - Harder, Christoffer Bugge
AU - Læssøe, Thomas
AU - Frøslev, Tobias G.
AU - Ekelund, Flemming
AU - Rosendahl, Søren
AU - Kjøller, Rasmus
PY - 2013/11
Y1 - 2013/11
N2 - 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 (645bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423bp) and RNA polymerase II (RPB1) (492bp) 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 treeshad 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.
AB - 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 (645bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423bp) and RNA polymerase II (RPB1) (492bp) 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 treeshad 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.
KW - Basidiomycete phylogeny
KW - Cryptic speciation
KW - DNA barcode
KW - Phylogenetic congruence
KW - Prunulus
U2 - 10.1016/j.funbio.2013.09.004
DO - 10.1016/j.funbio.2013.09.004
M3 - Journal article
C2 - 24295915
SN - 1878-6146
VL - 117
SP - 764
EP - 775
JO - Fungal Biology
JF - Fungal Biology
IS - 11-12
ER -