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Contribution to the Taxonomy and Biodiversity of Crustose Lichens from the Family Teloschistaceae

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School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Contribution to the taxonomy and biodiversity of crustose lichens from the family Teloschistaceae Ph.D. Thesis Ivan Frolov Supervisor: Jan Vondrák, Ph.D. Faculty of Science, University of South Bohemia and Institute of Botany of the Czech Academy of Sciences České Budějovice, 2021 This thesis should be cited as: Frolov I., 2021: Contribution to the taxonomy and biodiversity of crustose lichens from the family Teloschistaceae. Ph.D. Thesis Series, No. 5. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 260 pp. Annotation The PhD thesis is composed of five published papers and one manuscript accepted for publication. The main research goal was the investigation of the taxonomy and diversity of crustose Teloschistaceae in Europe and Northern Asia with special emphasis on the genus Pyrenodesmia . The first paper investigated the delimitation of the genus Pyrenodesmia and its relationships with the closely related Caloplaca haematites and C. xerica groups and some other species. The second paper proposed standardized methods for the measurement of the morphological characters of the crustose Teloschistaceae and suggested a phenotype evaluation process for the delimitation of species that are difficult to phenotypically distinguish. The method was practically employed in the third paper for the separation of three seemingly cryptic species from the genus Pyrenodesmia , which were formally described in the paper. Another new Pyrenodesmia species was described in the fourth paper. Investigations presented in the fifth paper substantially extended the known geographical distribution of several species of crustose Teloschistaceae in Europe and Northern Asia. The accepted manuscripts proposes the description of the new species of crustose Teloschistaceae in Siberia and the Russian Far East. Our studies provide a basis for future summarizing papers on the taxonomy and diversity of the genus Pyrenodesmia in the Holarctic and the family Teloschistaceae in Russia. Declaration I hereby declare that I am the author of this dissertation and that I have used only those sources and literature detailed in the list of references. České Budějovice, …………………….. ............................................... Ivan Frolov Financial support This work was supported by: The Grant Agency of the University of South Bohemia, grant 04−133/2014/P Visegrad Fund Scholarship 51100848 Russian Foundation for Fundamental Research, grant 19-04-00074 Acknowledgements During my work on the thesis, I received valuable help from many people. First, I would like to express my sincere gratitude to my supervisor Jan Vondrák. Without his help my research and the writing of this thesis would not have been possible. I deeply appreciate the time he has spent discussing our results, his patience and support. He has willingly shared his wide knowledge on Teloschistaceae diversity. I am grateful to Jiří Košnar who was always ready to help me with my work in the molecular lab as well as with the phylogenetic analyses. I would like to acknowledge Jan Kučera, Martina Vašutová, and Marie Šmilauerová for their help and guidance during my postgraduate study. I am grateful to Milan Štech, Karel Prach, Petr Koutecký, and Libor Ekrt, who gave me the opportunity to look at a large part of Europe during the interdisciplinary excursions of the University of South Bohemia they organized. During several of those trips, I got to know local biomes, collected a lot of material for my thesis, and had a lot of fun. I am also grateful to all participants of the excursions for the friendly and cheerful atmosphere on those journeys. My friend and colleague Liudmila Konoreva supported me a lot during my postgraduate study and often helped to organize the field trips. Trips to the regions of Southern Siberia, the Mediterranean, and the Macaronesia were possible largely thanks to my supervisor Jan Vondrák. Many friends shared the joys and difficulties of the field trips with me: Olga Flegontova, Pavel Flegontov, Václav Mikeš, Ilnur Baygildin. I would like to acknowledge Helmut Mayrhofer (Graz), Anton Igersheim (Vienna), Harrie Sipman (Berlin), Lucyna Śliwa (Krakow), and Mikhail Andreev (Saint Petersburg) for their help during my work in the local herbaria. I also thank Philipp Resl and Toby Spribille for their hospitality during my stays in Graz, and Karina Wilk and Natalia Matura in Krakow. My friends Olga Flegontova and Iosif Kaurov gave me much useful advice during the writing and formatting of the thesis. Olga Flegontova also helped me a lot during the remote stage of my postgraduate study. I thank Olga Flegontova, Mikhail Buldakov, and Iraida Dolgova for their revision of the first version of the thesis. My friend and teacher Christopher Steer kindly revised the English. I also thank Olga Vondráková for her hospitality and help during my life in České Budějovice. Finally yet importantly, I would like to thank my relatives and especially my mother, father and brother, who have supported me throughout my long-standing postgraduate study. List of papers and author’s contribution The thesis is based on the following papers: Paper 1 Frolov I. , Vondrák J., Košnar J., Arup U. 2020. Phylogenetic relationships within Pyrenodesmia sensu lato and the role of pigments in its taxonomic interpretation. Journal of Systematics and Evolution. doi: 10.1111/jse.12717. Ivan Frolov made 70 % of the study: he designed the study, participated in the collection of the material, production, analysis, and interpretation of the data, and wrote the manuscript. Paper 2 Vondrák J., Frolov I., Arup U., Khodosovtsev A. 2013. Methods for phenotypic evaluation of crustose lichens with emphasis on Teloschistaceae. Chornomorskiy botanichniy zhurnal 9: 382–405. Ivan Frolov made 20 % of the study: he participated in the study design and editing of the manuscript. Paper 3 Frolov I. , Vondrák J., Fernández-Mendoza F., Wilk K., Khodosovtsev A., Halıcı M.G. 2016. Three new, seemingly-cryptic species in the lichen genus Caloplaca (Teloschistaceae) distinguished in two-phase phenotype evaluation. Annales Botanici Fennici 53: 243–262. Ivan Frolov made 60 % of the study: he participated in the study design, collection of the material, production, analysis, and interpretation of the data, and writing of the manuscript. Paper 4 Vondrák J., Frolov I. , Říha P., Hrouzek P., Palice Z., Nadyeina O., Halıcı G., Khodosovtsev A., Roux C. 2013. New crustose Teloschistaceae in Central Europe. The Lichenologist 45: 701–722. Ivan Frolov made 20 % of the study: he participated in the collection of the material, production, analysis and interpretation of the data, and writing of the manuscript. Paper 5 Vondrák J., Frolov I. , Davydov E.A., Urbanavichene I., Chesnokov S., Zhdanov I., Muchnik E., Konoreva L., Himelbrant D., Tchabanenko S. 2016. The extensive geographical range of several species of Teloschistaceae: evidence from Russia. The Lichenologist 48: 181–189. Ivan Frolov made 20 % of the study: he participated in the collection of the material and production of the molecular data. Paper 6 Frolov I. , Vondrák J., Konoreva L.A., Chesnokov S.V., Himelbrant D.E., Arup U., Stepanchikova I.S., Prokopiev I.A., Yakovchenko L., Davydov E.A. (accepted manuscript). Three new species of crustose Teloschistaceae in Siberia and the Far East. The Lichenologist. Ivan Frolov made 70 % of the study: he designed the study, participated in the collection of the material, produced and analyzed the data, participated in the interpretation of the data, and wrote the manuscript. ____________________________________________________________________ Co-author agreement Jan Vondrák, the supervisor of this Ph.D. thesis, on behalf of all the co-authors, fully acknowledges the contribution of Ivan Frolov. …………………………………………. Jan Vondrák, Ph.D. Contents 1 Introduction ........................................................................................................... 1 1.1 Lichen symbiosis and the taxonomy of lichens as complex organisms ..... 1 1.2 Species concepts and their application in lichenology .............................. 2 1.3 Species complexes in lichenized fungi ..................................................... 7 1.4 Molecular phylogenetic methods applied in the species delimitation of lichenized fungi .................................................................................... 11 1.5 Generic delimitation in lichenized fungi ................................................ 14 1.6 Taxonomy and diversity of the family Teloschistaceae .......................... 17 2 Aims of the study ................................................................................................ 21 3 Summary ............................................................................................................. 22 4 References ........................................................................................................... 26 5 Original publications ........................................................................................... 43 5.1 Paper 1 .................................................................................................. 43 5.2 Paper 2 .................................................................................................. 89 5.3 Paper 3 ...............................................................................................
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  • Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two

    Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two

    (topsheet) Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113. Fieldiana, Botany H. Thorsten Lumbsch Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7881 fax: 312-665-7158 e-mail: [email protected] Sabine M. Huhndorf Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7855 fax: 312-665-7158 e-mail: [email protected] 1 (cover page) FIELDIANA Botany NEW SERIES NO 00 Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 H. Thorsten Lumbsch Sabine M. Huhndorf [Date] Publication 0000 PUBLISHED BY THE FIELD MUSEUM OF NATURAL HISTORY 2 Table of Contents Abstract Part One. Outline of Ascomycota - 2009 Introduction Literature Cited Index to Ascomycota Subphylum Taphrinomycotina Class Neolectomycetes Class Pneumocystidomycetes Class Schizosaccharomycetes Class Taphrinomycetes Subphylum Saccharomycotina Class Saccharomycetes Subphylum Pezizomycotina Class Arthoniomycetes Class Dothideomycetes Subclass Dothideomycetidae Subclass Pleosporomycetidae Dothideomycetes incertae sedis: orders, families, genera Class Eurotiomycetes Subclass Chaetothyriomycetidae Subclass Eurotiomycetidae Subclass Mycocaliciomycetidae Class Geoglossomycetes Class Laboulbeniomycetes Class Lecanoromycetes Subclass Acarosporomycetidae Subclass Lecanoromycetidae Subclass Ostropomycetidae 3 Lecanoromycetes incertae sedis: orders, genera Class Leotiomycetes Leotiomycetes incertae sedis: families, genera Class Lichinomycetes Class Orbiliomycetes Class Pezizomycetes Class Sordariomycetes Subclass Hypocreomycetidae Subclass Sordariomycetidae Subclass Xylariomycetidae Sordariomycetes incertae sedis: orders, families, genera Pezizomycotina incertae sedis: orders, families Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 Introduction Literature Cited 4 Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota.