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Experimental Evolution of Chlamydomonas Reinhardtii Under Salt Stress

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Experimental Evolution of Chlamydomonas Reinhardtii Under Salt Stress Experimental evolution of Chlamydomonas reinhardtii under salt stress Chase Curtis Moser Department of Biology McGill University, Montreal June 2010 A thesis submitted to McGill University in partial fulfilment of the requirements of the degree of Master of Science. © Chase Moser 2010 Library and Archives Bibliothèque et Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l’édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre référence ISBN: 978-0-494-72799-7 Our file Notre référence ISBN: 978-0-494-72799-7 NOTICE: AVIS: The author has granted a non- L’auteur a accordé une licence non exclusive exclusive license allowing Library and permettant à la Bibliothèque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par télécommunication ou par l’Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans le loan, distribute and sell theses monde, à des fins commerciales ou autres, sur worldwide, for commercial or non- support microforme, papier, électronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L’auteur conserve la propriété du droit d’auteur ownership and moral rights in this et des droits moraux qui protège cette thèse. Ni thesis. Neither the thesis nor la thèse ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent être imprimés ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author’s permission. In compliance with the Canadian Conformément à la loi canadienne sur la Privacy Act some supporting forms protection de la vie privée, quelques may have been removed from this formulaires secondaires ont été enlevés de thesis. cette thèse. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n’y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. Contributions of Authors The following thesis is made up of a review chapter and two manuscripts to be submitted for publication in peer-reviewed journals. The experimental design in each chapter was provided by Dr. Graham Bell. I performed the experiments and the data analysis. Each manuscript was drafted in collaboration with Dr. Graham Bell. 2 Abstract The environment is now changing much faster than in recent geological time, causing increasing population extinctions. Experiments have shown that extinction can be avoided by adaptation through natural selection leading to evolutionary rescue. I first determined the response of Chlamydomonas to stressful environments by growing populations over a range of salinity. The population growth is halved at 5 g/L salt (NaCl), and 8 g/L is lethal. In this experiment, the genetic correlation between environments increases with environmental similarity. I then manipulated the genotypic diversity in experimental populations and cultured them by serial transfer at 5 g/L salt. The outcome of adaptation is not influenced by initial genetic variation. Instead, populations adapted mainly through the spread of new beneficial mutations. These results suggest that populations have a greater chance of adapting when new environments are similar to current conditions and that adaptation is sometimes dominated by the spread of new mutations, even in the presence of a substantial amount of standing genetic variation. 3 Résumé Notre environnement change maintenant beaucoup plus rapidement que dans le passé géologique récent, précipitant l’extinction de plus en plus d’espèces. Des chercheurs ont démontré que, grâce à l’adaptation par la sélection naturelle, des espèces peuvent éviter l’extinction, un processus nommé sauvetage évolutif. J’ai d’abord étudié la capacité de Chlamydomonas à croitre dans des environnements dont la salinité augmente. J’ai trouvé que 5 g/L de sel diminue la croissance de moitié tandis que 8 g/L est suffisant pour empêcher toute croissance. Ici, la corrélation génétique entre environnement augmente avec la similarité des environnements comparés. J’ai ensuite soumis des populations contenant différentes quantités de diversité génétique initiale à une salinité de 5 g/L. La diversité génétique initiale ne semble pas influencer la capacité d’adaptation. Cependant, les populations semblent plutôt s’adapter en utilisant de nouvelles mutations dont l’effet est bénéfique. Ces résultats suggèrent que les populations s’adapteront plus facilement à des environnements similaires aux conditions présentes. De plus, ce processus sera dominé par la fixation de nouvelles mutations, même dans des populations contenant de la diversité génétique. 4 Acknowledgements I was able to complete this thesis only with the help and support of some very fine people to whom I am grateful. Foremost I owe a debt of gratitude my supervisor Dr. Graham Bell, for initially putting faith in me and having since provided me with guidance, encouragement, as well as patience at every stage of the project. He provided experimental designs, help with analysis, and draft edits along the way. I am very appreciative of his support and encouragement. Kathy Tallon provided invaluable assistance in the lab in many ways including lending her technical knowledge and support. Thanks for taking care of all of us in the lab and not letting our (my) messes get out of hand. Thank you also to Sonja and Anne- Marie for their help, friendly faces, and positive attitudes. My lab mates, Etienne and Pedram, have provided thought-provoking discussions, friendship, and emotional support over the last 2½ years. Etienne helped me during the writing process, draft edits, and abstract translation. I thank him for not letting me get away with anything and encouraging me to keep looking. Mark Jewell helped me with some demanding lab work for my experiment in Chapter 3; I thank him for his endurance and patience. The Leung lab welcomed me into their office space for 2 months during the spring of 2010. They helped me with my troubles with the statistical package R and with portions of my statistical analysis. Special thanks to Dr. Brian Leung, Corey, Paul, Erin, and Sylvia. 5 Michael Pedruski provided helpful comments and feedback on my literature review. I owe my parents for my interest in the natural world and how it operates; thanks for making sure the apple didn’t fall far from the tree. Thank you Mom, Dad, Shasta, and Scott, for your continuous love and support. My group of friends who have put up with me in one way or another, discussing Chlamydomonas or how to bring back dinosaurs, thanks for being there and being wonderful, especially the “Choose-Day” crew and Erica Strange. Most importantly, Katie, without your constant support, love, and faith in me, I wouldn’t be where I am. 6 Table of contents Contributions of Authors 2 Abstract 3 Résumé 4 Acknowledgements 5 General Introduction 9 References 12 Chapter 1 Evolutionary response to deteriorating environments 15 References 32 Figures and legends 38 Linking statement between Chapters 1 and 2 41 Chapter 2 Genetic correlation in relation to differences in dosage of a stressor 43 References 55 Figure legends 57 Figures 58 7 Linking statement between Chapters 2 and 3 65 Chapter 3 The contribution of standing genetic variation and novel mutation to adaptation and evolutionary rescue in a simple laboratory system 67 References 86 Figure legends 89 Figures 91 General Conclusions and Summary 100 8 General Introduction Rates of environmental change are increasing as human activities increase (Solomon, 2007) and as a result populations are responding to these changes to a greater extent than natural changes alone (Hendry et al., 2008). Severe environmental changes can cause extinctions, but in certain circumstances populations may avoid extinction through evolutionary processes (Bradshaw & McNeilly, 1991; Gomulkiewicz & Holt, 1995). Evolutionary biology provides a framework to understand how populations adapt to severe change and thereby avoid extinction. There has been a recent call for evolutionary biologists to turn the focus of their studies toward evolutionary processes influencing extinction (Bell & Collins, 2008; Hendry et al., 2010). The theory of evolutionary rescue involves a decline in abundance caused by a severe environmental stress resulting in the death or sterilization of most of the individuals, followed by a population recovery driven by the survival and reproduction of individuals that are able to withstand the stress (Gomulkiewicz & Holt, 1995). Recovery may occur even if there are only a few individuals which survive, although when populations are reduced to small population sizes there is an increased risk of extinction through stochastic processes (Lande, 1993). The probability of evolutionary rescue depends on several factors: the strength and rate of the environmental change, the population size, and the availability of variation. Genetic variation in the population can come from two main sources, standing variation that is already present and novel variation caused by beneficial mutations arising after the 9 stress has been applied. Novel mutation and standing genetic variation lead to somewhat different processes of adaptation (Barrett & Schluter, 2008). Adaptation from standing variation
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