A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

@article{Miadlikowska2014AMP,
  title={A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.},
  author={Jolanta Miadlikowska and Frank Kauff and Filip H{\"o}gnabba and Jeffrey C. Oliver and Katalin Moln{\'a}r and Emily Fraker and Ester Gaya and Josef Hafellner and Val{\'e}rie Hofstetter and C{\'e}cile Gueidan and M{\'o}nica A G Ot{\'a}lora and Brendan P. Hodkinson and Martin Kukwa and Robert L{\"u}cking and Curtis Bj{\"o}rk and Harrie J. M. Sipman and Ana Rosa Burgaz and Arne Thell and Alfredo Passo and Leena Myllys and Trevor Goward and Samantha Fern{\'a}ndez-Brime and Geir Hestmark and James C. Lendemer and H. Thorsten Lumbsch and Michaela Schmull and Conrad L. Schoch and Emmanu{\"e}l S{\'e}rusiaux and David R. Maddison and A. Elizabeth Arnold and François Lutzoni and Soili Stenroos},
  journal={Molecular phylogenetics and evolution},
  year={2014},
  volume={79},
  pages={
          132-68
        }
}
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae… Expand
Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence
TLDR
The phylogenetic relationship of lecanoroid lichens is studied and the presence of additional clades of species currently placed in Lecanora sensu lato that warrant taxonomic recognition is indicated but additional data will be necessary before the circumscription of these entities is fully understood. Expand
The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae)
TLDR
Five conserved mitochondrial genes were used to infer a best estimate maximum likelihood phylogeny among these five Usnea and other relatives, which yielded relationships consistent with prior published phylogenies. Expand
Phylogeny of the family Cladoniaceae (Lecanoromycetes, Ascomycota) based on sequences of multiple loci
TLDR
A new phylogeny of Cladoniaceae is constructed using five loci from a worldwide sample of 643 specimens representing 304 species and proposes the new genera Pulchrocladia and Rexia, as segregates of Cladia, five new combinations, and the resurrection of the genus Heterodea. Expand
Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).
TLDR
This study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae. Expand
Hidden diversity of marine borderline lichens and a new order of fungi: Collemopsidiales (Dothideomyceta)
TLDR
Observations suggest rock-boring ability evolved in parallel in the different lineages within this group of fungi, as well as comparing the two alternative species models by means of Bayes factors, and estimating the marginal likelihood of each model. Expand
Two new classes of Ascomycota: Xylobotryomycetes and Candelariomycetes
TLDR
The new class Xylobotryomycetes is described, containing the new order Xylabotryales with the two new families XylOBotryaceae and Cirrosporiaceae, and the new class CandelariomycETes is proposed. Expand
Dominikia bonfanteae and Glomus atlanticum, two new species in the Glomeraceae (phylum Glomeromycota) with molecular phylogenies reconstructed from two unlinked loci
Examination of morphological characters of two arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which produced clusters with glomoid spores in single-species cultures, suggested that theyExpand
Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni
TLDR
A culture-based survey of staining fungi on oil-treated timber after outdoor exposure in Australia and the Netherlands uncovered new taxa in Pezizomycotina that could not be classified reliably at the class and lower taxonomic ranks by sequencing from the substrate directly or based solely on culture-dependent morphological investigations. Expand
Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.
TLDR
The cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. Expand
Taxonomy and Phylogeny of Aspiciliella, a Resurrected genus of Megasporaceae, Including the New Species A. portosantana
TLDR
Morphological and chemotaxonomic surveys showed that the genus Aspiciliella is characterized by a thallus that is crustose, rimose-areolate, partially continuous, K+ red; a green, olive-green to greenish-brown N+ light green epihymenium; 8-spored asci, ellipsoid, colourless, simple ascospores and very small conidia. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 213 REFERENCES
New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
TLDR
The phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi and conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data. Expand
Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota)
TLDR
The phylogenetic placement of members of this heterogeneous group of lichen-forming fungi is elucidated to improve the classification and phylogeny of Lecanoromycetes and the new combination Frutidella pullata is proposed here. Expand
Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.
TLDR
The various phylogenetic analyses carried out on the data sets allowed us to conclude that: the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient. Expand
Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).
TLDR
A new, but provisional, classification is proposed for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae andTeloschistineae, respectively), and it is reported here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the TelosChistales in a strict sense. Expand
Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes.
TLDR
A phylogeny based on nucleotide sequences of the nuclear large subunit (nu LSU) and the mitochondrial small sub unit (mt SSU) rRNA genes is generated and the genus Pertusaria in its current circumscription is polyphyletic comprising three major clades: the Pertuaria s.str.-group, the Variolaria-group and the Varicellaria- group. Expand
Phylogenetic Revision of the Genus Peltigera (Lichen‐Forming Ascomycota) Based on Morphological, Chemical, and Large Subunit Nuclear Ribosomal DNA Data
TLDR
The monophyly of these seven morpho‐chemical Peltigera groups is tested and a classification based on a phylogenetic approach is proposed and Hydrothyria is transferred to Pelt Tigera and a new combination Peltigersa hydrothyria Miadlikowska & Lutzoni is proposed. Expand
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
TLDR
A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented. Expand
A molecular phylogeny of Graphidaceae (Ascomycota, Lecanoromycetes, Ostropales) including 428 species
TLDR
A comprehensive molecular phylogeny of the lichen family Graphidaceae (subfamilies Graphidoideae and Fissurinoideae) based on partial sequences of the mtSSU, nuLSU rDNA, and RPB2 loci confirms that rounded and lirellate ascomata evolved multiple times in unrelated clades within the family. Expand
Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales).
TLDR
The most intriguing find is the correlation between gall-forming thalli and vertical columns of calcium oxalate crystals, suggesting that these crystals do not function as light distributors, as previously assumed, but instead stabilize the thalli which are usually hollow beneath, similar to a dome-shaped structure. Expand
Phylogenetic study of Diploschistes (lichen-forming Ascomycota: Ostropales: Graphidaceae), based on morphological, chemical, and molecular data
TLDR
This work inferred phylogenetic relationships within Diploschistes, with a special emphasis on the D. scruposus complex, using a combined dataset consisting of morphological, chemical, nrITS, and mtSSU data to determine if these species groups and phenotypically based species delimitations were monophyletic. Expand
...
1
2
3
4
5
...