@article {4798, title = {Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence}, journal = {Taxon}, volume = {59}, year = {2010}, pages = {1735-1753}, url = {http://www.jstor.org/stable/41059870}, author = {Crespo, A. and Kauff, F. and Divakar, P.K. and del Prado, R. and P{\'e}rez-Ortega, S. and Amo de Paz, G. and Ferencova, Z. and Blanco, O. and Roca-Valiente, B. and N{\'u}{\~n}ez-Zapata, J. and Cubas, P. and Arg{\"u}ello, A. and Elix, J.A. and Esslinger, T.L. and Hawksworth, D.L. and Millanes, A.M. and Molina, M. Carmen and Wedin, M. and Ahti, T. and Aptroot, A. and Barreno, E. and Bungartz, F. and Calvelo, S. and Candan, M. and Cole, M. and Ertz, D. and Goffinet, B. and Lindblom, L. and L{\"u}cking, R. and Lutzoni, F. and Mattsson, J.-E. and Messuti, M.I. and Miadlikowska, J. and Piercey-Normore, M.D. and Rico, V.J. and Sipman, H.J.M. and Schmitt, I. and Spribille, T. and Thell, A. and Thor, G. and Upreti, D. and Lumbsch, H.T.} } @article {4721, title = {Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in Graphidaceae (Ascomycota)}, journal = {PLoS ONE}, volume = {7}, year = {2012}, pages = {e51392}, doi = {10.1371/journal.pone.0051392}, url = {http://dx.plos.org/10.1371/journal.pone.0051392}, author = {Parnmen, S. and L{\"u}cking, R. and Lumbsch, H.T.}, editor = {O{\textquoteright}Grady, P.} } @article {4689, title = {Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions}, journal = {BMC Evolutionary Biology}, volume = {12}, year = {2012}, pages = {18 pp.}, issn = {1471-2148}, doi = {10.1186/1471-2148-12-176}, url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-12-176}, author = {Leavitt, S.D. and Esslinger, T.L. and Divakar, P.K. and Lumbsch, H.T.} } @article {4688, title = {The sister-group relationships of the largest family~of~lichenized fungi, Parmeliaceae (Lecanorales,~Ascomycota)}, journal = {Fungal Biology}, volume = {117}, year = {2013}, pages = {715-721}, issn = {18786146}, doi = {10.1016/j.funbio.2013.08.001}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1878614613001177}, author = {Singh, G. and Divakar, P.K. and Dal Grande, F. and Otte, J. and Parnmen, S. and Wedin, M. and Crespo, A. and Lumbsch, H.T. and Schmitt, I.} } @article {4666, title = {Diversification of the newly recognized lichen-forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events}, journal = {American Journal of Botany}, volume = {99}, year = {2012}, pages = {2014-2026}, issn = {0002-9122}, doi = {10.3732/ajb.1200258}, url = {http://doi.wiley.com/10.3732/ajb.1200258}, author = {Divakar, P.K. and Del-Prado, R. and Lumbsch, H.T. and Wedin, M. and Esslinger, T.L. and Leavitt, S.D. and Crespo, A.} } @article {4660, title = {Anatomical and ontogenetic studies on the lichen family Schaereriaceae (Agyriineae, Lecanorales)}, journal = {Bryologist}, volume = {99}, year = {1996}, pages = {53-63}, issn = {00072745}, doi = {10.2307/3244438}, url = {http://www.jstor.org/stable/3244438}, author = {Lunke, T. and Lumbsch, H.T. and Feige, G.B.} } @article {4645, title = {Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)}, journal = {PLOS ONE}, volume = {10}, year = {2015}, pages = {e0124625}, doi = {10.1371/journal.pone.0124625}, url = {http://dx.plos.org/10.1371/journal.pone.0124625}, author = {Singh, G. and Dal Grande, F. and Divakar, P.K. and Otte, J. and Leavitt, S.D. and Szczepanska, K. and Crespo, A. and Rico, V.J. and Aptroot, A. and C{\'a}ceres, M.E. da Silva and Lumbsch, H.T. and Schmitt, I.}, editor = {Fontaneto, D.} } @article {4637, title = {New insights into relationships of lichen-forming Dothideomycetes}, journal = {Fungal Diversity}, volume = {51}, year = {2011}, pages = {155-162}, issn = {1560-2745}, doi = {10.1007/s13225-011-0144-7}, url = {http://link.springer.com/10.1007/s13225-011-0144-7}, author = {Nelsen, M.P. and L{\"u}cking, R.T. and Mbatchou, J.S. and Andrew, C.J. and Spielmann, A.A. and Lumbsch, H.T.} } @article {4614, title = {Towards an integrated phylogenetic classification of the Tremellomycetes}, journal = {Studies in Mycology}, volume = {81}, year = {2015}, pages = {85-147}, issn = {01660616}, doi = {10.1016/j.simyco.2015.12.001}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0166061615000275}, author = {Liu, X.-Z. and Wang, Q.-M. and G{\"o}ker, M. and Groenewald, M. and Kachalkin, A.V. and Lumbsch, H.T. and Millanes, A.M. and Wedin, M. and Yurkov, A.M. and Boekhout, T. and Bai, F.-Y.} } @article {4573, title = {Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation}, journal = {Molecular Phylogenetics and Evolution}, volume = {56}, year = {2010}, pages = {125-133}, issn = {10557903}, doi = {10.1016/j.ympev.2010.04.014}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790310001685}, author = {Del-Prado, R. and Cubas, P. and Lumbsch, H.T. and Divakar, P.K. and Blanco, O. and de Paz, G. Amo and Molina, M.C. and Crespo, A.} } @article {4495, title = {Circumscription of the genus Lepra, a recently resurrected genus to accommodate the {\textquotedblleft}Variolaria{\textquotedblright}-group of Pertusaria sensu lato (Pertusariales, Ascomycota)}, journal = {PLoS ONE}, volume = {12}, year = {2017}, pages = {e0180284}, doi = {10.1371/journal.pone.018028410}, url = {http://dx.plos.org/10.1371/journal.pone.0180284}, author = {Wei, X.-l. and Schmitt, I. and Hodkinson, B. and Flakus, A. and Kukwa, M. and Divakar, P.K. and Kirika, P.M. and Otte, J. and Meiser, A. and Lumbsch, H.T.}, editor = {Baruffini, E.} } @article {4454, title = {Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi}, journal = {Fungal Diversity}, volume = {84}, year = {2017}, pages = {101-117}, issn = {1560-2745}, doi = {10.1007/s13225-017-0379-z}, url = {http://link.springer.com/10.1007/s13225-017-0379-z}, author = {Divakar, P.K. and Crespo, A. and Kraichak, E. and Leavitt, S.D. and Singh, G. and Schmitt, I. and Lumbsch, H.T.} } @article {4453, title = {The cetrarioid core group revisited (Lecanorales: Parmeliaceae)}, journal = {Lichenologist}, volume = {43}, year = {2011}, pages = {537-551}, issn = {0024-2829}, doi = {10.1017/S0024282911000508}, url = {https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0024282911000508}, author = {Nelsen, M.P. and Chavez, N. and Sackett-Hermann, E. and Thell, A. and Randlane, T. and Divakar, P.K. and Rico, V.J. and Lumbsch, H.T.} } @article {4372, title = {A DNA barcoding approach for identification of hidden diversity in Parmeliaceae (Ascomycota): Parmelia sensu stricto as a case study}, journal = {Botanical Journal of the Linnean Society}, volume = {180}, year = {2016}, pages = {21-29}, doi = {10.1111/boj.12358}, url = {https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/boj.12358}, author = {Divakar, P.K. and Leavitt, S.D. and Molina, M. Carmen and Del-Prado, R. and Lumbsch, H.T. and Crespo, A.