TY - JOUR T1 - Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence JF - Taxon Y1 - 2010 A1 - Crespo, A. A1 - Kauff, F. A1 - Divakar, P.K. A1 - del Prado, R. A1 - Pérez-Ortega, S. A1 - Amo de Paz, G. A1 - Ferencova, Z. A1 - Blanco, O. A1 - Roca-Valiente, B. A1 - Núñez-Zapata, J. A1 - Cubas, P. A1 - Argüello, A. A1 - Elix, J.A. A1 - Esslinger, T.L. A1 - Hawksworth, D.L. A1 - Millanes, A.M. A1 - Molina, M. Carmen A1 - Wedin, M. A1 - Ahti, T. A1 - Aptroot, A. A1 - Barreno, E. A1 - Bungartz, F. A1 - Calvelo, S. A1 - Candan, M. A1 - Cole, M. A1 - Ertz, D. A1 - Goffinet, B. A1 - Lindblom, L. A1 - Lücking, R. A1 - Lutzoni, F. A1 - Mattsson, J.-E. A1 - Messuti, M.I. A1 - Miadlikowska, J. A1 - Piercey-Normore, M.D. A1 - Rico, V.J. A1 - Sipman, H.J.M. A1 - Schmitt, I. A1 - Spribille, T. A1 - Thell, A. A1 - Thor, G. A1 - Upreti, D. A1 - Lumbsch, H.T. SP - 1735 EP - 1753 VL - 59 UR - http://www.jstor.org/stable/41059870 ER - TY - JOUR T1 - Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in Graphidaceae (Ascomycota) JF - PLoS ONE Y1 - 2012 DO - 10.1371/journal.pone.0051392 A1 - Parnmen, S. A1 - Lücking, R. A1 - Lumbsch, H.T. ED - O’Grady, P. SP - e51392 VL - 7 UR - http://dx.plos.org/10.1371/journal.pone.0051392 IS - 12 ER - TY - JOUR T1 - Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions JF - BMC Evolutionary Biology Y1 - 2012 DO - 10.1186/1471-2148-12-176 A1 - Leavitt, S.D. A1 - Esslinger, T.L. A1 - Divakar, P.K. A1 - Lumbsch, H.T. SP - 18 pp. VL - 12 UR - http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-12-176 IS - 176 ER - TY - JOUR T1 - The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota) JF - Fungal Biology Y1 - 2013 DO - 10.1016/j.funbio.2013.08.001 A1 - Singh, G. A1 - Divakar, P.K. A1 - Dal Grande, F. A1 - Otte, J. A1 - Parnmen, S. A1 - Wedin, M. A1 - Crespo, A. A1 - Lumbsch, H.T. A1 - Schmitt, I. SP - 715 EP - 721 VL - 117 UR - http://linkinghub.elsevier.com/retrieve/pii/S1878614613001177 ER - TY - JOUR T1 - Diversification of the newly recognized lichen-forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events JF - American Journal of Botany Y1 - 2012 DO - 10.3732/ajb.1200258 A1 - Divakar, P.K. A1 - Del-Prado, R. A1 - Lumbsch, H.T. A1 - Wedin, M. A1 - Esslinger, T.L. A1 - Leavitt, S.D. A1 - Crespo, A. SP - 2014 EP - 2026 VL - 99 UR - http://doi.wiley.com/10.3732/ajb.1200258 ER - TY - JOUR T1 - Anatomical and ontogenetic studies on the lichen family Schaereriaceae (Agyriineae, Lecanorales) JF - Bryologist Y1 - 1996 DO - 10.2307/3244438 A1 - Lunke, T. A1 - Lumbsch, H.T. A1 - Feige, G.B. SP - 53 EP - 63 VL - 99 UR - http://www.jstor.org/stable/3244438 ER - TY - JOUR T1 - Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota) JF - PLOS ONE Y1 - 2015 DO - 10.1371/journal.pone.0124625 A1 - Singh, G. A1 - Dal Grande, F. A1 - Divakar, P.K. A1 - Otte, J. A1 - Leavitt, S.D. A1 - Szczepanska, K. A1 - Crespo, A. A1 - Rico, V.J. A1 - Aptroot, A. A1 - Cáceres, M.E. da Silva A1 - Lumbsch, H.T. A1 - Schmitt, I. ED - Fontaneto, D. SP - e0124625 VL - 10 UR - http://dx.plos.org/10.1371/journal.pone.0124625 IS - 5 ER - TY - JOUR T1 - New insights into relationships of lichen-forming Dothideomycetes JF - Fungal Diversity Y1 - 2011 DO - 10.1007/s13225-011-0144-7 A1 - Nelsen, M.P. A1 - Lücking, R.T. A1 - Mbatchou, J.S. A1 - Andrew, C.J. A1 - Spielmann, A.A. A1 - Lumbsch, H.T. SP - 155 EP - 162 VL - 51 UR - http://link.springer.com/10.1007/s13225-011-0144-7 ER - TY - JOUR T1 - Towards an integrated phylogenetic classification of the Tremellomycetes JF - Studies in Mycology Y1 - 2015 DO - 10.1016/j.simyco.2015.12.001 A1 - Liu, X.-Z. A1 - Wang, Q.-M. A1 - Göker, M. A1 - Groenewald, M. A1 - Kachalkin, A.V. A1 - Lumbsch, H.T. A1 - Millanes, A.M. A1 - Wedin, M. A1 - Yurkov, A.M. A1 - Boekhout, T. A1 - Bai, F.-Y. SP - 85 EP - 147 VL - 81 UR - http://linkinghub.elsevier.com/retrieve/pii/S0166061615000275 ER - TY - JOUR T1 - Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation JF - Molecular Phylogenetics and Evolution Y1 - 2010 DO - 10.1016/j.ympev.2010.04.014 A1 - Del-Prado, R. A1 - Cubas, P. A1 - Lumbsch, H.T. A1 - Divakar, P.K. A1 - Blanco, O. A1 - de Paz, G. Amo A1 - Molina, M.C. A1 - Crespo, A. SP - 125 EP - 133 VL - 56 UR - http://linkinghub.elsevier.com/retrieve/pii/S1055790310001685 ER - TY - JOUR T1 - Circumscription of the genus Lepra, a recently resurrected genus to accommodate the “Variolaria”-group of Pertusaria sensu lato (Pertusariales, Ascomycota) JF - PLoS ONE Y1 - 2017 DO - 10.1371/journal.pone.018028410 A1 - Wei, X.-l. A1 - Schmitt, I. A1 - Hodkinson, B. A1 - Flakus, A. A1 - Kukwa, M. A1 - Divakar, P.K. A1 - Kirika, P.M. A1 - Otte, J. A1 - Meiser, A. A1 - Lumbsch, H.T. ED - Baruffini, E. SP - e0180284 VL - 12 UR - http://dx.plos.org/10.1371/journal.pone.0180284 IS - 7 ER - TY - JOUR T1 - Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi JF - Fungal Diversity Y1 - 2017 DO - 10.1007/s13225-017-0379-z A1 - Divakar, P.K. A1 - Crespo, A. A1 - Kraichak, E. A1 - Leavitt, S.D. A1 - Singh, G. A1 - Schmitt, I. A1 - Lumbsch, H.T. SP - 101 EP - 117 VL - 84 UR - http://link.springer.com/10.1007/s13225-017-0379-z ER - TY - JOUR T1 - The cetrarioid core group revisited (Lecanorales: Parmeliaceae) JF - Lichenologist Y1 - 2011 DO - 10.1017/S0024282911000508 A1 - Nelsen, M.P. A1 - Chavez, N. A1 - Sackett-Hermann, E. A1 - Thell, A. A1 - Randlane, T. A1 - Divakar, P.K. A1 - Rico, V.J. A1 - Lumbsch, H.T. SP - 537 EP - 551 VL - 43 UR - https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0024282911000508 ER - TY - JOUR T1 - A DNA barcoding approach for identification of hidden diversity in Parmeliaceae (Ascomycota): Parmelia sensu stricto as a case study JF - Botanical Journal of the Linnean Society Y1 - 2016 DO - 10.1111/boj.12358 A1 - Divakar, P.K. A1 - Leavitt, S.D. A1 - Molina, M. Carmen A1 - Del-Prado, R. A1 - Lumbsch, H.T. A1 - Crespo, A. SP - 21 EP - 29 VL - 180 UR - https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/boj.12358 