EVOLUTIONARY CONSEQUENCES OF COLONIZATION IN THE GENUS CAPSELLA GESSECA GOS A DISSERTATION SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOLOGY YORK UNIVERSITY TORONTO, ONTARIO JUNE 2012 © Gesseca Gos, 2012 Library and Archives Bibliotheque et Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-90373-5 Our file Notre reference ISBN: 978-0-494-90373-5 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque 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 telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distrbute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non­ support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author's permission. In compliance with the Canadian Conformement a la loi canadienne sur la Privacy Act some supporting forms protection de la vie privee, quelques may have been removed from this formulaires secondaires ont ete enleves de thesis. cette these. 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. Canada Abstract The establishment of a species in a new geographic range has profound implications for its evolution. A colonizing species may encounter founder effects such decreased genetic diversity and drift, as well as new selection pressures in the environment. Other genetic changes that frequently accompany range expansion, such as shifts in mating system and chromosome copy number, can also influence the evolutionary processes of the founding population. In this thesis, I have investigated the consequences of colonization for two different plant species, Capsella rubella and Capsella bursa-pastoris, following divergence from their range-stable progenitor Capsella grandiflora. To investigate the relationship between ecological stoichiometry and colonization ability, I compared nitrogen use efficiency and other plant performance-related traits under three different soil nitrogen levels in the three Capsella species that differ in their colonization histories. No differences in the traits were found between species, but a large degree of between-population variation was observed. This variation indicates a large potential for local adaptation that was likely present prior to species divergence. To investigate the genetic diversity of disease resistance genes following colonization and a population bottleneck, I partially sequenced 9 NBS-LRR disease resistance genes in the outcrossing Capsella grandiflora and the recently derived, bottlenecked selfing species Capsella rubella, and compared patterns of nucleotide diversity and divergence with genome-wide reference loci. Average diversity at ii resistance loci was comparable between C. rubella and C. grandiflora, indicating a retention of genetic diversity at disease resistance genes in Capsella rubella, despite the genome-wide diversity reduction following a population bottleneck. Finally, I investigated the genome-wide consequences of polyploidy in the world­ wide colonizer Capsella bursa-pastoris. Indications of the past population bottleneck were apparent, as was a large-scale reduction in the prevalence of purifying selection. This implies a lighter load of deleterious mutations in the polyploid C. bursa-pastoris compared to its progenitor C. grandiflora, which has implications for its evolution and may be related to its colonization success. These results provide an overview of the evolutionary consequences that the colonization process has had in the Capsella genus, with regard to nitrogen use, disease resistance, and polyploidy. iii This thesis is dedicated to my parents, Silvana and Elci, who always knew I could accomplish this, and to my supervisor, Stephen, who gave me the chance. Thank you. iv Acknowledgements I would like to thank the members of my Supervisory Committee, Dr. Joel Shore, Dr. Bridget Stutchbury, and Dr. Norman Yan for their continued guidance throughout my time as a graduate student. I would also like to thank the members of my Examining Committee, for agreeing to be a part of the most important step in my career. I would also like to thank my Supervisor, Dr. Stephen Wright, for giving me the opportunity to study in his laboratory, and for providing such strong guidance along the way. I want to thank the members of the Wright lab, especially Khaled Hazzouri, not only for help in the laboratory, but also for a great friendship throughout our time as graduate students together. v Author Contributions Chapters 2, 3 and 4 of this thesis are being prepared as refereed journal articles. I am the first author in each case, however, those with whom I share authorship must be acknowledged. My supervisor, Stephen Wright, is a co-author on all journal articles. For Chapter 3, Tanja Slotte contributed partially to the data collection by providing the sequences from the 283 reference genes, which I used for comparison to the disease resistance genes. For Chapter 4, Khaled Hazzouri performed the CTAB DNA extraction protocol on leaf material for both Capsella species. Robert Williamson wrote several of the computer program scripts that were either used, or modified for use in my analysis. vi Table of Contents Abstract Dedication Acknowledgments..., Author Contributions Table of Contents List of Tables List of Figures Chapter One: Introduction to the evolutionary consequenes of colonization References 15 Chapter Two: No relationship between species' colonization history and plant performance in the genus Capsella 26 Abstract 27 Introduction 28 Materials and Methods 34 Results 36 vii Discussion 39 References 53 Appendix and Supplementary Material 59 Chapter Three: Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella 73 Abstract 74 Introduction 75 Materials and Methods 82 Results 86 Discussion 88 Conclusions 92 Supplementary Material 98 References 102 Chapter Four: Genome-wide relaxation of purifying selection in the recent polyploid Capsella bursa- pastoris 110 Introduction 111 Materials and Methods 118 viii Results 123 Discussion 127 References 154 Chapter Five: Conclusions 161 ix List of Tables Chapter 2 Table 1: Log likelihood values for the first full model and its explanatory factors, as predictors of the measurements 45 Table 2: Log likelihood values for the second full model and its explanatory factors, as predictors of the measurements 46 Appendix SI: Seed sample genotype labels and collecting locations 59 Chapter 3 Table 1: Individual and average summary statistics for the disease resistance genes 95 Table 2: Differentiation of individual and average disease resistance genes between species 96 Table 3: Percentages of shared, unique and fixed polymorphisms by category for individual and average disease resistance genes 97 x Table SI: Locations of the individuals from which the R-gene sequences were sampled 98 Table S2: Primers used for PCR amplification of R-gene fragments 99 Table S3: BlastX Coordinates and protein coding domains for the R-gene fragments 100 Table S4: Locations of the individuals from which the genome-wide sequences were sampled 101 xi List of Figures Chapter 2 Figure 1: Nitrogen use efficiency for (A) the three Capsella species and (B) the eight Capsella populations under three different levels of nitrogen fertilization 47 Figure 2: Total biomass (grams) for (A) the three Capsella species and (B) the eight Capsella populations under three different levels of nitrogen fertilizan 50 Figure 3: Root to Shoot ratio (grams) for (A) the three Capsella species and (B) the eight Capsella populations under three different levels of nitrogen fertilization 52 Appendix S2: A branch diagram representing the sampling design for this study 60 Appendix S3: Randomized Latin Square design used in the greenhouse 61 Appendix S4: Nutrient Solution Recipes 62 Appendix S5: Aboveground (shoot) biomass (grams) for (A) the three Capsella species and (B) the eight Capsella populations under three different levels of nitrogen fertilization 63 Appendix S6: xii Root biomass (grams) for (A) the three Capsella species and (B) the eight Capsella populations under three different levels of nitrogen fertilization 65 Appendix S7: Percent carbon contained in leaves for (A) the three Capsella species and (B) the eight Capsella populations under three different