} } @article {4369, title = {Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data}, journal = {Lichenologist}, volume = {37}, year = {2005}, pages = {37-46}, issn = {0024-2829}, doi = {10.1017/S0024282904014641}, url = {http://www.journals.cambridge.org/abstract_S0024282904014641}, author = {Divakar, Pradeep K. and Molina, M. Carmen and Lumbsch, H.T. and Crespo, A.} } @article {4368, title = {Phylogenetic relationships and species concepts in Parmelia s. str. (Parmeliaceae) inferred from nuclear ITS rDNA and beta-tubulin sequences}, journal = {Lichenologist}, volume = {36}, year = {2004}, pages = {37-54}, issn = {0024-2829}, doi = {10.1017/S0024282904013933}, url = {http://www.journals.cambridge.org/abstract_S0024282904013933}, author = {Molina, M. del Carmen and Crespo, A. and Blanco, O. and Lumbsch, H.T. and Hawksworth, D.L.} } @article {4320, title = {Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy}, journal = {Molecular Ecology Resources}, volume = {13}, year = {2013}, pages = {1058-1068}, doi = {10.1111/1755-0998.12086}, url = {http://doi.wiley.com/10.1111/1755-0998.12086}, author = {Pino-Bodas, R. and Mart{\'\i}n, M.P. and Burgaz, A.R. and Lumbsch, H.T.} } @article {4303, title = {Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters}, journal = {Antarctic Science}, volume = {22}, year = {2010}, pages = {727-741}, issn = {0954-1020}, doi = {10.1017/S0954102010000477}, url = {http://www.journals.cambridge.org/abstract_S0954102010000477}, author = {Ruprecht, U. and Lumbsch, H.T. and Brunauer, G. and Green, T.G.A. and T{\"u}rk, R.} } @article {4198, title = {Major clades and phylogenetic relationships between lichenized and non-lichenized lineages in Ostropales (Ascomycota: Lecanoromycetes)}, journal = {Taxon}, volume = {59}, year = {2010}, pages = {1483-1494}, url = {http://www.jstor.org/stable/20774043}, author = {Baloch, E. and L{\"u}cking, R. and Lumbsch, H.T. and Wedin, M.} } @article {4186, title = {The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited}, journal = {Mycological Research}, volume = {111}, year = {2007}, pages = {257-267}, abstract = {

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.

}, keywords = {Ascomycota, Fungal Proteins, Genes, Fungal, Phylogeny, Species Specificity}, issn = {0953-7562}, doi = {10.1016/j.mycres.2007.01.006}, author = {Lumbsch, H.T. and Schmitt, I. and L{\"u}cking, R. and Wiklund, E. and Wedin, M.} } @article {4180, title = {Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes}, journal = {Molecular Phylogenetics and Evolution}, volume = {33}, year = {2004}, pages = {43-55}, issn = {10557903}, doi = {10.1016/j.ympev.2004.04.014}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790304001435}, author = {Schmitt, I. and Lumbsch, H.T.