ER - TY - JOUR T1 - Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data JF - Lichenologist Y1 - 2005 DO - 10.1017/S0024282904014641 A1 - Divakar, Pradeep K. A1 - Molina, M. Carmen A1 - Lumbsch, H.T. A1 - Crespo, A. SP - 37 EP - 46 VL - 37 UR - http://www.journals.cambridge.org/abstract_S0024282904014641 ER - TY - JOUR T1 - Phylogenetic relationships and species concepts in Parmelia s. str. (Parmeliaceae) inferred from nuclear ITS rDNA and beta-tubulin sequences JF - Lichenologist Y1 - 2004 DO - 10.1017/S0024282904013933 A1 - Molina, M. del Carmen A1 - Crespo, A. A1 - Blanco, O. A1 - Lumbsch, H.T. A1 - Hawksworth, D.L. SP - 37 EP - 54 VL - 36 UR - http://www.journals.cambridge.org/abstract_S0024282904013933 ER - TY - JOUR T1 - Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy JF - Molecular Ecology Resources Y1 - 2013 DO - 10.1111/1755-0998.12086 A1 - Pino-Bodas, R. A1 - Martín, M.P. A1 - Burgaz, A.R. A1 - Lumbsch, H.T. SP - 1058 EP - 1068 VL - 13 UR - http://doi.wiley.com/10.1111/1755-0998.12086 ER - TY - JOUR T1 - Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters JF - Antarctic Science Y1 - 2010 DO - 10.1017/S0954102010000477 A1 - Ruprecht, U. A1 - Lumbsch, H.T. A1 - Brunauer, G. A1 - Green, T.G.A. A1 - Türk, R. SP - 727 EP - 741 VL - 22 UR - http://www.journals.cambridge.org/abstract_S0954102010000477 ER - TY - JOUR T1 - Major clades and phylogenetic relationships between lichenized and non-lichenized lineages in Ostropales (Ascomycota: Lecanoromycetes) JF - Taxon Y1 - 2010 A1 - Baloch, E. A1 - Lücking, R. A1 - Lumbsch, H.T. A1 - Wedin, M. SP - 1483 EP - 1494 VL - 59 UR - http://www.jstor.org/stable/20774043 ER - TY - JOUR T1 - The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited JF - Mycological Research Y1 - 2007 DO - 10.1016/j.mycres.2007.01.006 A1 - Lumbsch, H.T. A1 - Schmitt, I. A1 - Lücking, R. A1 - Wiklund, E. A1 - Wedin, M. SP - 257 EP - 267 KW - Ascomycota KW - Fungal Proteins KW - Genes, Fungal KW - Phylogeny KW - Species Specificity AB -

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.

VL - 111 ER - TY - JOUR T1 - Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes JF - Molecular Phylogenetics and Evolution Y1 - 2004 DO - 10.1016/j.ympev.2004.04.014 A1 - Schmitt, I. A1 - Lumbsch, H.T. SP - 43 EP - 55 VL - 33 UR - http://linkinghub.elsevier.com/retrieve/pii/S1055790304001435 ER - TY - JOUR T1 - A class-wide phylogenetic assessment of Dothideomycetes JF - Studies in Mycology Y1 - 2009 DO - 10.3114/sim.2009.64.01 A1 - Schoch, C.L. A1 - Crous, P.W. A1 - Groenewald, J.Z. A1 - Boehm, E.W.A. A1 - Burgess, T.I. A1 - de Gruyter, J. A1 - de Hoog, G.S. A1 - Dixon, L.J. A1 - Grube, M. A1 - Gueidan, C. A1 - Harada, Y. A1 - Hatakeyama, S. A1 - Hirayama, K. A1 - Hosoya, T. A1 - Huhndorf, S.M. A1 - Hyde, K.D. A1 - Jones, E.B.G. A1 - Kohlmeyer, J. A1 - Kruys, Å. A1 - Li, Y.M. A1 - Lücking, R. A1 - Lumbsch, H.T. A1 - Marvanová, L. A1 - Mbatchou, J.S. A1 - McVay, A.H. A1 - Miller, A.N. A1 - Mugambi, G.K. A1 - Muggia, L. A1 - Nelsen, M.P. A1 - Nelson, P. A1 - Owensby, C.A. A1 - Phillips, A.J.L. A1 - Phongpaichit, S. A1 - Pointing, S.B. A1 - Pujade-Renaud, V. A1 - Raja, H.A. A1 - Plata, E. Rivas A1 - Robbertse, B. A1 - Ruibal, C. A1 - Sakayaroj, J. A1 - Sano, T. A1 - Selbmann, L. A1 - Shearer, C.A. A1 - Shirouzu, T. A1 - Slippers, B. A1 - Suetrong, S. A1 - Tanaka, K. A1 - Volkmann-Kohlmeyer, B. A1 - Wingfield, M.J. A1 - Wood, A.R. A1 - Woudenberg, J.H.C. A1 - Yonezawa, H. A1 - Zhang, Y. A1 - Spatafora, J.W. SP - 1 EP - 15 VL - 64 UR - http://linkinghub.elsevier.com/retrieve/pii/S0166061614600956 ER - TY - JOUR T1 - Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota) JF - Mycologia Y1 - 2011 DO - 10.3852/10-234 A1 - Schmull, M. A1 - Miadlikowska, J. A1 - Pelzer, M. A1 - Stocker-Worgotter, E. A1 - Hofstetter, V. A1 - Fraker, E. A1 - Hodkinson, B.P. A1 - Reeb, V. A1 - Kukwa, M. A1 - Lumbsch, H.T. A1 - Kauff, F. A1 - Lutzoni, F. SP - 983 EP - 1003 VL - 103 UR - http://www.mycologia.org/cgi/doi/10.3852/10-234 ER - TY - JOUR T1 - Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta JF - Studies in Mycology Y1 - 2009 DO - 10.3114/sim.2009.64.07 A1 - Nelsen, M.P. A1 - Lücking, R. A1 - Grube, M. A1 - Mbatchou, J.S. A1 - Muggia, L. A1 - Rivas Plata, E. A1 - Lumbsch, H.T. SP - 135 EP - 144 VL - 64 UR - http://linkinghub.elsevier.com/retrieve/pii/S0166061614601019 ER - TY - JOUR T1 - New molecular data on Pyrenulaceae from Sri Lanka reveal two well-supported groups within this family JF - Lichenologist Y1 - 2012 DO - 10.1017/S0024282912000333 A1 - Weerakoon, G. A1 - Aptroot, A. A1 - Lumbsch, H.T. A1 - Wolseley, P.A. A1 - Wijeyaratne, S.C. A1 - Gueidan, C. SP - 639 EP - 647 VL - 44 UR - http://www.journals.cambridge.org/abstract_S0024282912000333 ER - TY - JOUR T1 - Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence JF - Fungal Diversity Y1 - 2016 DO - 10.1007/s13225-015-0354-5 A1 - Zhao, X. A1 - Leavitt, S.D. A1 - Zhao, Z.T. A1 - Zhang, L.L. A1 - Arup, U. A1 - Grube, M. A1 - Pérez-Ortega, S. A1 - Printzen, C. A1 - Śliwa, L. A1 - Kraichak, E. A1 - Divakar, P.K. A1 - Crespo, A. A1 - Lumbsch, H.T. SP - 293 EP - 304 VL - 78 UR - http://link.springer.com/10.1007/s13225-015-0354-5 ER - TY - JOUR T1 - A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales) JF - Taxon Y1 - 2004 A1 - Blanco, O. A1 - Crespo, A. A1 - Elix, J.A. A1 - Hawksworth, D.L. A1 - Lumbsch, H.T. SP - 959 EP - 975 VL - 53 UR - http://www.ingentaconnect.com/content/iapt/tax/2004/00000053/00000004/art00010 ER - TY - JOUR T1 - Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene JF - Molecular and Phylogenetic Evolution Y1 - 2007 DO - 10.1016/j.ympev.2006.11.029 A1 - Crespo, A. A1 - Lumbsch, H.T. A1 - Mattsson, J.-E. A1 - Blanco, O. A1 - Divakar, P.K. A1 - Articus, K. A1 - Wiklund, E. A1 - Bawingan, P.A. A1 - Wedin, M. SP - 812 EP - 824 AB -

Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.

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