Demography and Polyploidy in Capsella

! " #$%!$!"!$$!" & '(')'&&'* !+ $ List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Slotte, T., H. Huang, K. Holm, A. Ceplitis, K.R. St. Onge, J. Chen, U. Lagercrantz, and M. Lascoux. (2009) Splicing variation at a FLOWERING LOCUS C Homeolog is associated with flowering time variation in the tetraploid Capsella bursa- pastoris. Genetics, 183: 337-345 II St. Onge, K.R., T. Källman, T. Slotte, M. Lascoux, A.E. Palmé. Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. (2010) Submitted manuscript III St.Onge, K.R., A.E. Palmé, S.I. Wright, and M. Lascoux. (2010) The impact of sampling schemes on demographic infer- ence: an empirical study in two species with different mating systems and histories. Submitted manuscript IV St.Onge, K.R.*, J.P. Foxe*, L. Junrui, L. Haipeng, K. Holm, P. Corcoran, T. Slotte, M. Lascoux and S.I. Wright. (2010) Novel coalescent-analysis distinguishesbetween allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris). Manuscript. *These authors contributed equally to this work. Reprints were made with permission from the respective publishers. Contents 1 Introduction...................................................................................................... 7 1.1 Capsella as a model for evolutionary genomic studies......................... 8 1.2 Sampling and identification of Capsella species................................... 9 1.3 Mating System....................................................................................... 12 1.4 Polyploidy.............................................................................................. 13 1.5 Searching for variation affecting flowering time in candidate genes. 14 2 Research Aims............................................................................................... 16 3 Results and Discussion.................................................................................. 17 3.1 Association Mapping of the quantitative flowering time trait in C. bursa-pastoris .............................................................................................. 17 3.2 Demographic history............................................................................. 19 3.2.1 Divergent histories and population structure in Capsella grandiflora and C. rubella (Paper II) .................................................... 19 3.2.2 What sampling strategy is most appropriate for demographic studies? (Paper III).................................................................................. 22 3.3 Autopolyploid speciation of Capsella bursa-pastoris (Paper IV)...... 26 4 Conclusions.................................................................................................... 30 5 Swedish summary.......................................................................................... 31 6 Acknowledgements ....................................................................................... 33 7 References...................................................................................................... 34 1 Introduction Searching for the signature of natural selection in genetic data has been a central goal of molecular evolutionary biology since the field was first estab- lished. Which mutations make an organism more fit? Like any scientific question a null hypothesis is required. Such a model was presented in 1968 by Kimura in the form of his neutral theory of evolution. The neutral theory assumes that the variation we observe is mostly due to neutral mutations on their way to fixation or loss under random drift as deleterious mutations quickly disappear from populations and advantageous ones are rare. From this theory the Standard Neutral Model (SNM) was created, which has been the dominant null hypothesis in molecular evolution and population genetics since its inception. The SNM describes a population, which is not experiencing selection, is mating randomly and is not experiencing population size changes. Depar- tures from this model can be caused by violation of any of these assumptions, which clearly leads to several alternative explanatory hypotheses, only one of which is selection. The assumptions of random mating and constant population size can be violated if there is population structure and complex demographic histories. Importantly, demographic departures from the SNM can leave signatures in the genome that are identical to those left by selection and demographic changes and selection often occur simultaneously. For in- stance colonization of new environments are often accompanied by population bottlenecks and expansions as well as new selective pressures. Here lies the importance of complementing studies searching for the signature of selection with information on population structure and demographic history. Studies of demography and population structure are also interesting in their own right, as they give insight into important evolutionary processes such as speciation and diversification. Mechanisms of speciation and diversification have always been of general interest to evolutionary biologists and are of importance to the more contemporary work of conservation biologists. Demographic studies using coalescent analysis are an important part of un- derstanding these processes. In the current work, I use coalescent analysis to study demographic history, population structure and speciation within the genus Capsella, laying the ground for future studies searching for the signature of selection in candidate genes. I use my empirical data in combination with simulated data to investigate what type of sampling strategy is most appropriate for such studies. Finally, I use an association mapping approach 7 that accounts for population structure to search for genetic variation which is associated with variation in flowering time, an important quantitative trait in plants. 1.1 Capsella as a model for evolutionary genomic studies Capsella is a small genus including only three species according to current classification. Capsella grandiflora (Fauche & Chaub) Boiss, is a self- incompatible diploid (2n=16) and this ploidy and mating system are likely the ancestral state of the genus (Paetsch et al. 2006). Capsella rubella Rent., which has recently evolved from C. grandiflora (Foxe et al 2009, Guo et al 2009, Paper II), is also a diploid (2n=16) but has lost its self-incompatibility system and become predominately selfing (0.90-0.94 Paper II). Finally, Capsella bursa-pastoris (L.) Medik, is also a selfer, but is a tetraploid species (2n=4x=32). Capsella is an excellent model for molecular evolutionary studies for several reasons. First, this small genus presents the opportunity to study several key phenomena in plant evolution and speciation. Important to this study are the change in mating system between C. grandiflora and both C. rubella and C. bursa-pastoris and the polyploidisation of C. bursa-pastoris. Both of these changes have occurred independently in many plant lineages, often leading to speciation. They can also have large effects on the amount and structure of genetic diversity. A second important advantage of working with Capsella is its phylogenetic relations within the Brassicaceae family. Capsella is closely related to the model plant species Arabidopsis thaliana, which has a two-fold advantage. Because of their close relation, many of the tools and methods developed for Arabidopsis work with little adjustment in Capsella; in fact most of the PCR primers that we have designed for the current work were designed using the Arabidopsis thaliana full genome se- quence. Additionally, because of the popularity of Arabidopsis in the past decade, quite a large amount of molecular work has been done on the genus and its close relatives, making comparative genomic studies between Arabi- dopsis, Capsella and their relatives possible. And finally, work within the Capsella genus has real tangible use to agriculture because it belongs to the Brassicaceae family, the major crop family which includes mustard, cabbage and oil seed rape, and also because C. bursa-pastoris is a common weed of agriculture. In fact, the evolution of polyploidy and weediness in C. bursa- pastoris is of direct interest to agricultural research. 8 1.2 Sampling and identification of Capsella species Capsella grandiflora has the most limited distribution of the three Capsella species. It occurs locally in northern Italy, but is mainly found in northern Greece and Albania, where it grows in disturbed habitats but also in less disturbed mountain meadows (Hurka and Neuffer, 1997; Paetsch et al. 2006). The natural distribution of C. rubella is thought to be Western Europe, the Balkans, Greece, North Africa and the Middle East, but it also occasionally followed settlers into

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