Taxonomic Principles, Reproductive Systems, Population Genetics And
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Univerzita Karlova — Charles University Přírodovědecká fakulta — Faculty of Science Studijní program: botanika — Study programme: botany Mgr. Vojtěch Zeisek [email protected], [email protected], https://trapa.cz/ Taxonomické principy, reprodukční systémy, populační genetika a vztahy mezi vybranými skupinami rodu Taraxacum (Asteraceae) Taxonomic principles, reproductive systems, population genetics and relationships within selected groups of genus Taraxacum (Asteraceae) Disertační práce — Doctoral thesis Školitel — supervisor: Doc. RNDr. Jan Kirschner, CSc. Botanický ústav Akademie věd ČR — Institute of Botany, Czech Academy of Sciences Praha — Prague 2018 Contents I Preface 1 1 Declaration — prohlášení 3 2 Acknowledgements 5 3 Summary — shrnutí 7 3.1 English abstract ................................. 7 3.2 Český abstrakt .................................. 8 4 Included papers 11 5 Author 13 5.1 Published papers ................................. 14 II Introduction 15 6 Species problem 21 6.1 Taxonomic concepts ............................... 21 6.2 Plant species concepts .............................. 22 7 The genus Taraxacum 27 7.1 Taraxacum modes of reproduction ....................... 29 8 Modern methods 31 8.1 Molecular genetic methods ........................... 31 8.2 Flow cytometry and karyology ......................... 35 8.3 Studies in Taraxacum .............................. 35 9 Evolution, microevolution and Taraxacum 43 9.1 Sexuality and asexuality and their implications to Taraxacum microevolution 43 9.2 Clone clustering and diversity ......................... 44 9.3 Autoploidy and alloploidy ........................... 46 9.4 Hybridity ..................................... 46 9.5 Epigenetic changes ............................... 48 I 9.6 Section as a group of species with common ancestry ............. 49 9.7 Plesiomorphic characters in Taraxacum sections ............... 50 10 Articles included in the thesis 51 III Section Dioszegia 53 11 Introduction 57 12 Material and methods 59 12.1 Plant material .................................. 59 12.2 Documentation and sources of information .................. 59 12.3 The nomenclature adopted in the present paper ............... 62 12.4 Methods used in the taxonomic revision of the section and identification of the mode of reproduction ............................ 62 12.5 Laboratory and statistical analyses ....................... 62 13 Results 65 13.1 Microsatellite analysis .............................. 65 13.2 Relationships among species and populations ................ 65 13.3 Morphology and the mode of reproduction .................. 69 14 Discussion 75 14.1 Sexuality and reproduction ........................... 75 14.2 Population analysis of widespread diploid outcrossing sexual species ... 76 14.3 New assessment of the taxonomy and relationships in Taraxacum sect. Di- oszegia ...................................... 77 14.4 Microevolution through shifts from allogamy to autogamy: Taraxacum se- rotinum subsp. tomentosum is a special case ................. 78 15 Taxonomic treatment: a revision 81 15.1 Excluded name .................................. 95 16 Acknowledgements 97 IV Identification of microspecies 99 17 Introduction 103 18 Material and methods 107 18.1 Material ..................................... 107 18.2 Ploidy analysis .................................. 121 18.3 DNA isolation .................................. 121 18.4 Microsatellite analysis .............................. 121 18.5 Statistical analyses ................................ 121 19 Results 125 20 Discussion 131 20.1 Elucidation of the nature of Taraxacum microspecies ............ 131 20.2 Clonal organisms and intraspecific variation ................. 133 20.3 Species-specific clone clusters ......................... 134 20.4 Genotype diversity ............................... 134 20.5 Utilization of molecular markers to distinguish closely related lineages .. 134 21 Acknowledgements 137 V Section Orientalia 139 22 Introduction 143 22.1 Basic outline of Taraxacum in the West Himalaya .............. 144 23 Material and Methods 147 24 Results 153 24.1 Interpretation of the name T. sect. Orientalia ................. 153 25 Taxonomic treatment 159 25.1 A new section to accommodate the West Himalayan T. stenolepium .... 159 25.1.1 Description ............................... 159 25.1.2 Phylogenetic position of T. sect. Squamulosa ............. 160 25.1.3 Comparison with morphologically similar taxa ........... 161 25.1.4 A key to the members of Taraxacum sect. Squamulosa ....... 162 25.2 Taxa with broadly ovate outer phyllaries and yellow stigmas ........ 172 25.3 Further Himalayan taxa reported as belonging to T. sect. Orientalia .... 