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Genetic and Ecological Investigations in the Thistle Genus Onopordum with Special Emphases on Hybridization and Evolution Peter

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Genetic and Ecological Investigations in the Thistle Genus Onopordum with Special Emphases on Hybridization and Evolution Peter Genetic and ecological investigations in the thistle genus Onopordum with special emphases on hybridization and evolution Peter O’Hanlon A thesis submitted for the degree of Doctor of Philosophy Australian National University Library copy February 2002 Declaration I certify that the substance of this thesis has not already been submitted for any degree and is not currently submitted for any other degree. I certify that the help received in preparing this thesis, and all sources used, have been acknowledged in this thesis. Peter O’Hanlon Acknowl edgent en ts Acknowledgements This project was funded by the Department of Employment, Education, Training and Youth Affairs, the Australian Research Council and the Cooperative Research Centre for Weed Management Systems through an Australian Postgraduate Award (Industry) scholarship. Additional funding from the CRC for Weed Management Systems and the French Government Scientific and Cultural Exchange Program administered by the French Embassy, Canberra was also appreciated. I would like to thank the following people for their support, advice and guidance; • Dr. Rod Peakall (Chair of supervisory panel and primary supervisor) for sharing his expertise, endless enthusiasm and knowledge with me, and for providing me with a rounded academic training. • Dr. David Briese (Co-supervisor) for providing the initial inspiration for this project, continual direction and assessment of my research in good humour and always being able to set my work within a context of Weed Science. • My two examiners who provided helpful final suggestions to this thesis. • My friends in BoZo and CSIRO: Occasionally you’ve made my life pretty normal. • My advisors Dr. Siegy Krauss and Dr. Mike Crisp for guidance. • A special thanks to Dr. Mike Ramsey, Dr. Richard Groves, Prof. Rick Roush and John Kerin for special encouragement and interest in my work. • The technical assistance from the workshop (Bmce and Allan), in photography (Keith) and in the laboratory (Simon, Wes, Jeanette, Ginny, Ian) • To my overseas friends and colleagues who added an extra dimension to my training and to this thesis; especially Stefan Böttcher, Isabelle Olivieri, John Scott, Eva Haeffner, Peter Hein (who also provided information on the distributions of Onopordum), Torsten, Thierry, and Jose. • To those who have read much of my work and provided editorial input; Mike Ramsey, Siegy Krauss and especially Rod Peakall and David Briese. • Seed for several analyses were provided by Thierry Thomann and Jose Serin (CSIRO European Laboratory, Montpellier, France), Eva Haeffner (Botanisches Museum and Botanische Garten, Berlin, Germany) and W. Richter (Botanisches Garten der Georg August Universität, Gottingen, Germany) and Isabelle Olivieri (University of Montpellier, France). • Personal thanks my family who have always been more interested in things other than my research. Ackno wledgem en ts 4 Table of Contents DECLARATION.......................................................................................................................................2 ACKNOWLEDGEMENTS.......................................................................................................................3 PREFACE................................................................................................................................................. 7 CHAPTER ONE ABSTRACT..................................................................................................................8 CHAPTER TWO A REVIEW OF NEW PCR-BASED GENETIC MARKERS AND THEIR UTILITY TO WEED ECOLOGY............................................................................................................................12 Recent developments in genetic marker technology.......................................................... 13 Sequence-Tagged-Site PCR.........................................................................................13 AFLPs..........................................................................................................................18 Other methods.............................................................................................................21 PCR SSR identification............................................................................................... 21 Intron PCR...................................................................................................................21 Sequencing...................................................................................................................23 Applications of PCR based genetic markers in weed ecology..........................................23 Patterns of genetic diversity in invasive populations..................................................24 Breeding systems.........................................................................................................26 Taxon identification and phylogenetic relationships..................................................27 Geographic origin/s.................................................................................................... 29 Note on statistical analysis.........................................................................................................31 Conclusions......................................................................................................................................... 33 Marker technology.......................................................................................................33 Applications to weed research.................................................................................... 34 Implications for studies in Onopordum...................................................................... 35 CHAPTER THREE A SIMPLE METHOD FOR THE DETECTION OF SIZE HOMOPLASY IN PCR BASED MULTILOCUS FINGERPRINTS................................................................................. 36 CHAPTER FOUR AN ASSESSMENT OF CPDNA SEQUENCE AND AFLPS FOR PHYLOGENETIC ANALYSES OF THE CARDUINAE THISTLES (ASTERACEAE: CARDUEAE) .................................................................................................................................................................. 45 Plant taxa and sampling..............................................................................................48 DNA methods...............................................................................................................49 cpDNA sequencing......................................................................................................50 AFLP fingerprinting....................................................................................................53 Identification of size homoplasy................................................................................. 53 Phylogenetic analyses..................................................................................................53 Results....................................................................................................................................................54 cpDNA variation..........................................................................................................54 AFLP polymorphism....................................................................................................56 Morphological phylogeny............................................................................................57 cpDNA sequence phylogeny....................................................................................... 58 AFLP phylogeny..........................................................................................................59 Reconciliation between data sets.................................................................................60 D iscussion.............................................................................................................................................. 63 Chloroplast variation..................................................................................................63 AFLP polymorphism....................................................................................................63 Reconciliation between cpDNA sequence, AFLP and morphological data................65 Implications for host-choice studies............................................................................66 Table of Contents 5 CHAPTER FIVE RECOLONIZA TION OF EUROPE FROM HYBRID RE FUG I A BY ONOPORDUM THISTLES: A PHYLOGEOGRAPHICANALYSIS................................................. 67 Materials and Methods..............................................................................................................72 Sampling...................................................................................................................... 72 DNA extraction............................................................................................................73 Chloroplast sequencing and AFLP fingerprinting..................................................... 73 Phylogenetic analysis..................................................................................................74 Results............................................................................................................................................. 75 Chloroplast and AFLP polymorphism........................................................................ 75 Phylogenetic analyses..................................................................................................76
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