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Glinka, Sascha (2005): Population Genetic Approaches to Detect Natural Selection in Drosophila melanogaster. Dissertation, LMU München: Faculty of Biology
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Abstract

This thesis intends to detect evidence of Darwinian selection and ultimately identify genes and substitutions that were involved in adaptation. The model organism Drosophila melanogaster was chosen as the study object, since the availability of the genome sequence and its evolutionary history allows us to investigate ancestral and derived populations. To identify the footprints of natural selection, the first objective was to locate genomic regions subject to selection. Such footprints involve a reduction in genetic variation along a recombining chromosome caused by a fixation of a beneficial mutation (i.e., so-called “selective sweep”) in a population under study. Single nucleotide polymorphisms of non-coding regions (i.e., 105 fragments) of the X chromosome in a putatively ancestral population of D. melanogaster from Zimbabwe were surveyed and compared to a derived European population in the first chapter. In contrast to the European population, evidence of selection was weak in the African population, but a strong signature of a population size expansion was observed. To examine the impact of demography and selection more deeply, an analysis of an enlarged DNA sequencing data set (i.e., 253 fragments) of the African population is presented in chapter two. A clear signature of a recent size expansion was observed and the time estimated of the expansion is 15,000 years before present, which was probably caused by drastic climatic changes. The enlarged data set revealed, in addition, that recombination is mutagenic in D. melanogaster. In the second part of this thesis, candidate regions of selective sweeps detected in the genome scan in both populations of D. melanogaster were investigated. In chapter three, a more detailed analysis of the region comprising an observed local reduction in variation in one X-linked fragment in the derived European population revealed significant evidence of recent Darwinian selection. The target of selection was attributed to three replacement sites leading to amino acid changes in two predicted genes, CG1677 and CG2059. In contrast, a lower number of haplotypes and a trend for low haplotype diversity suggesting the recent action of a selective sweep was examined in chapter four in the ancestral D. melanogaster population. An enlarged DNA sequencing data set revealed another feature unique to a selective sweep, namely the decay in haplotype structure. The target of selection was localized at the 5’ region of gene CG4661. In the third part of this thesis, the genetic variation of D. melanogaster populations from Southeast Asia were examined to provide first insights into these derived populations and the groundwork for future studies. Since no population genetic approach was done in natural D. melanogaster populations from this region, inversions were used as genetic markers. Other than a high frequency of the four common cosmopolitan inversions, there were neither signs for genetic differentiation between populations nor for natural selection. These findings can best be explained by a homogeneous habitat and a joint history of these populations revealing the existence of a panmictic population on Sundaland ~18,000 years ago.