@article {5665,
	title = {Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {66},
	year = {2013},
	pages = {628-644},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2012.10.021},
	url = {http://dx.doi.org/10.1016/j.ympev.2012.10.021},
	author = {Vialle, A. and Feau, N. and Frey, P. and Bernier, L. and Hamelin, R.C.}
}
@article {4672,
	title = {A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {59},
	year = {2011},
	pages = {603-614},
	issn = {10557903},
	doi = {10.1016/j.ympev.2011.03.021},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790311001606},
	author = {Spribille, T. and Klug, B. and Mayrhofer, H.}
}
@article {4634,
	title = {Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {117},
	year = {2017},
	pages = {10-29},
	issn = {10557903},
	doi = {10.1016/j.ympev.2017.08.013},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S105579031730636X},
	author = {Magain, N. and Miadlikowska, J. and Mueller, O. and Gajdeczka, M. and Truong, C. and Salamov, A.A. and Dubchak, I. and Grigoriev, I.V. and Goffinet, B. and S{\'e}rusiaux, E. and Lutzoni, F.}
}
@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 {4304,
	title = {Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {32},
	year = {2004},
	pages = {66-82},
	issn = {10557903},
	doi = {10.1016/j.ympev.2003.11.012},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S105579030300424X},
	author = {Buschbom, J. and Mueller, G.}
}
@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 {4107,
	title = {Coordinated ultrastructural and phylogenomic analyses shed light on the hidden phycobiont diversity of Trebouxia microalgae in Ramalina fraxinea},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {94},
	year = {2016},
	pages = {765-777},
	issn = {10557903},
	doi = {10.1016/j.ympev.2015.10.021},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790315003243},
	author = {Catal{\'a}, S. and del Campo, E.M. and Barreno, E. and Garc{\'\i}a-Breijo, F.J. and Reig-Armi{\~n}ana, J. and Casano, L.M.}
}
@article {3878,
	title = {Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {32},
	year = {2004},
	pages = {1036-1060},
	issn = {10557903},
	doi = {10.1016/j.ympev.2004.04.012},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S105579030400140X},
	author = {Reeb, V. and Lutzoni, F. and Roux, C.}
}
@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 {3257,
	title = {Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {63},
	year = {2012},
	pages = {374-387},
	issn = {10557903},
	doi = {10.1016/j.ympev.2012.01.012},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790312000292},
	author = {Gaya, E. and H{\"o}gnabba, F. and Holguin, {\'A}. and Molnar, K. and Fern{\'a}ndez-Brime, S. and Stenroos, S. and Arup, U. and S{\o}chting, U. and Boom, P. van den and L{\"u}cking, R. and Sipman, H.J.M. and Lutzoni, F.}
}
@article {2970,
	title = {Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences.},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {39},
	year = {2006},
	pages = {587-597},
	abstract = {<p>Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.</p>
},
	keywords = {DNA, Ribosomal, Fungi, Phylogeny, Polymerase Chain Reaction},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2006.01.025},
	author = {Tsui, C.K.M. and Berbee, M.L.}
}
@article {2925,
	title = {A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {67},
	year = {2013},
	pages = {311-335},
	issn = {10557903},
	doi = {10.1016/j.ympev.2013.01.014},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790313000511},
	author = {Hansen, K. and Perry, B.A. and Dranginis, A.W. and Pfister, D.H.}
}
@article {2912,
	title = {Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {27},
	year = {2003},
	pages = {58-69},
	issn = {10557903},
	doi = {10.1016/S1055-7903(02)00398-6},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790302003986},
	author = {Myllys, L. and Stenroos, S. and Thell, A. and Ahti, T.}
}
@article {2857,
	title = {Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {61},
	year = {2011},
	pages = {12-28},
	issn = {10557903},
	doi = {10.1016/j.ympev.2011.05.014},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790311002569},
	author = {Millanes, A.M. and Diederich, P. and Ekman, S. and Wedin, M.}
}
@article {2808,
	title = {Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {39},
	year = {2006},
	pages = {587-597},
	issn = {10557903},
	doi = {10.1016/j.ympev.2006.01.025},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790306000327},
	author = {Tsui, C.K.M. and Berbee, M.L.}
}
@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 {2629,
	title = {Phylogenetic status of Xylaria subgenus Pseudoxylaria among taxa of the subfamily Xylarioideae (Xylariaceae) and phylogeny of the taxa involved in the subfamily},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {54},
	year = {2010},
	pages = {957-969},
	issn = {10557903},
	doi = {10.1016/j.ympev.2009.12.015},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790309005211},
	author = {Hsieh, H.-M. and Lin, C.-R. and Fang, M.-J. and Rogers, J.D. and Fournier, J. and Lechat, C. and Ju, Y.-M.}
}
@article {2618,
	title = {Phylogenetic diversity of lichen-associated homobasidiomycetes},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {44},
	year = {2007},
	pages = {778-789},
	issn = {10557903},
	doi = {10.1016/j.ympev.2006.12.023},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790306005148},
	author = {Lawrey, J.D. and Binder, M. and Diederich, P. and Molina, M.C. and Sikaroodi, M. and Ertz, D.}
}
@article {2479,
	title = {Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {68},
	year = {2013},
	pages = {357-372},
	issn = {10557903},
	doi = {10.1016/j.ympev.2013.04.005},
	author = {Truong, C. and Divakar, P.K. and Yahr, R. and Crespo, A. and Clerc, P.}
}
@article {122,
	title = {Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {35},
	year = {2005},
	pages = {60-75},
	author = {Miller, A.N. and Huhndorf, S.M.}
}