175 26 Acknowledgements 183 VI T. bicorne and natural rubber 185 27 Introduction 189 27.1 Relatives of Taraxacum koksaghyz on the basis of morphology ....... 189 28 Material and Methods 191 28.1 Taxonomy .................................... 191 28.2 Plant material .................................. 191 28.3 Cultivation and reproduction system ..................... 192 28.4 Hybridization .................................. 192 28.5 Molecular analysis ................................ 193 28.6 Statistical evaluation .............................. 195 28.7 Flow cytometry (FCM) ............................. 195 28.8 Rubber content quantification ......................... 195 29 Results 197 29.1 Evolutionary relationships of Taraxacum koksaghyz and T. bicorne ..... 197 29.2 Population genetic statistics .......................... 197 29.3 FCM ....................................... 199 29.4 Rubber content of T. bicorne .......................... 199 29.5 Hybridization between T. koksaghyz (TKS) and T. bicorne (TBI) ....... 200 29.6 Taxonomy of T. bicorne ............................. 202 29.7 Distribution and ecology ............................ 204 29.8 Selected specimens studied ........................... 204 29.9 Reliable literature records ............................ 208 30 Discussion 209 30.1 Population genetic analysis of sexual dandelions ............... 209 30.2 Rubber content in T. bicorne and T. koksaghyz ................ 211 31 Acknowlegments 215 VII What is and is not T. bithynicum 217 32 Introduction 221 33 Material and methods 223 34 Results 225 34.1 Identity of Taraxacum bithynicum ....................... 225 34.2 Problems associated with the name Taraxacum bithynicum ......... 225 34.3 Collections of R. Aucher-Éloy and T. bithynicum ............... 226 34.4 Chromosome number of T. bithynicum .................... 228 34.5 Achene micromorphology of T. bithynicum .................. 228 34.6 Relationships of T. bithynicum on the basis of the nrDNA .......... 229 35 Taxonomy of T. bithynicum 233 35.1 Specimens examined .............................. 234 35.2 Distribution, endemism and ecology ...................... 234 36 An apomictic congener 237 36.1 Chromosome number and karyotype ..................... 237 36.2 Micromorphology of achenes .......................... 237 37 T. pseudobithynicum 239 37.1 Chromosome number .............................. 241 37.2 Habitat and distribution ............................. 241 37.3 Additional specimens examined ........................ 241 38 Acknowlegments 243 Bibliography 290 List of Figures 12.1 Map showing the locations where the samples were collected ....... 64 13.1 Results of STRUCTURE analysis for K = 5 ................... 67 13.2 Results of STRUCTURE analysis for K = 16 .................. 68 13.3 PCoA of Taraxacum sect. Dioszegia ...................... 70 13.4 Unrooted neighbour-joining tree ........................ 71 15.1 Taraxacum serotinum subsp. serotinum .................... 83 15.2 Involucres of T. sect. Dioszegia ......................... 85 15.3 Taraxacum serotinum subsp. tomentosum ................... 87 15.4 Taraxacum haussknechtii ............................ 90 15.5 Distribution of Taraxacum haussknechtii ................... 92 19.1 Bayesian clustering of individuals performed in BAPS ............ 125 19.2 K-means Bayesian clustering .......................... 127 19.3 NJ tree based on Nei’s distance ......................... 128 19.4 Minimum Spanning Network (MSN) ...................... 129 19.5 PCoA based on Nei’s genetic distance ..................... 130 25.1 A detail of the characteristic achene squamulosity in T. sect. Squamulosa . 160 25.2 A Neigbour Net constructed from uncorrected P-distances ......... 161 25.3 Taraxacum coronatum .............................. 163 25.4 Achenes of the representatives of T. sect. Squamulosa ............ 164 25.5 Taraxacum stenotegulatum ........................... 166 25.6 Distribution of Taraxacum stenotegulatum. .................. 167 25.7 Taraxacum persquamulosum .......................... 168 25.8 Distribution of Taraxacum persquamulosum. ................. 169 25.9 Taraxacum tenuiculum ............................. 170 25.10 Distribution of Taraxacum tenuiculum. .................... 171 25.11 Distribution of Taraxacum amblylepidocarpum. ................ 173 25.12 Distribution of Taraxacum baltistanicum. ................... 174 25.13 Distribution of Taraxacum melleum. ...................... 175 25.14 Taraxacum tricolor ................................ 177 25.15 Distribution of Taraxacum tricolor. ....................... 178 25.16 Achenes of T. tricolor and T. wendelboanum .................. 179 VII 28.1 The Kokpek region in the SE Kazakhstan, ................... 192 28.2 Flower beds and cages covered with a plexiglass ............... 193