} } @article {4148, title = {A class-wide phylogenetic assessment of Dothideomycetes}, journal = {Studies in Mycology}, volume = {64}, year = {2009}, pages = {1-15}, issn = {01660616}, doi = {10.3114/sim.2009.64.01}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0166061614600956}, author = {Schoch, C.L. and Crous, P.W. and Groenewald, J.Z. and Boehm, E.W.A. and Burgess, T.I. and de Gruyter, J. and de Hoog, G.S. and Dixon, L.J. and Grube, M. and Gueidan, C. and Harada, Y. and Hatakeyama, S. and Hirayama, K. and Hosoya, T. and Huhndorf, S.M. and Hyde, K.D. and Jones, E.B.G. and Kohlmeyer, J. and Kruys, {\r A}. and Li, Y.M. and L{\"u}cking, R. and Lumbsch, H.T. and Marvanov{\'a}, L. and Mbatchou, J.S. and McVay, A.H. and Miller, A.N. and Mugambi, G.K. and Muggia, L. and Nelsen, M.P. and Nelson, P. and Owensby, C.A. and Phillips, A.J.L. and Phongpaichit, S. and Pointing, S.B. and Pujade-Renaud, V. and Raja, H.A. and Plata, E. Rivas and Robbertse, B. and Ruibal, C. and Sakayaroj, J. and Sano, T. and Selbmann, L. and Shearer, C.A. and Shirouzu, T. and Slippers, B. and Suetrong, S. and Tanaka, K. and Volkmann-Kohlmeyer, B. and Wingfield, M.J. and Wood, A.R. and Woudenberg, J.H.C. and Yonezawa, H. and Zhang, Y. and Spatafora, J.W.} } @article {4090, title = {Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota)}, journal = {Mycologia}, volume = {103}, year = {2011}, pages = {983-1003}, issn = {0027-5514}, doi = {10.3852/10-234}, url = {http://www.mycologia.org/cgi/doi/10.3852/10-234}, author = {Schmull, M. and Miadlikowska, J. and Pelzer, M. and Stocker-Worgotter, E. and Hofstetter, V. and Fraker, E. and Hodkinson, B.P. and Reeb, V. and Kukwa, M. and Lumbsch, H.T. and Kauff, F. and Lutzoni, F.} } @article {4070, title = {Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta}, journal = {Studies in Mycology}, volume = {64}, year = {2009}, pages = {135-144}, issn = {01660616}, doi = {10.3114/sim.2009.64.07}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0166061614601019}, author = {Nelsen, M.P. and L{\"u}cking, R. and Grube, M. and Mbatchou, J.S. and Muggia, L. and Rivas Plata, E. and Lumbsch, H.T.} } @article {3971, title = {New molecular data on Pyrenulaceae from Sri Lanka reveal two well-supported groups within this family}, journal = {Lichenologist}, volume = {44}, year = {2012}, pages = {639-647}, issn = {0024-2829}, doi = {10.1017/S0024282912000333}, url = {http://www.journals.cambridge.org/abstract_S0024282912000333}, author = {Weerakoon, G. and Aptroot, A. and Lumbsch, H.T. and Wolseley, P.A. and Wijeyaratne, S.C. and Gueidan, C.} } @article {3867, title = {Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence}, journal = {Fungal Diversity}, volume = {78}, year = {2016}, pages = {293-304}, issn = {1560-2745}, doi = {10.1007/s13225-015-0354-5}, url = {http://link.springer.com/10.1007/s13225-015-0354-5}, author = {Zhao, X. and Leavitt, S.D. and Zhao, Z.T. and Zhang, L.L. and Arup, U. and Grube, M. and P{\'e}rez-Ortega, S. and Printzen, C. and {\'S}liwa, L. and Kraichak, E. and Divakar, P.K. and Crespo, A. and Lumbsch, H.T.} } @article {3445, title = {A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales)}, journal = {Taxon}, volume = {53}, year = {2004}, pages = {959-975}, url = {http://www.ingentaconnect.com/content/iapt/tax/2004/00000053/00000004/art00010}, author = {Blanco, O. and Crespo, A. and Elix, J.A. and Hawksworth, D.L. and Lumbsch, H.T.} } @article {3384, title = {Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene}, journal = {Molecular and Phylogenetic Evolution}, volume = {44}, year = {2007}, pages = {812-824}, abstract = {

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.

