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Title: Effects of recombination rate and mating system on genome evolution and diversity in Arabidopsis
Author: Wright, Stephen Isaac
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2003
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High levels of inbreeding are expected to cause a strong reduction in levels of genetic variability, effective recombination rates and in adaptation compared with related outcrossing populations. The evolution of mating systems can thus have profound effects on the evolution of genome structure and diversity. In this thesis I test these predictions, using the plant genus Arabidopsis as a model system. I examine patterns of genome organisation, DNA sequence polymorphism and divergence in the highly self-fertilizing Arabidopsis thaliana, and compare them to those of its self-incompatible, outcrossing relative Arabidopsis lyrata. From comparisons of rates of substitution, there is no evidence for a higher rate of amino acid substitution in A. thaliana, suggesting that slightly deleterious amino acid mutations may not be the primary source of protein evolution in these species. In contrast with results from published data, analysis including polymorphism data also reveals no difference in the ratio of nonsynonymous to synonymous polymorphism between species, suggesting that there may not be a general elevation of amino acid polymorphism in A. thaliana. Comparisons of intron length reveal evidence for consistently smaller introns in A. thaliana, perhaps reflecting the action of directional selection on noncoding DNA length in an annual plant. Analysis of codon usage bias at orthologous loci shows evidence for consistently higher GC content at third codon positions in A. lyrata. Comparisons of base composition in introns and polymorphism patterns for preferred and unpreferred synonymous mutations show no evidence for a shift in mutation pattern or rates of biased gene conversion between species, suggesting that the difference in codon bias might reflect a relaxation of natural selection in A. thaliana. However, comparisons of codon usage between species using a measure of codon bias based on relative abundance of tRNA genes reveals no significant difference between species, and there is no evidence for a difference in the relative rates of preferred and unpreferred substitutions. As there is a good correlation between the frequency of preferred codons defined by tRNA abundance and levels of gene expression, these results suggest a neutral explanation for the difference in GC content. Comparisons of multilocus neutral variability between A. thaliana and A. lyrata show the expected decrease in average within-population diversity in A. thaliana, but this is complicated by strong geographic structuring of variability in A. lyrata, probably associated with recent demographic history. Consistent with an influence of demographic history, analysis of intralocus linkage disequilibrium suggests a strong deficiency of the effective rate of recombination in A. lyrata. In contrast, A. thaliana shows approximately the amount of linkage disequilibrium expected in a highly self-fertilising species. These results suggest a possible role for population admixture in northern, postglacial populations of A. lyrata. A whole-genome analysis of transposable elements in A. thaliana indicates that recombination rate heterogeneity does not play an important role in driving their distribution in this species, and that gene density is the primary determinant of TE abundance in the genome. Combined with evidence from other complete eukaryotic genomes, this pattern is consistent with a role of inbreeding in reducing effective rates of recombination genome-wide, and thereby reducing the effect of recombination rate heterogeneity on genome structure. Polymorphism analysis of 18 foci located in regions of contrasting recombination rate in an Icelandic population of Arabidopsis lyrata reveals no evidence for the expected positive correlation between recombination rate and nucleotide diversity. A maximum likelihood analysis of polymorphism and divergence for these data shows evidence for significantly elevated diversity compared with divergence at a centromeric locus, suggesting the possibility of balancing selection in this region. Alternatively, recent demographic history may have contributed to an uncoupling of the expected relationship between recombination and variability, and an inflation of the variance in diversity across loci. The results of this thesis provide some evidence for the evolution of genome structure between related Arabidopsis species, but no strong evidence for differences in the efficacy of natural selection. These results emphasize the importance of understanding the influence of population history on the action of natural selection at the molecular level.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available