@article {5638,
	title = {Biodiversity assessment of ascomycetes inhabiting Lobariella lichens in Andean cloud forests led to one new family, three new genera and 13 new species of lichenicolous fungi},
	journal = {Plant and Fungal Systematics},
	volume = {64},
	year = {2019},
	pages = {283-344},
	abstract = {<p><jats title="">Abstract</jats><jats p="">Neotropical mountain forests are characterized by having hyperdiverse and unusual fungi inhabiting lichens. The great majority of these lichenicolous fungi (i.e., detectable by light microscopy) remain undescribed and their phylogenetic relationships are mostly unknown. This study focuses on lichenicolous fungi inhabiting the genus <jats italic="">Lobariella</jats> (<jats italic="">Peltigerales</jats>), one of the most important lichen hosts in the Andean cloud forests. Based on molecular and morphological data, three new genera are introduced: <jats italic="">Lawreyella</jats> gen. nov. (<jats italic="">Cordieritidaceae</jats>, for <jats italic="">Unguiculariopsis lobariella</jats>), <jats italic="">Neobaryopsis</jats> gen. nov. (<jats italic="">Cordycipitaceae</jats>), and <jats italic="">Pseudodidymocyrtis</jats> gen. nov. (<jats italic="">Didymosphaeriaceae</jats>). Nine additional new species are described (<jats italic="">Abrothallus subhalei</jats> sp. nov., <jats italic="">Atronectria lobariellae</jats> sp. nov., <jats italic="">Corticifraga microspora</jats> sp. nov., <jats italic="">Epithamnolia rugosopycnidiata</jats> sp. nov., <jats italic="">Lichenotubeufia cryptica</jats> sp. nov., <jats italic="">Neobaryopsis andensis</jats> sp. nov., <jats italic="">Pseudodidymocyrtis lobariellae</jats> sp. nov., <jats italic="">Rhagadostomella hypolobariella</jats> sp. nov., and <jats italic="">Xylaria lichenicola</jats> sp. nov.). Phylogenetic placements of 13 lichenicolous species are reported here for <jats italic="">Abrothallus</jats>, <jats italic="">Arthonia</jats>, <jats italic="">Globonectria</jats>, <jats italic="">Lawreyella</jats>, <jats italic="">Monodictys</jats>, <jats italic="">Neobaryopsis</jats>, <jats italic="">Pseudodidymocyrtis</jats>, <jats italic="">Sclerococcum</jats>, <jats italic="">Trichonectria</jats> and <jats italic="">Xylaria</jats>. The name <jats italic="">Sclerococcum ricasoliae</jats> comb. nov. is reestablished for the neotropical populations formerly named <jats italic="">S. lobariellum</jats> (<jats italic="">Sclerococcales</jats>). A key to sexual and asexual states of 40 species of lobariellicolous ascomycetous fungi is provided. Teleomorph-anamorph connections were established for several species using molecular methods and/or visual observations in nature. Additionally, we found that the anamorphic species <jats italic="">Cornutispora ophiurospora</jats> inhabiting <jats italic="">Lobariella</jats> was often accompanied by ascomata of <jats italic="">Spirographa</jats>. Results of phylogenetic analyses, including newly generated sequences of several <jats italic="">Cornutispora</jats> and <jats italic="">Spirographa</jats> species inhabiting various host lichens, support the conclusion that <jats italic="">Cornutispora</jats> is a synonym of <jats italic="">Spirographa</jats>. Our Maximum Likelihood inference based on multiple loci show that all studied <jats italic="">Spirographa</jats> (including <jats italic="">Cornutispora</jats>) belong to a new lineage within <jats italic="">Ostropales</jats>. Based on these highly supported phylogenetic placements and the distinct character states of their conidiomata, in comparison with other <jats italic="">Lecanoromycetes</jats>, a new family is proposed \&ndash; <jats italic="">Spirographaceae</jats> fam. nov. This new lineage includes broadly distributed mycoparasites, inhabiting various lichen and fungal hosts, and representing an early diversification event preceding the lichen-forming clade of <jats italic="">Fissurinaceae</jats>, <jats italic="">Gomphillaceae</jats> and <jats italic="">Graphidaceae</jats>. Two lichenicolous species, <jats italic="">Asteroglobulus giselae</jats> and <jats italic="">Pleoscutula arsenii</jats>, were found to be nested within the <jats italic="">Spirographa</jats> clade, and their teleomorph-anamorph connections were confirmed based on genotypic and phenotypic data. This phylogenetic result is corroborated by their highly similar ascomata anatomy. Together