}, issn = {1055-7903}, doi = {10.1016/j.ympev.2006.11.029}, author = {Crespo, A. and Lumbsch, H.T. and Mattsson, J.-E. and Blanco, O. and Divakar, P.K. and Articus, K. and Wiklund, E. and Bawingan, P.A. and Wedin, M.} } @article {3352, title = {A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families}, journal = {Molecular Phylogenetics and Evolution}, volume = {79}, year = {2014}, pages = {132-168}, issn = {10557903}, doi = {10.1016/j.ympev.2014.04.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790314001298}, author = {Miadlikowska, J. and Kauff, F. and H{\"o}gnabba, F. and Oliver, J.C. and Molnar, K. and Fraker, E. and Gaya, E. and Hafellner, J. and Hofstetter, V. and Gueidan, C. and Ot{\'a}lora, M.A.G. and Hodkinson, B. and Kukwa, M. and L{\"u}cking, R. and Bj{\"o}rk, C. and Sipman, H.J.M. and Burgaz, A.R. and Thell, A. and Passo, A. and Myllys, L. and Goward, T. and Fern{\'a}ndez-Brime, S. and Hestmark, G. and Lendemer, J. and Lumbsch, H.T. and Schmull, M. and Schoch, C.L. and S{\'e}rusiaux, E. and Maddison, D.R. and Arnold, A. E. and Lutzoni, F. and Stenroos, S.} } @article {3327, title = {Phylogenetic patterns of morphological and chemical characters and reproductive mode in the Heterodermia obscurata group in Costa Rica (Ascomycota, Physciaceae)}, journal = {Systematics and Biodiversity}, volume = {6}, year = {2008}, pages = {31-41}, issn = {1477-2000}, doi = {10.1017/S1477200007002629}, url = {http://www.tandfonline.com/doi/abs/10.1017/S1477200007002629}, author = {L{\"u}cking, R. and del Prado, R. and Lumbsch, H.T. and Will-Wolf, S. and Aptroot, A. and Sipman, H.J.M. and Uma{\~n}a, L. and Chaves, J.L.} } @article {3227, title = {New combinations and names in Gyalecta for former Belonia and Pachyphiale (Ascomycota, Ostropales) species}, journal = {Lichenologist}, volume = {45}, year = {2013}, pages = {723-727}, issn = {0024-2829}, doi = {10.1017/S0024282913000492}, url = {http://www.journals.cambridge.org/abstract_S0024282913000492}, author = {Baloch, E. and Lumbsch, H.T. and L{\"u}cking, R. and Wedin, M.} } @article {2689, title = {Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene}, journal = {Molecular Phylogenetics and Evolution}, volume = {44}, year = {2007}, pages = {812-824}, issn = {10557903}, doi = {10.1016/j.ympev.2006.11.029}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790306004854}, author = {Crespo, A. and Lumbsch, H.T. and Mattsson, J.-E. and Blanco, O. and Divakar, P.K. and Articus, K. and Wiklund, E. and Bawingan, P.A. and Wedin, M.} } @article {2132, title = {One hundred new species of lichenized fungi: a signature of undiscovered global diversity}, journal = {Phytotaxa}, volume = {18}, year = {2011}, pages = {1-127}, url = {http://www.mapress.com/phytotaxa/content/2011/f/pt00018p127.pdf}, author = {Lumbsch, H.T. and Ahti, T. and Altermann, S. and Amo de Paz, G. and et al} } @article {76, title = {A class-wide phylogenetic assessment of Dothideomycetes}, journal = {Studies in Mycology}, volume = {64}, year = {2009}, pages = {1-15}, doi = {10.3114/sim.2009.64.01}, author = {Schoch, C.L. and Crous, P.W. and Groenewald, J.Z. and Boehm, E.W.A. and Burgess, T.I. and de Gruyter, J. and de Hoog, G.S. and Dixon, L.J. and Grube, M. and Gueidan, C. and Harada, Y. and Hatakeyama, S. and Hirayama, K. and Hosoya, T. and Huhndorf, S.M. and Hyde, K.D. and Jones, E.B.G. and Kohlmeyer, J. and Kruys, {\r A}. and Li, Y.M. and L{\"u}cking, R. and Lumbsch, H.T. and Marvanov{\'a}, L. and Mbatchou, J.S. and McVay, A.H. and Miller, A.N. and Mugambi, G.K. and Muggia, L. and Nelsen, M.P. and Nelson, P. and Owensby, C.A. and Philips, A.J.L. and Phongpaichit, S. and Pointing, S.B. and Pujade-Renaud, V. and Raja, H.A. and Rivas Plata, E. and Robbertse, B. and Ruibal, C. and Sakayaroj, J. and Sano, T. and Selbmann, L. and Shearer, C.A. and Shirouzu, T. and Slippers, B. and Suetrong, S. and Tanaka, K. and Volkmann-Kohlmeyer, B. and Wingfield, M.J. and Wood, A.R. and Woudenberg, J.H.C. and Yonezawa, H. and Zhang, Y. and Spatafora, J.W.} }