Phylogenetic analyses in St. John’s wort (Hypericum) Inferring character evolution and historical biogeography Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) eingereicht im Fachbereich Biologie, Chemie, Pharmazie der Freien Universität Berlin vorgelegt von NICOLAI M. NÜRK aus Filderstadt 2011 Die Arbeit wurde im Zeitraum von September 2007 bis August 2011 angefertigt unter der Leitung von Herrn Dr. F. R. Blattner am Leibniz-Institute für Pflanzengenetik und Kulturpflanzenforschung IPK Gatersleben. 1. Gutachter: Dr. F. R. Blattner 2. Gutachter: Prof. Dr. T. Borsch Disputation 17.11.2011 C. Darwin (Notebook No B, 1837) Nothing in biology makes sense except in the light of evolution T. Dobzhansky (1973) Contents 1 Introduction ............................................................................................................................................... 1 1.1 The genus Hypericum .............................................................................................................................. 1 1.1.1 Origin of the name, phytochemistry & economic importance ................................................ 2 1.1.2 Biology of Hypericum .............................................................................................................................. 7 1.1.3 Distribution and biogeography ....................................................................................................... 13 1.2 Objectives of this study ....................................................................................................................... 15 1.2.1 Phylogeny .................................................................................................................................................15 1.2.2 Character evolution and ecology .................................................................................................... 15 1.2.3 Historical biogeography ..................................................................................................................... 16 1.2.4 Diversification ......................................................................................................................................... 16 1.3 Methods .................................................................................................................................................... 17 1.3.1 Phylogenetic inference ........................................................................................................................ 17 1.3.2 Character evolution .............................................................................................................................. 21 1.3.3 The molecular clock .............................................................................................................................. 21 1.3.4 Biogeography ......................................................................................................................................... 23 1.3.5 Diversification rates .............................................................................................................................. 24 2 Cladistic analysis of morphological characters in Hypericum (Hypericaceae) .................. 25 2.1 Introduction ............................................................................................................................................ 25 2.2 Materials & methods ............................................................................................................................ 28 2.2.1 Character coding ................................................................................................................................... 29 2.2.2 Phylogenetic inference ....................................................................................................................... 29 2.3 Results ....................................................................................................................................................... 30 2.4 Discussion ................................................................................................................................................ 35 2.4.1 Character coding ................................................................................................................................... 35 2.4.2 Phylogeny of Hypericaceae ............................................................................................................... 35 2.4.3 Phylogenetic inference within Hypericum .................................................................................... 36 2.4.4 Character evolution .............................................................................................................................. 37 2.4.5 Biogeography ......................................................................................................................................... 38 2.5 Conclusions ............................................................................................................................................. 39 3 Molecular phylogeny and character evolution in St. John’s wort (Hypericum) ................ 41 3.1 Introduction ............................................................................................................................................ 41 3.2 Materials & methods ............................................................................................................................ 42 3.2.1 Taxon sampling ...................................................................................................................................... 42 3.2.2 Molecular methods ............................................................................................................................... 43 3.2.3 Phylogenetic inference ....................................................................................................................... 44 3.2.4 Character reconstruction .................................................................................................................... 45 3.3 Results ....................................................................................................................................................... 45 3.4 Discussion ................................................................................................................................................ 51 v Contents 3.4.1 Phylogeny of Hypericaceae ............................................................................................................... 51 3.4.2 Character evolution .............................................................................................................................. 54 3.4.3 Phylogeny and classification ............................................................................................................. 57 3.5 Conclusions ............................................................................................................................................. 59 4 Out of the tropics? Historical biogeography of the temperate genus Hypericum .......... 61 4.1 Introduction ............................................................................................................................................ 61 4.2 Methods .................................................................................................................................................... 64 4.2.1 Divergence time estimations ............................................................................................................ 64 4.2.2 Diversification rates .............................................................................................................................. 65 4.2.3 Biogeographic analyses ...................................................................................................................... 65 4.3 Results & discussion .............................................................................................................................. 68 4.3.1 Age estimations ..................................................................................................................................... 68 4.3.2 Ancestral area reconstructions: model comparison ................................................................. 70 4.3.3 Historical biogeography ..................................................................................................................... 72 4.3.4 Diversification rate shifts .................................................................................................................... 75 4.4 Conclusions ............................................................................................................................................. 75 5 Synthesis .................................................................................................................................................... 79 5.1 Phylogeny and biogeography .......................................................................................................... 80 5.2 Character evolution .............................................................................................................................. 81 5.3 Nuclear rDNA internal transcribed spacer, hybridization and concerted evolution ..... 81 5.4 Evolutionary scenario of Hypericum s. l. ........................................................................................