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Hutter, Stephan (2007): Natural variation in Drosophila melanogaster: A survey of genome-wide DNA sequence polymorphism and gene expression diversity, and the development of new bioinformatic tools. Dissertation, LMU München: Faculty of Biology
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Abstract

This work is dedicated to studying natural variation in D. melanogaster at the DNA sequence and gene expression level. In addition I present a new version of the DNA polymorphism analysis program VariScan, which includes significant improvements. In CHAPTER 1 I describe a genome scan of single nucleotide polymorphism in two natural D. melanogaster populations (from Africa and Europe) on the third chromosome. Together with polymorphism data previously published for the X chromosome of the same populations, this allows a comparative study of the polymorphism patterns of the X chromosome and an autosome. The frequency spectrum of mutations and the patterns of linkage disequilibrium are investigated. The observed patterns indicate that there is a significant difference in the behavior of the two chromosomes, as has already been suggested by previous studies. To uncover the reasons for this a coalescent based maximum likelihood method is applied that incorporates the effects of demographic history and unequal sex ratios. For the African population the differential behavior of the chromosomes can be explained by its demographic history and an excess of females. In Europe, a population bottleneck and an excess of males alone cannot explain the patterns we observe. The additional action of positive selection in this population is proposed as a possible explanation. In CHAPTER 2 I investigate the variation in gene expression of the two aforementioned populations. Whole-genome microarrays are used to study levels of expression for 88% of all known genes in eight adult males from both populations. The observed levels of expression variation are equal in Africa and Europe, despite the fact that DNA sequence variation is much higher in Africa. This is evidence for the action of stabilizing selection governing levels of expression polymorphism. Supporting this view, genes involved in many different functions, and are therefore on strong selective constraint, show less variation than do genes with only few functions. The experimental design allows the search for genes which differ in their expression patterns between Europe and Africa and might therefore have undergone adaptive evolution. Detected candidates include genes putatively involved in insecticide resistance and food choice. Surprisingly, many genes over-expressed in Africa are involved in the formation and function of the flying apparatus. In CHAPTER 3 I present version 2 of the program VariScan. This program was designed to analyse patterns of DNA sequence polymorphism on a chromosomal scale. The functionality of the core analysis tool, the wavelet decomposition, is described. In addition, multiple improvements to the previous version are presented. The program now supports the “pairwise deletion” option. This is essential for analysing data at the chromosome scale, since such data often contains incomplete information. It is now possible to add outgroup information, which allows the calculation of additional statistics. Furthermore, the separate analysis of different predefined chromosomal regions is added as an option. To increase the user friendliness, a graphical user interface is now included as part of the software package. Finally, VariScan is applied to published and computer-generated data and the ability of the wavelet-based analysis to uncover chromosomal regions with interesting DNA polymorphism patterns is demonstrated.