Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies

The evolutionary history of the phytopathogenic Gibberella fujikuroi complex of Fusarium and related species was investigated by cladistic analysis of DNA sequences obtained from multiple unlinked loci. Gene phylogenies inferred from the mitochondrial small subunit (mtSSU) rDNA, nuclear 28S rDNA, and beta-tubulin gene were generally concordant, providing strong support for a fully resolved phylogeny of all biological and most morphological species. Discordance of the nuclear rDNA internal transcribed spacer 2 (ITS2) gene tree is due to paralogous or xenologous ITS2 sequences. PCR and sequence analysis demonstrated that every strain of the ingroup species tested possesses two highly divergent nonorthologous ITS2 types designated type I and type II. Only the major ITS2 type, however, is discernable when PCR products are amplified and sequenced directly with conserved primers. The minor ITS2 type was recovered using ITS2 type-specific PCR primers. Distribution of the major ITS2 type within the species lineages exhibits a homoplastic pattern of evolution, thus obscuring true phylogenetic relationships. The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium. The results also indicate that current morphological-based taxonomic schemes for these fungi are unnatural and a new classification is required.

A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors. Taxonomic novelties: Cladosporium allicinum (Fr.: Fr.) Bensch, U. Braun & Crous, comb. nov., C. astroideum var. catalinense U. Braun, var. nov., Fusicladium tectonicola (Yong H. He & Z.Y. Zhang) U. Braun & Bensch, comb. nov., Septoidium uleanum (Henn.) U. Braun, comb. nov., Zasmidium adeniae (Hansf.) U. Braun, comb. nov., Zasmidium dianellae (Sawada & Katsuki) U. Braun, comb. nov., Zasmidium lythri (Westend.) U. Braun & H.D. Shin, comb. nov., Zasmidium wikstroemiae (Petch) U. Braun, comb. nov.