these results strongly indicate that both species are congeneric with <jats italic="">Spirographa</jats>. As a result, four new species (<jats italic="">S. aggregata</jats> sp. nov., <jats italic="">S. galligena</jats> sp. nov., <jats italic="">S. maroneae</jats> sp. nov., and <jats italic="">S. parmotrematis</jats> sp. nov.) and 15 new combinations are proposed (<jats italic="">Spirographa ascaridiella</jats> comb. nov., <jats italic="">S. arsenii</jats> comb. nov., <jats italic="">S. ciliata</jats> comb. nov., <jats italic="">S. giselae</jats> comb. nov., <jats italic="">S. herteliana</jats> comb. nov., <jats italic="">S. hypotrachynae</jats> comb. nov., <jats italic="">S. intermedia</jats> comb. nov., <jats italic="">S. lichenicola</jats> comb. nov., <jats italic="">S. limaciformis</jats> comb. nov., <jats italic="">S. ophiurospora</jats> comb. nov., <jats italic="">S. pittii</jats> comb. nov., <jats italic="">S. pyramidalis</jats> comb. nov., <jats italic="">S. triangularis</jats> comb. nov., <jats italic="">S. tricupulata</jats> comb. nov., and <jats italic="">S. vermiformis</jats> comb. nov.). Species of the genus <jats italic="">Spirographa</jats>, as outlined here, are strongly host-specific, mainly at the generic level of their host. Some host genera can harbour more than one <jats italic="">Spirographa</jats> species.</jats></p>
},
	issn = {2657-5000},
	doi = {10.2478/pfs-2019-0022},
	url = {http://dx.doi.org/10.2478/pfs-2019-0022},
	author = {Flakus, A. and Etayo, J. and Miadlikowska, J. and Lutzoni, F. and Kukwa, M. and Matura, N. and Rodriguez-Flakus, P.}
}
@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 {4635,
	title = {Macroevolution of specificity in cyanolichens of the genus Peltigera section Polydactylon (Lecanoromycetes, Ascomycota)},
	journal = {Systematic Biology},
	volume = {66},
	year = {2016},
	pages = {74-99},
	issn = {1063-5157},
	doi = {10.1093/sysbio/syw065},
	url = {https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syw065},
	author = {Magain, N. and Miadlikowska, J. and Goffinet, B. and S{\'e}rusiaux, E. and Lutzoni, F.}
}
@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 {4600,
	title = {Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges},
	journal = {Taxon},
	volume = {58},
	year = {2009},
	pages = {184-208},
	author = {Gueidan, C. and Savic, S. and Th{\"u}s, H. and Roux, C. and Keller, C. and Tibell, L. and Prieto, M. and Hei{\dh}marsson, S. and Breuss, O. and Orange, A. and Fr{\"o}berg, L. and Wynns, A.A. and Navarro-Rosin{\'e}s, P. and Krzewicka, B. and Pyk{\"a}l{\"a}, J. and Grube, M. and Lutzoni, F.}
}
@article {4564,
	title = {Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study},
	journal = {Mycologia},
	volume = {103},
	year = {2011},
	pages = {361-378},
	issn = {0027-5514},
	doi = {10.3852/10-120},
	url = {https://www.tandfonline.com/doi/pdf/10.3852/10-120},
	author = {Gaya, E. and Redelings, B.D. and Navarro-Rosin{\'e}s, P. and Llimona, X. and De C{\'a}ceres, M. and Lutzoni, F.}
}
@article {4462,
	title = {Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera},
	journal = {Mycological Research},
	volume = {112},
	year = {2008},
	pages = {1307-1318},
	issn = {09537562},
	doi = {10.1016/j.mycres.2008.05.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0953756208001202},
	author = {Savic, S. and Tibell, L. and Gueidan, C. and Lutzoni, F.}
}
@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 {4060,
	title = {Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota)},
	journal = {Mycologia},
	volume = {102},
	year = {2010},
	pages = {279-290},
	issn = {0027-5514},
	doi = {10.3852/09-114},
	url = {http://www.mycologia.org/cgi/doi/10.3852/09-114},
	author = {Ot{\'a}lora, M.A.G. and Arag{\'o}n, G. and Molina, M.C. and Mart{\'\i}nez, I. and Lutzoni, F.}
}
@article {4046,
	title = {Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic?},
	journal = {Bryologist},
	volume = {115},
	year = {2012},
	pages = {265-277},
	issn = {0007-2745},
	doi = {10.1639/0007-2745-115.2.265},
	url = {http://www.bioone.org/doi/abs/10.1639/0007-2745-115.2.265},
	author = {{\'S}liwa, L. and Miadlikowska, J. and Redelings, B.D. and Molnar, K. and Lutzoni, F.}
}
@article {4031,
	title = {Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis},
	journal = {Mycologia},
	volume = {102},
	year = {2010},
	pages = {291-304},
	issn = {0027-5514},
	doi = {10.3852/09-168},
