Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma

Abstract

The phylogenetically most derived group of the genus Trichoderma - section Longibrachiatum, includes some of the most intensively studied species, such as the industrial cellulase producer T. reesei (teleomorph Hypocrea jecorina), or the facultative opportunistic human pathogens T. longibrachiatum and H. orientalis. At the same time, the phylogeny of this clade is only poorly understood. Here we used a collection of 112 strains representing all currently recognized species and isolates that were tentatively identified as members of the group, to analyze species diversity and molecular evolution. Bayesian phylogenetic analyses based on several unlinked loci in individual and concatenated datasets confirmed 13 previously described species and 3 previously recognized phylogenetic species all of which were not yet described formally. When the genealogical concordance criterion, the K/θ method and comparison of frequencies of pairwise nucleotide differences were applied to the data sample, 10 additional new phylogenetic species were recognized, seven of which consisted only of a single lineage. Our analysis thus identifies 26 putative species in section Longibrachiatum, what doubles the currently estimated taxonomic diversity of the group, and illustrates the power of combining genealogical concordance and population genetic analysis for dissecting species in a recently diverged group of fungal species.

Fig. 1

Bayesian phylograms obtained from the concatenated alignment of tef1, cal1 and chi18-5 loci. Branches leading to formally described or previously recognized phylogenetic species are marked by filled single and double arrows respectively; phylogenetic species recognized in this study are shown by open arrows. The color code corresponds to the map insert and indicates geographic origin of isolates. Nodes supported by posterior probability >0.94 are shown in circles: black circles indicate supports obtained in both analyses after removal of ambiguous areas of the alignment using unconstrained gblocks (Castresana, 2000) and without such treatment, while white circles indicate supports obtained based on the complete concatenated alignment only. Sexual recombination is shown by vertical bars with a ‘rec+’ sign. Type strains of formally described species are underlined. Strains isolated from teleomorphs are given in bold.

Fig. 2

Frequency distribution of uncorrected pairwise sequence differences, in bins of 1%. The gray bars show values detected between isolates of the same species. Arrows with strain numbers identify the lowest difference value detected for this isolate against isolates from any other taxon.