Genome Divergence in Progress - a population genetic analysis of the allopolyploid Arabidopsis suecica and its maternal parent A. thaliana

The evolutionary history of the allotetraploid Arabidopsis suecica and its maternal parent Arabidopsis thaliana is analyzed in the thesis in terms of genetic variation in the natural populations of the two species. The earliest phase of the speciation event in which the genomes of A. thaliana and A. suecica are in the process of diverging was investigated using population genetic methods. Evolutionary and demographic hypotheses were tested on the basis of sequence and microsatellite variation in the nuclear and chloroplast genomes. It was shown that the maternally inherited chloroplast originated in all investigated A. suecica individuals from A. thaliana, identifying A. thaliana as A. suecica's maternal parent. A Bayesian multi-locus method based on coalescent theory was developed to infer the evolutionary history of polyploids in general and specifically of A. suecica. It provides a rigorous statistical framework allowing the confidence in one's conclusions to be quantified. The origins of allopolyploid species, in contrast to those of most species, can be considered to be well defined discrete events. Both the nuclear and the chloroplast genome of A. suecica were shown to have a single origin, implying there to be a single origin for the entire species. Its origin was estimated to have been 10 thousand to 65 thousand years ago. The A. thaliana and the A. suecica populations were shown to both be genetically structured, although the A. thaliana population, unlike the A. suecica population, clearly was geographically structured too. A. suecica and A. thaliana were also found to differ in terms of Linkage Disequilibrium, it extends further and the levels are higher in A. suecica than in A. thaliana. These findings showed that a species of recent, single origin has quite different patterns of genetic variation than of more distant origin. In the first genome-wide study ever of sequence polymorphisms in a eukaryote organism, here A. thaliana, it was found that the data failed to fit standard neutral models. This means that attempts to infer natural selection on the basis of polymorphism data will require genome-wide surveys of polymorphism in order to identify regions that are anomalous. Certain theoretical models of microsatellite evolution were shown to fit the distribution of mononucleotide microsatellites in the A. thaliana genome. These models were also able to predicted empirical levels of microsatellite variation in the A. thaliana chloroplast genome. This thesis is based on the following papers: I. Säll, T., Jakobsson, M., Lind-Halldén, C. & Halldén, C. (2003) Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica. J. Evol. Biol. 16: 1019 1029. II. Jakobsson, M., Säll, T., Lind-Halldén, C. & Halldén, C. The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica. (Submitted). III. Jakobsson, M., Hagenblad, J., Tavaré, S., Nordborg, M., Halldén, C., Säll, T. & Lind-Halldén, C. A recent unique origin of the allotetraploid species Arabidopsis suecica evidence from nuclear DNA markers. (Manuscript). IV. Jakobsson, M., Säll, T., Halldén, C. & Lind-Halldén, C. Genome evolution in progress: Linkage disequilibrium and population structure in Arabidopsis suecica and A. thaliana. (Manuscript). V. Nordborg, M., Hu, T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Tomer, E., Calabrese, P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N., A., Shah, C., Wall, J., Zhao, K., Kalbfleisch, T., Schultz, V., Kreitman, M. & Bergelson, J. (2005) The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biology (in Press). VI. Jakobsson, M., Säll, T., Lind-Halldén, C. & Halldén, C. Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. (Submitted)