	url = {http://www.mycologia.org/cgi/doi/10.3852/09-168},
	author = {Prieto, M. and Mart{\'\i}nez, I. and Arag{\'o}n, G. and Ot{\'a}lora, M.A.G. and Lutzoni, F.}
}
@article {4022,
	title = {Phylogenetic study of Diploschistes (lichen-forming Ascomycota: Ostropales: Graphidaceae), based on morphological, chemical, and molecular data},
	journal = {Taxon},
	volume = {62},
	year = {2013},
	pages = {267-280},
	issn = {00400262},
	doi = {10.12705/622.10},
	url = {http://www.lutzonilab.org/publications/lutzoni_file650.pdf},
	author = {Fern{\'a}ndez-Brime, S. and Llimona, X. and Lutzoni, F. and Gaya, E.}
}
@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 {3817,
	title = {Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).},
	journal = {Molecular and Phylogenetic Evolution},
	volume = {98},
	year = {2016},
	pages = {210-232},
	abstract = {<p>The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.</p>
},
	issn = {1095-9513},
	doi = {10.1016/j.ympev.2016.02.010},
	author = {U{\textquoteright}Ren, J.M. and Miadlikowska, J. and Zimmerman, N.B. and Lutzoni, F. and Stajich, J.E. and Arnold, A.E.}
}
@article {3529,
	title = {Single origin and subsequent diversification of central Andean endemic Umbilicaria species},
	journal = {Mycologia},
	volume = {103},
	year = {20112011},
	pages = {45-56},
	issn = {0027-5514},
	doi = {10.3852/10-012},
	url = {http://www.mycologia.org/cgi/doi/10.3852/10-012},
	author = {Hestmark, G. and Miadlikowska, J. and Kauff, F. and Fraker, E. and Molnar, K. and Lutzoni, F.}
}
@article {3474,
	title = {Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data},
	journal = {International Journal of Plant Science},
	volume = {161},
	year = {2000},
	pages = {925-958},
	url = {http://www.lutzonilab.org/publications/lutzoni_file208.pdf},
	author = {Miadlikowska, J. and Lutzoni, F.}
}
@article {3473,
	title = {Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes)},
	journal = {American Journal of Botany},
	volume = {101},
	year = {2014},
	pages = {1141-1156},
	issn = {0002-9122},
	doi = {10.3732/ajb.1400267},
	url = {http://www.amjbot.org/cgi/doi/10.3732/ajb.1400267},
	author = {Miadlikowska, J. and Richardson, D. and Magain, N. and Ball, B. and Anderson, F. and Cameron, R. and Lendemer, J. and Truong, C. and Lutzoni, F.}
}
@article {3385,
	title = {Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure},
	journal = {Bryologist},
	volume = {114},
	year = {2011},
	pages = {392-400},
	issn = {0007-2745},
	doi = {10.1639/0007-2745-114.2.392},
	url = {http://www.bioone.org/doi/abs/10.1639/0007-2745-114.2.392},
	author = {Miadlikowska, J. and Schoch, C.L. and Kageyama, S.A. and Molnar, K. and Lutzoni, F. and McCune, B.}
}
@article {3355,
	title = {The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {112},
	year = {2015},
	pages = {11600-11605},
	issn = {0027-8424},
	doi = {10.1073/pnas.1507072112},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1507072112},
	author = {Gaya, E. and Fern{\'a}ndez-Brime, S. and Vargas, R. and Lachlan, R.F. and Gueidan, C. and Ram{\'\i}rez-Mej{\'\i}a, M. and Lutzoni, F.}
}
@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 {2866,
	title = {Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha},
	journal = {Mycological Research},
	volume = {113},
	year = {2009},
	pages = {141-152},
	issn = {09537562},
	doi = {10.1016/j.mycres.2008.09.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0953756208002219},
	author = {Ertz, D. and Miadlikowska, J. and Lutzoni, F. and Dessein, S. and Rasp{\'e}, O. and Vigneron, N. and Hofstetter, V. and Diederich, P.}
}
@article {2614,
	title = {Molecular phylogeny of Heteroplacidium, Placidium, and related catapyrenioid genera (Verrucariaceae, lichen-forming Ascomycota)},
	journal = {American Journal of Botany},
	volume = {99},
	year = {2012},
	pages = {23-35},
	issn = {0002-9122},
	doi = {10.3732/ajb.1100239},
	url = {http://www.amjbot.org/cgi/doi/10.3732/ajb.1100239},
	author = {Prieto, M. and Mart{\'\i}nez, I. and Arag{\'o}n, G. and Gueidan, C. and Lutzoni, F.}
}
@article {2613,
	title = {Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota)},
	journal = {Mycological Research},
	volume = {111},
	year = {2007},
	pages = {1145-1168},
	issn = {09537562},
	doi = {10.1016/j.mycres.2007.08.010},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0953756207001943},
	author = {Gueidan, C. and Roux, C. and Lutzoni, F.}
}
