Robert A. Shoemaker

Reconstructing the early evolution of Fungi using a six-gene phylogeny

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

The systematic position of Phaeocryptopus gaeumannii

Phaeocryptopus gaeumannii, causal agent of the Douglas-fir foliar disease Swiss needle cast, is the only known pathogenic species of the genus. Current classifications place Phaeocryptopus in the Venturiaceae (Pleosporales), typified by the apple-scab pathogen Venturia inaequalis. All core members of this family have hyphomycetous anamorphs. We sought to confirm these relationships by means of phylogenetic analyses of the small (SSU) and large (LSU) subunits and internal transcribed spacer (ITS) region of nuclear ribosomal gene sequences (nrDNA). Analyses indicated that both the genus Phaeocryptopus and the family Venturiaceae, as currently defined, are unnatural groups. Phaeocryptopus nudus, type of the genus, is aligned in the Dothioraceae (Dothideales) and P. gaeumannii in the Mycosphaerellaceae (Capnodiales) near species of Mycosphaerella and Rasutoria. Core representatives of Venturiaceae formed an unambiguous clade but ordinal placement was unresolved. The family apparently is not included in the Pleosporales, Dothideales, Myriangiales or Capnodiales. Coelomycetous Rhizosphaera form-species are accepted generally as anamorphic states of Phaeocryptopus, however the relationship never has been established conclusively. Species of Rhizosphaera are closely related to P. nudus but not to P. gaeumannii, supporting an anamorphteleomorph connection between Rhizosphaera and Phaeocryptopus and providing further evidence that P. gaeumanii is not congeneric with P. nudus.

Molecular phylogenetic support from ribosomal DNA sequences for origin of Helminthosporium from Leptosphaeria-like loculoascomycete ancestors

Internal transcribed spacer (ITS) regions and 5.8S rDNA were PCR-amplified and sequenced for 17 isolates of Helminthosporium solani, cause of the potato disease silver scurf, and for 10 other iso- lates obtained from culture collections as Helminthos- porium spp. Of these, five isolates had been incor- rectly identified as Helminthosporium spp. and be- longed in the genera Cochliobolus (anamorphs Bipo- laris, Curvularia), Cladosporium, and Pyrenophora (anamorph Drechslera). Sequence alignment and analyses of ITS regions and 5.8S rDNA of four true Helminthosporium species and more than 45 fungi formerly grouped in the genus Helminthosporium s. 1. revealed that the segregated Helminthosporium spe- cies did not group with Helminthosporium s. s. Three species of Helminthosporium s. s. (H. solani, type spe- cies H. velutinum, and H. chlorophorae) grouped tightly and were most closely related to the teleo- morph Leptosphaeria bicolor. For H. solani and H. ve- lutinum, 18SrDNA sequences were also determined. Phylogenetic analyses of the 18S rDNA sequences of 33 euascomycetous species confirmed the close rela- tionship of H. solani and H. velutinum to L. bicolor and placed Helminthosporium in the Pleosporales with 100% parsimony bootstrap support. Helminthos- porium asterinum did not group closely with the other species of Helminthosporium s. s., but was as closely related to discomycetes in the Leotiales as to other

Pyrigemmula, a novel hyphomycete genus on grapevine and tree bark.

The anamorphic taxon Pyrigemmula aurantiaca gen. et sp. nov. is described and illustrated from specimens that were collected from the inner bark of living woody hosts (Vitis vinifera, Pyrus communis, Mespilus germanica, Platanus hybrida, Elaeagnus angustifolia) and plant debris in Hungary. The fungus is generically distinct in the nature of the pyriform, golden conidiogenous cell with a solitary terminal pore and the ellipsoidal, distoseptate, phragmoconidia that germinate from each end and that have a rarely noted internal hilum quite unlike the hilum of the conidiogenous cell. The new fungus is compared with the type species of a number of allied genera of hyphomycetes. Free spores of the fungus were trapped in air, honeydew sap and rainwater samples. Aerobiological studies showed that the spores are infrequent in the air, whereas their concentration increased with higher atmospheric pressure. Pyrigemmula aurantiaca lives in bark fissures and rarely becomes airborne and the spores are mainly dispersed by rain splash.