Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Towards an integrated phylogenetic classification of the Tremellomycetes.

Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.

Polygynous supercolonies of the acacia-ant Pseudomyrmex peperi, an inferior colony founder.

In ant-plant protection mutualisms, plants provide nesting space and nutrition to defending ants. Several plant-ants are polygynous. Possessing more than one queen per colony can reduce nestmate relatedness and consequently the inclusive fitness of workers. Here, we investigated the colony structure of the obligate acacia-ant Pseudomyrmex peperi, which competes for nesting space with several congeneric and sympatric species. Pseudomyrmex peperi had a lower colony founding success than its congeners and thus, appears to be competitively inferior during the early stages of colony development. Aggression assays showed that P. peperi establishes distinct, but highly polygynous supercolonies, which can inhabit large clusters of host trees. Analysing queens, workers, males and virgin queens from two supercolonies with eight polymorphic microsatellite markers revealed a maximum of three alleles per locus within a colony and, thus, high relatedness among nestmates. Colonies had probably been founded by one singly mated queen and supercolonies resulted from intranidal mating among colony-derived males and daughter queens. This strategy allows colonies to grow by budding and to occupy individual plant clusters for time spans that are longer than an individual queen's life. Ancestral states reconstruction indicated that polygyny represents the derived state within obligate acacia-ants. We suggest that the extreme polygyny of Pseudomyrmex peperi, which is achieved by intranidal mating and thereby maintains high nestmate relatedness, might play an important role for species coexistence in a dynamic and competitive habitat.

Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota).

Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.

Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta.

We present a revised phylogeny of lichenised Dothideomyceta (Arthoniomycetes and Dothideomycetes) based on a combined data set of nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA data. Dothideomyceta is supported as monophyletic with monophyletic classes Arthoniomycetes and Dothideomycetes; the latter, however, lacking support in this study. The phylogeny of lichenised Arthoniomycetes supports the current division into three families: Chrysothrichaceae (Chrysothrix), Arthoniaceae (Arthonia s. l., Cryptothecia, Herpothallon), and Roccellaceae (Chiodecton, Combea, Dendrographa, Dichosporidium, Enterographa, Erythrodecton, Lecanactis, Opegrapha, Roccella, Roccellographa, Schismatomma, Simonyella). The widespread and common Arthonia caesia is strongly supported as a (non-pigmented) member of Chrysothrix. Monoblastiaceae, Strigulaceae, and Trypetheliaceae are recovered as unrelated, monophyletic clades within Dothideomycetes. Also, the genera Arthopyrenia (Arthopyreniaceae) and Cystocoleus and Racodium (Capnodiales) are confirmed as Dothideomycetes but unrelated to each other. Mycomicrothelia is shown to be unrelated to Arthopyrenia s.str., but is supported as a monophyletic clade sister to Trypetheliaceae, which is supported by hamathecium characters. The generic concept in several groups is in need of revision, as indicated by non-monophyly of genera, such as Arthonia, Astrothelium, Cryptothecia, Cryptothelium, Enterographa, Opegrapha, and Trypethelium in our analyses.

New primers for promising single-copy genes in fungal phylogenetics and systematics.

Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

A class-wide phylogenetic assessment of Dothideomycetes.

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Phylogeny of filamentous ascomycetes.

Phylogenetic studies of higher ascomycetes are enhanced by the introduction of molecular markers. Most studies employed sequences of the SSU rRNA gene, but recently data from additional genes (RPB2, LSU rRNA) have become available. Several groups defined by their ascoma-type, such as Pyrenomycetes, are supported while others, like the Discomycetes, appear to be paraphyletic. The Pezizales with operculate asci are basal to other eu-ascomycetes, while other Discomycetes appear to be derived eu-ascomycetes. The reevaluation of classical characters using molecular data is discussed using three examples. Ascus types are often regarded as being of major importance in ascomycete systematics, but prototunicate asci were found to be of poor taxonomic value, since ascomycetes with prototunicate asci are polyphyletic. The independence of the Agyriales, assumed from their morphological characters, is supported by sequence data but the relationship to supposed sister groups remains dubious. The phylogeny of ascolocularous fungi and their circumscription requires further study. While a circumscription based on bitunicate asci can be rejected, it remains unclear whether fungi with ascolocularous ascoma development represent a monophyletic entity.

Molecular evidence for the diversification of extant lichens in the late cretaceous and tertiary.

A molecular clock based on ITS sequence data from the lichen genera Biatora and Phyllopsora is calibrated with the help of paleoclimatic data and evidence of forest history. The clock indicates that diversification within Biatora started as early as in the Late Cretaceous and took place during periods of climatic cooling, when new types of forest evolved and spread in the Northern Hemisphere. Arctic-alpine species of the genus appear to be of considerable age, dating back to the Late Eocene-Oligocene climatic cooling. By using calibrated phylogenies of epiphytic lichens it may become possible to date many paleoenvironmental events, for which little fossil evidence exists.

Genetic variation of Usnea filipendula (Parmeliaceae) populations in western Germany investigated by RAPDs suggests reinvasion from various sources.

Random amplified polymorphic DNA (RAPD) markers were characterized for 25 specimens of Usnea filipendula to evaluate the genetic diversity of populations reinvading formerly uninhabited regions in Northrhine-Westphalia due to decreasing sulfur dioxide levels. With six 10-mer randomly amplified polymorphic DNA (RAPD) primers, a 66 character by 25 specimens matrix was generated. Phenetic analysis (UPGMA) showed no obvious groupings. The reinvading populations are distributed over the phenogram and are not genetically closely related. The results suggest that the reinvading populations of this usually sterile species are derived from different sources and do not consist of a particular clone capable of re-entering the area.