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A Poly Approach to Ploidy: Polyploid Evolution and Taxonomic Implications

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A Poly Approach to Ploidy: Polyploid Evolution and Taxonomic Implications A poly approach to ploidy: Polyploid evolution and taxonomic implications Marte Holten Jørgensen Dissertation presented for the degree of Philosophiae Doctor Centre for Ecological and Evolutionary Synthesis, Department of Biology Faculty of Mathematics and Natural Sciences University of Oslo 2011 © Marte Holten Jørgensen, 2011 Series of dissertations submitted to the Faculty of Mathematics and Natural Sciences, University of Oslo No. 1136 ISSN 1501-7710 All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission. Cover: Inger Sandved Anfinsen. Printed in Norway: AIT Oslo AS. Produced in co-operation with Unipub. The thesis is produced by Unipub merely in connection with the thesis defence. Kindly direct all inquiries regarding the thesis to the copyright holder or the unit which grants the doctorate. Kan du'kke bare levere'a? Lille far, januar 2011. Contents Preface .................................................................................................................................. 6 List of papers ........................................................................................................................ 9 Background ........................................................................................................................ 11 Case studies ........................................................................................................................ 18 Papers 1 and 2: The Saxifraga rivularis complex ................................................. 18 Paper 3: The Cardamine digitata aggregate .......................................................... 19 Papers 4 and 5: Arabidopsis kamchatica ............................................................... 19 Paper 6: Arabidopsis arenosa and A. lyrata .......................................................... 21 Discussion ........................................................................................................................... 22 Pros and cons of markers - is there a perfect one? ................................................ 22 Recurrence of polyploidy - is there a rule?............................................................ 29 Taxonomy in a polyploid world ............................................................................ 33 Literature cited .................................................................................................................. 36 Papers I-VI..........................................................................................................................47 5 Preface When my project is about to finish, it's time for acknowledgements: Annen. ANNEANNEANNE! Fineste sjefstøsen! My main supervisor Anne K. Brysting. Best supervisor in the world, I'm sure. You are my colleague, my friend, my third mum (I have a modern family), and my hero. As well as scientifically strong, you show a care for and a faith in your students that is really remarkable. Your door is always open, even literally, for all kinds of problems, personal as well as scientifical. If I didn't have you, I would have quitted a long time ago. But you were there, and you kept your faith in me when I didn't. Thanks for all your chatter, your support, and your hugs! I wonder if you'll ever be able to say Vålenga kjærke! Barbs. My wonderful co-supervisor Barbara Mable at the Glasgow Uni. Your hospitality when welcoming me to Glasgow meant a lot. And your patience with my ignorance on S-alleles and inheritage and crossings. From now on, my focus will be on our joint project! Hilde, agent Empetrum, thanks for always being there. Thanks for sharing my tears and my laughter. Thanks to you, Julie, Ragnhild, Flua, Helge, and Einar for quiz nights every Tuesday. And thanks to you, Vir, and Inger for wine colloquia and a nice master period. Snilleskrede: thanks for reading! Torbæibi, my wise and nice colleague Tor Carlsen, thanks for all the nice scientific discussions and all the coffea! Thanks to Svend-Ole Nielsen (my Danish friend), Elisabeth Hubbuck, and Cecilia Leslie for professional help with a messy brain. Thanks to my family, particularly my father for being supportive, taking me on boat trips, trips to our cottage, and for using me as a source of knowledge in molecular 6 biology. Thanks to my sister for always being there, and letting me use her kids in hug therapy. Thanks to my brother for breaks in Svalbard and particularly for taking me to Paris on a two day's notice. Thanks to my grandpa for financial help throughout my studies. I'm sorry you couldn't be there to see me finish, farfar! Thanks to all my