Evolutionary patterns and processes in the genus Potentilla L. (Rosaceae) Dissertation Juraj PAULE 2010 Dissertation submitted to the Combined Faculties for Natural Sciences and for Mathematics of the Ruperto‐Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Mgr. Juraj PAULE, M.Sc. born in Zvolen, Slovakia Oral examination: 23 July 2010 Evolutionary patterns and processes in the genus Potentilla L. (Rosaceae) Referees: Prof. Dr. Marcus A. Koch Prof. RNDr. Karol Marhold, CSc. to my family Contents CONTENTS.......................................................................................................................................... 7 SUMMARY......................................................................................................................................... 11 ZUSAMMENFASSUNG.................................................................................................................. 13 INTRODUCTION............................................................................................................................. 15 1.1 SOURCES OF PLANT VARIATION AND EVOLUTION ................................................................... 15 1.2 HYBRIDISATION, POLYPLOIDISATION AND APOMIXIS.............................................................. 16 1.3 POTENTILLA AS A RESEARCH TARGET....................................................................................... 17 1.4 OVERVIEW OF THE CHAPTERS ................................................................................................... 18 1.5 REFERENCES ............................................................................................................................... 19 A COMPREHENSIVE CHLOROPLAST DNA‐BASED PHYLOGENY OF THE GENUS POTENTILLA (ROSACEAE): IMPLICATIONS FOR ITS GEOGRAPHIC ORIGIN, PHYLO‐GEOGRAPHY AND GENERIC CIRCUMSCRIPTION............................................. 23 2.1 INTRODUCTION .......................................................................................................................... 23 2.2 MATERIAL AND METHODS........................................................................................................ 25 2.2.1 Plant material ...................................................................................................................... 25 2.2.2 DNA extraction................................................................................................................... 26 2.2.3 PCR and DNA sequencing ................................................................................................. 26 2.2.4 Phylogenetic reconstruction ................................................................................................ 27 2.2.5 Molecular clock estimates.................................................................................................... 28 2.2.6 Biogeography ....................................................................................................................... 29 2.2.7 Diversity.............................................................................................................................. 30 2.3 RESULTS ...................................................................................................................................... 30 2.3.1 Sequence variation............................................................................................................... 30 2.3.2 Phylogenetic relationships................................................................................................... 31 2.3.4 Diversification in time......................................................................................................... 35 2.3.5 Biogeography ....................................................................................................................... 35 2.4 DISCUSSION ................................................................................................................................40 2.4.1 Phylogenetic relationships and taxonomic implications ..................................................... 40 2.4.2 Biogeographic and evolutionary history.............................................................................. 43 2.4.2.1 Biogeographic history of the Potentillinae and Potentilla s.str........................... 44 2.4.2.2 The colonization of North America ........................................................................ 45 2.4.2.3 Biogeography of the Potentilla core group............................................................ 47 2.4.2.4 The fossil record......................................................................................................... 47 2.4.2.5 Pliocenic radiations ................................................................................................... 49 2.5 CONCLUSIONS............................................................................................................................ 50 2.6 REFERENCES ............................................................................................................................... 51 POLYPLOIDY IN POTENTILLA ARGENTEA L. GROUP ........................................................ 57 3.1 INTRODUCTION .......................................................................................................................... 57 3.2 MATERIAL AND METHODS........................................................................................................ 60 3.2.1 Plant material ...................................................................................................................... 60 7 3.2.2 Chromosome counts and DNA ploidy level estimation....................................................... 60 3.2.3 DNA extraction................................................................................................................... 61 3.2.4 CpDNA amplification and sequencing ............................................................................... 61 3.2.5 AFLP analysis ..................................................................................................................... 62 3.2.6 Data Analyses...................................................................................................................... 63 3.2.6.1 Chloroplast sequence data analysis and phylogenetic inference ....................... 63 3.2.6.2 AFLP data analyses................................................................................................... 63 3.3 RESULTS ...................................................................................................................................... 65 3.3.1 DNA ploidy level and cytotype distribution ....................................................................... 65 3.3.2 CpDNA sequence data and haplotype distribution............................................................. 66 3.3.2 CpDNA sequence data and haplotype distribution............................................................. 67 3.3.3 AFLP analyses..................................................................................................................... 68 3.3.3.1 Strong genetic division of cytotypes....................................................................... 68 3.3.3.2 Population genetic structure and diversity ........................................................... 72 3.3.3.3 Clonal assignment analysis and genotypic variability of populations.............. 72 3.4 DISCUSSION ................................................................................................................................78 3.4.1 Ploidy differentiation........................................................................................................... 78 3.4.2 Origin of polyploid cytotypes .............................................................................................. 79 3.4.3 Reproductive modes and population genetic structure ....................................................... 80 3.4.4 Phylogeographic implications.............................................................................................. 82 3.4.5 Taxonomic assumptions ...................................................................................................... 84 3.5 CONCLUSIONS............................................................................................................................ 85 3.6 REFERENCES ............................................................................................................................... 85 HYBRIDISATION IN THE GENUS POTENTILLA – A CASE STUDY OF P. ALPICOLA ....... 93 4.1 INTRODUCTION .......................................................................................................................... 93 4.2 MATERIAL AND METHODS........................................................................................................ 95 4.2.1 Plant material ...................................................................................................................... 95 4.2.2 Chromosome counts and DNA ploidy level estimation....................................................... 96 4.2.3 DNA extraction................................................................................................................... 96 4.2.4 CpDNA amplification and sequencing ............................................................................... 96 4.2.5 AFLP analysis ....................................................................................................................