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Francois Lutzoni - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic comparison of protein coding versus ribosomal rna coding sequence data a case study of the lecanoromycetes Ascomycota
Molecular Phylogenetics and Evolution, 2007Co-Authors: Valerie Hofstetter, Frank Kauff, Jolanta Miadlikowska, Francois LutzoniAbstract:The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.
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assembling the fungal tree of life progress classification and evolution of subcellular traits
American Journal of Botany, 2004Co-Authors: Francois Lutzoni, Timothy Y. James, David S Hibbett, David J. Mclaughlin, Mahajabeen Padamsee, Frank Kauff, Cymon J Cox, Gail Celio, Bryn T M Dentinger, Elisabeth BalochAbstract:Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.
Benjamin D Hall - One of the best experts on this subject based on the ideXlab platform.
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loss of the flagellum happened only once in the fungal lineage phylogenetic structure of kingdom fungi inferred from rna polymerase ii subunit genes
BMC Evolutionary Biology, 2006Co-Authors: Yajuan J Liu, Matthew C Hodson, Benjamin D HallAbstract:At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.
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phylogenetic relationships among ascomycetes evidence from an rna polymerse ii subunit
Molecular Biology and Evolution, 1999Co-Authors: Yajuan J Liu, Sally Whelen, Benjamin D HallAbstract:In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi.
Mats Wedin - One of the best experts on this subject based on the ideXlab platform.
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collolechia revisited and a re assessment of ascus characteristics in placynthiaceae peltigerales Ascomycota
Lichenologist, 2016Co-Authors: Alica Kosuthova, Martin Westberg, Samantha Fernandezbrime, Mats WedinAbstract:Collolechia revisited and a re-assessment of ascus characteristics in Placynthiaceae (Peltigerales, Ascomycota)
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dating the diversification of the major lineages of Ascomycota fungi
PLOS ONE, 2013Co-Authors: Maria Prieto, Mats WedinAbstract:Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated.
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phylogenetic relationships of lecanoromycetes Ascomycota as revealed by analyses of mtssu and nlsu rdna sequence data
Fungal Biology, 2005Co-Authors: Mats Wedin, Elisabeth Wiklund, Anna T Crewe, Heidi Doring, Stefan Ekman, Asa Nyberg, Imke Schmitt, Thorsten H LumbschAbstract:The phylogeny of Lecanoromycetes (Ascomycota, Fungi) is investigated utilizing parsimony and Bayesian Markov Chain Monte Carlo analyses, of combined nLSU rDNA and mtSSU rDNA sequence datasets. The results suggest that Acarosporaceae, Candelariaceae, Phlyctis and Pycnora are not members of the monophyletic Lecanorales, and that Timdalia and Pleopsidium are members of a monophyletic Acarosporaceae. Pycnora, Candelariaceae and Acarosporaceae form a monophyletic group. Umbilicariaceae, Hypocenomyce scalaris, H. friesii, Ophioparmaceae, Boreoplaca, Elixia and Fuscidea form either a basal paraphyletic assemblage in Lecanoromycetes, or a monophyletic group which is the sister-group to Lecanorales and the rest of Lecanoromycetes (excluding Acarosporaceae). The Acarosporaceae forms a group with Pycnora and Candelariaceae, which may be outside the Lecanoromycetes. Chaetothyriales, Verrucariales, Eurotiales, Lichinales and Mycocaliciales form a monophyletic group, but with low support. We briefly discuss incongruence between datasets from different genetic markers, comparing the differences between the separate parsimony analyses, where the ILD test indicated a very significant incongruence. The phylogenetic significance of ascus-types that have influenced most recent Ascomycota classifications heavily is also discussed, and we finally point out risks with formalizing classifications too early.
Thorsten H Lumbsch - One of the best experts on this subject based on the ideXlab platform.
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kalbionora palaeotropica a new genus and species from coastal forests in southeast asia and australia malmideaceae Ascomycota
MycoKeys, 2017Co-Authors: Mattika Sodamuk, Steven D Leavitt, Kansri Boonpragob, Pachara Mongkolsuk, Anders Tehler, Thorsten H LumbschAbstract:Kalbionora palaeotropica , a new genus and species from coastal forests in Southeast Asia and Australia (Malmideaceae, Ascomycota)
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myconet volume 14 part one outline of Ascomycota 2009 part two notes on ascomycete systematics nos 4751 5113
Fieldiana Life and Earth Sciences, 2010Co-Authors: Thorsten H Lumbsch, Sabine M HuhndorfAbstract:Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota. It is based on the changes listed in Myconet notes 4751–5113. In the current outline, three subphyla (Pezizomycotina, Saccharomycotina, Taphrinomycotina) are accepted. Taphrinomycotina includes four classes (Neolectomycetes, Pneumocystidomycetes, Schizosaccharomyces, Taphrinomycetes). Saccharomycotina consists of one class and Pezizomycotina includes eleven classes (Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Laboulbeniomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, Orbiliomycetes, Pezizomycetes, Sordariomycetes). Part Two presents 363 notes on the taxonomy and nomenclature of ascomycetes (Ascomycota) at the generic and higher levels. Numerous changes in higher levels resulted from multi-authored phylogenetic papers resulting from the AFTOL and Deep Hyphae projects, especially a publication on a revised fungal classifica...
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outline of Ascomycota 2007
2007Co-Authors: Thorsten H Lumbsch, Sabine M HuhndorfAbstract:Lumbsch, H. T. and S.M. Huhndorf (ed.) 2007. Outline of Ascomycota – 2007. Myconet 13: 1 58. The present classification contains all accepted genera and higher taxa above the generic level in phylum Ascomycota.
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phylogenetic relationships of lecanoromycetes Ascomycota as revealed by analyses of mtssu and nlsu rdna sequence data
Fungal Biology, 2005Co-Authors: Mats Wedin, Elisabeth Wiklund, Anna T Crewe, Heidi Doring, Stefan Ekman, Asa Nyberg, Imke Schmitt, Thorsten H LumbschAbstract:The phylogeny of Lecanoromycetes (Ascomycota, Fungi) is investigated utilizing parsimony and Bayesian Markov Chain Monte Carlo analyses, of combined nLSU rDNA and mtSSU rDNA sequence datasets. The results suggest that Acarosporaceae, Candelariaceae, Phlyctis and Pycnora are not members of the monophyletic Lecanorales, and that Timdalia and Pleopsidium are members of a monophyletic Acarosporaceae. Pycnora, Candelariaceae and Acarosporaceae form a monophyletic group. Umbilicariaceae, Hypocenomyce scalaris, H. friesii, Ophioparmaceae, Boreoplaca, Elixia and Fuscidea form either a basal paraphyletic assemblage in Lecanoromycetes, or a monophyletic group which is the sister-group to Lecanorales and the rest of Lecanoromycetes (excluding Acarosporaceae). The Acarosporaceae forms a group with Pycnora and Candelariaceae, which may be outside the Lecanoromycetes. Chaetothyriales, Verrucariales, Eurotiales, Lichinales and Mycocaliciales form a monophyletic group, but with low support. We briefly discuss incongruence between datasets from different genetic markers, comparing the differences between the separate parsimony analyses, where the ILD test indicated a very significant incongruence. The phylogenetic significance of ascus-types that have influenced most recent Ascomycota classifications heavily is also discussed, and we finally point out risks with formalizing classifications too early.
Franck Richard - One of the best experts on this subject based on the ideXlab platform.
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2289 proposal to conserve the name morchella semilibera against phallus crassipes p gigas and p undosus Ascomycota conserve morchella semilibera
Taxon, 2014Co-Authors: Pierrearthur Moreau, Kerry Odonnell, Jeanmichel Bellanger, Philippe Clowez, Regis Courtecuisse, Karen Hansen, Henning Knudsen, Franck RichardAbstract:(2289) Proposal to conserve the name Morchella semilibera against Phallus crassipes, P. gigas and P. undosus (Ascomycota) : Conserve Morchella semilibera