co-authors, particularly Doro, Andi (my hero! Thanks for the title!), Tor, and Reidar. Thanks to Cecilie for help in the lab and all the chatter and cigarettes. Thanks to my supervisors in my master; Christian, Reidar, Brita, and Tove, for making me learn enough to be able to do a PhD (I hope!). Thanks to Mika, Ola, Unni, Inger, and the rest of the botanical group at Blindern for all your support and all the discussions. And Ave for chatter in the office. Thanks to Karin for giving me an anxiety attack and sweeping up the remains. Thanks to the Department of Biology and the CEES for giving me three months extra salary. Thanks to Kristine Bonnevie travelling stipend, S. G. Sønneland Foundation, and Hans Henrik Maschmann's legacy for financial support. Thanks to the people at the phytotron for taking care of all my plants. Thanks to Marc, Katya, Liza, Barry, Peter, Clair, Ash, Andy, and Katherine at the Glasgow Uni for making my stays in Glasgow full of joy. Thanks to Hege, Hilde L., Anette, Martha, Helle, Heidi, Gard, and other dear old friends for their patience with a depressed PhD student. Thanks to Herr Trøst for all the hugs throughout this period of trial! And to my father for giving him to me. Oslo, 080811, 7 8 List of papers I. Jørgensen MH, Elven R, Tribsch A, Gabrielsen TM, Stedje B, Brochmann C. 2006. Taxonomy and evolutionary relationships in the Saxifraga rivularis complex. Systematic Botany, 31: 702-729. II. Westergaard K, Jørgensen MH, Gabrielsen TM, Alsos IG, Brochmann C. 2010. The extreme Beringian/Atlantic disjunction in Saxifraga rivularis (Saxifragaceae) has formed at least twice. Journal of Biogeography, 37: 1262-1276. III. Jørgensen MH, Carlsen T, Skrede I, Elven R. 2008. Microsatellites resolve the taxonomy of the polyploid Cardamine digitata aggregate (Brassicaceae). Taxon, 57: 882-892. IV. Schmickl R, Jørgensen MH, Brysting AK, Koch MA. 2010. The evolutionary history of the Arabidopsis lyrata complex: A hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier. BMC Evolutionary Biology, 10: 98. V. Jørgensen MH, Brysting AK, Takebayashi N, Steets JA, Beecher JJ, Wolf DE. Digging deeper into the allopolyploid origin of Arabidopsis kamchatica and its effect on molecular diversity. Manuscript. VI. Jørgensen MH, Ehrich D, Schmickl R, Koch MA, Brysting AK. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae). Manuscript submitted to BMC Evolutionary Biology. 9 10 Background In school I learned about evolution as a gradual change of states. I remember memorising the jingle mutation - adaptation - selection - evolution: random mutations sometimes lead to adaptation, advantageous character changes which increase an organism's chance of survival and reproduction, i.e. fitness. Natural selection will spread the character state in the population until it becomes fixed. Evolution is then the process from mutation to fixation. Speciation, or the origin of species, was illustrated as a process where a population is split into two by a geographical barrier, and the two are gradually changed by adaptation to different environments. When they have accumulated so many differences that they no longer can reproduce if the barrier is removed, then they are considered different species. Horses and donkeys are different species because the mule is sterile. Furthermore the evolutionary relationship among organisms was presented as a tree where the root represents the beginning of life, the nodes are ancestors, and the leaves are extant organisms (Fig. 1). Now, this childhood learning of mine is not erroneous. The speciation description is the book example of allopatric speciation (Fig. 2), which accounts for the majority of speciation events in animals (Coyne and Orr, 2004). Reproductive isolation is the only defining criteria of Mayr's biological species concept (e.g., Mayr, 2000), widely Figure 1. Darwin's Tree of Life. From The Origin of Species (1859). accepted and used 11 among zoologists. And finally, trees are unquestionably the most common way of illustrating evolutionary ancestor-descendant or sibling relationships. However, moving from animals to the Plant Kingdom complicates the matter, and the primary reason is the prevalence of polyploidy among plants. Figure 2. Different modes of speciation. From Wikipedia (http://en.wikipedia.org/wiki/Allopatric_speciation). The word polyploidy is derived from Greek. The literal meaning is manifold and refers to number of chromosome sets in an organism, i.e. a diploid has two chromosome sets, a triploid has three and a polyploid has many (Fig. 3A). Throughout most of the 20th century it was generally believed that polyploids mostly arose through a somatic increase in chromosome number (e.g. Levin, 2002), i.e. through a chromosome replication without subsequent cell division in the mitotic
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