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Taxonomy and Symbiosis in Associations of Physciaceae and Trebouxia

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Taxonomy and Symbiosis in Associations of Physciaceae and Trebouxia Taxonomy and Symbiosis in Associations of Physciaceae and Trebouxia Dissertation zur Erlangung des Doktorgrades der Biologischen Fakultät der Georg-August Universität Göttingen Vorgelegt von Gert W.F. Helms aus Tübingen Göttingen 2003 1 D7 1. Gutachter: Prof. Dr. T. Friedl 2. Gutachter: Prof. Dr. G. Rambold Tag der Einreichung: 22. September 2003 Tag der mündlichen Prüfung: 6. November 2003 2 Contents Contents 1 GENERAL INTRODUCTION.........................................................................................5 1.1 The lichen concept ................................................................................................................................................ 5 2 GENERAL MATERIALS & METHODS .........................................................................6 2.1 Lichen samples, DNA extraction, PCR, sequencing .......................................................................................... 6 2.1.1 Lichen samples ............................................................................................................................................... 6 2.1.2 DNA extraction............................................................................................................................................... 6 2.1.3 PCR................................................................................................................................................................. 7 2.1.4 Agarose gel electrophoresis ............................................................................................................................ 7 2.1.5 Cloning ........................................................................................................................................................... 8 2.1.6 PCR product purification ................................................................................................................................ 8 2.1.7 DNA quantification......................................................................................................................................... 8 2.1.8 Sequencing...................................................................................................................................................... 8 2.2 Phylogenetic analyses ......................................................................................................................................... 10 2.2.1 Alignment ..................................................................................................................................................... 10 2.2.2 Assessing the model of evolution ................................................................................................................. 10 2.2.3 Phylogenetic inference.................................................................................................................................. 11 2.2.4 Significance measurement ............................................................................................................................ 11 2.2.5 Outgroup analysis ......................................................................................................................................... 11 3 PHYSCIACEAE TAXONOMY .....................................................................................12 3.1 Summary ............................................................................................................................................................. 12 3.2 Introduction ........................................................................................................................................................ 12 3.2.1 Taxonomic history and circumscription of the Physciaceae......................................................................... 12 3.3 Materials & Methods.......................................................................................................................................... 14 3.3.1 Alignment and phylogenetic analyses........................................................................................................... 16 3.3.1.1 Phylogenetic analyses of nrSSU sequence data ........................................................................................ 16 3.3.1.2 Phylogenetic analyses of nrITS sequence data ......................................................................................... 18 3.3.2 Testing alternative tree topologies ................................................................................................................ 18 3.3.3 Sources of phenotypic information............................................................................................................... 18 3.4 Results.................................................................................................................................................................. 19 3.4.1 nrSSU analyses, phylogenetic positioning of Physciaceae and Caliciaceae within the Lecanorales............ 19 3.4.1.1 A phylogenetic marker motive in the Physciaceae/Caliciaceae clade....................................................... 21 3.4.2 nrITS analyses, phylogentic structure within the Physciaceae...................................................................... 21 3.4.2.1 Clades and Genera .................................................................................................................................... 21 3.5 Discussion ............................................................................................................................................................ 25 3.5.1 nrSSU phylogeny.......................................................................................................................................... 25 3.5.1.1 General aspects ......................................................................................................................................... 25 3.5.1.2 Outgroup................................................................................................................................................... 26 3.5.1.3 Monophyly of a clade uniting Caliciaceae and Physciaceae..................................................................... 26 3.5.1.4 The taxonomic significance of ascus types............................................................................................... 26 3.5.2 nrITS phylogeny ........................................................................................................................................... 27 3.5.2.1 Outgroup................................................................................................................................................... 27 3.5.2.2 Two major clades...................................................................................................................................... 27 3.5.2.3 Ascus structures ........................................................................................................................................ 28 1 Contents 3.5.2.4 Ascospore characters ................................................................................................................................ 29 3.5.2.5 Hypothecium pigmentation....................................................................................................................... 30 3.5.2.6 Excipulum type......................................................................................................................................... 30 3.5.2.7 Upper cortex structure............................................................................................................................... 31 3.5.2.8 Growth habit ............................................................................................................................................. 31 3.5.2.9 Secondary compounds .............................................................................................................................. 32 3.5.2.10 Monophyly of genera................................................................................................................................ 33 3.5.2.11 Diplotomma and the delimitation of Subclade III and Subclade IV ......................................................... 34 3.5.2.12 The systematic position of Dirinaria and Pyxine ..................................................................................... 35 3.5.2.13 Misplacement of Buellia and Rinodina species ........................................................................................ 36 3.5.2.14 Plesiomorphy of ascus types and hypothecium pigmentation................................................................... 36 3.6 Taxonomy............................................................................................................................................................ 37 3.6.1 Emendations ................................................................................................................................................. 38 3.6.1.1 Caliciaceae Chevall................................................................................................................................... 38 3.6.1.2 Physciaceae Zahlbr. .................................................................................................................................. 38 3.6.1.3 Alternative concepts ................................................................................................................................
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