Journal ArticleDOI
Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene.
Ana Crespo,H. Thorsten Lumbsch,Jan-Eric Mattsson,Oscar Blanco,Pradeep K. Divakar,Kristina Articus,Elisabeth Wiklund,Paulina A. Bawingan,Mats Wedin +8 more
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TLDR
Testing morphology-based groupings using DNA sequence data from 120 taxa that include 59 genera and represent the morphological and chemical diversity in Parmeliaceae supports morphological characters as important for the identification of monophyletic clades within the family.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2007-08-01. It has received 138 citations till now. The article focuses on the topics: Parmeliaceae & Monophyly.read more
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Journal ArticleDOI
Myconet Volume 14. Part One. Outline of Ascomycota—2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113
TL;DR: The current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota is presented, based on the changes listed in Myconet notes 4751–5113.
Journal ArticleDOI
A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Jolanta Miadlikowska,Frank Kauff,Filip Högnabba,Jeffrey C. Oliver,Katalin Molnár,Emily Fraker,Ester Gaya,Josef Hafellner,Valérie Hofstetter,Cécile Gueidan,Monica Garcia Otalora,Brendan P. Hodkinson,Martin Kukwa,Robert Lücking,Curtis R. Björk,Harrie J. M. Sipman,Ana Rosa Burgaz,Arne Thell,Alfredo Passo,Leena Myllys,Trevor Goward,Samantha Fernández-Brime,Geir Hestmark,James C. Lendemer,H. Thorsten Lumbsch,Michaela Schmull,Conrad L. Schoch,Emmanuël Sérusiaux,David R. Maddison,A. Elizabeth Arnold,François Lutzoni,Soili Stenroos +31 more
TL;DR: A multigene phylogenetic synthesis of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences revealing relatively stable relationships for many families and orders is provided.
Journal ArticleDOI
New primers for promising single-copy genes in fungal phylogenetics and systematics.
Imke Schmitt,Ana Crespo,Pradeep K. Divakar,Johnathon D. Fankhauser,E. Herman-Sackett,Klaus Kalb,Matthew P. Nelsen,N.A. Nelson,E. Rivas-Plata,A.D. Shimp,Todd J. Widhelm,H. T. Lumbsch +11 more
TL;DR: Degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota) are reported and analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotins, Taphrinomycotinas and Basidiomycota.
Journal ArticleDOI
International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.
Laszlo Irinyi,Carolina Serena,Dea Garcia-Hermoso,Michael Arabatzis,Marie Desnos-Ollivier,Duong Vu,Gianluigi Cardinali,Ian Arthur,Anne-Cécile Normand,Alejandra Giraldo,Keith Cássia da Cunha,Marcelo Sandoval-Denis,Marijke Hendrickx,Angela Satie Nishikaku,Analy Salles de Azevedo Melo,Karina Bellinghausen Merseguel,Aziza Khan,Juliana Alves Parente Rocha,Paula Sampaio,Marcelo R. S. Briones,Renata C. Ferreira,Mauro de Medeiros Muniz,Laura Rosio Castañón-Olivares,Daniel Estrada-Bárcenas,Carole Cassagne,Charles Mary,Shu Yao Duan,Fanrong Kong,Annie Ying Sun,Xianyu Zeng,Zuotao Zhao,Nausicaa Gantois,Françoise Botterel,Barbara Robbertse,Conrad L. Schoch,Walter Gams,David Ellis,Catriona Halliday,Sharon C.-A. Chen,Sharon C.-A. Chen,Tania C. Sorrell,Renaud Piarroux,Arnaldo Lopes Colombo,Célia Pais,Sybren de Hoog,Rosely Maria Zancopé-Oliveira,Maria Lucia Taylor,Conchita Toriello,Célia Maria de Almeida Soares,Laurence Delhaes,Dirk Stubbe,Françoise Dromer,Stéphane Ranque,Josep Guarro,José F. Cano-Lira,Vincent Robert,Aristea Velegraki,Wieland Meyer +57 more
TL;DR: An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool to rapidly and reliably identify most agents of mycoses.
Journal ArticleDOI
Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence
Ana Crespo,Frank Kauff,Pradeep K. Divakar,Ruth del Prado,Sergio Pérez-Ortega,Guillermo Amo de Paz,Ferencova Suzana,Oscar Blanco,Beatriz Roca-Valiente,Jano Núñez-Zapata,Paloma Cubas,Arturo Argüello,J. A. Elix,Theodore L. Esslinger,David L. Hawksworth,Ana M. Millanes,M. Carmen Molina,Mats Wedin,Teuvo Ahti,André Aptroot,Eva Barreno,Frank Bungartz,Susana Calvelo,Mehmet Candan,Mariette S. Cole,Damien Ertz,Bernard Goffinet,Louise Lindblom,Robert Lücking,François Lutzoni,Jan-Eric Mattsson,María Inés Messuti,Jolanta Miadlikowska,Michele D. Piercey-Normore,Víctor J. Rico,Harrie J. M. Sipman,Imke Schmitt,Toby Spribille,Arne Thell,Göran Thor,Dalip K. Upreti,H. Thorsten Lumbsch +41 more
TL;DR: An overview of current knowledge of the major clades of all parmelioid lichens is given and 27 genera within nine main clades are accepted, including 31 of 33 currently accepted parMelioid genera (and 63 of 84 accepted genera of Parmeliaceae).
References
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Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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