Evolution of gene expression and gene-regulatory sequences in Drosophila melanogaster

Saminadin-Peter, Sarah S. (2008): Evolution of gene expression and gene-regulatory sequences in Drosophila melanogaster. Dissertation, LMU München: Fakultät für Biologie

Abstract

In this work, I investigate the role of gene regulatory changes in the evolution of Drosophila melanogaster. As a first step, I performed a survey of gene expression variation in the species using whole-genome microarrays. I surveyed eight strains from an ancestral African population and eight strains from a derived European population using an experimental design that allowed for the detection of expression differences within and between populations. Levels of gene expression variation were nearly equal within the two populations, but a higher amount of variation was detected in comparisons between the two populations. Most gene expression variation within populations appears to be limited by stabilizing selection. However, some genes that are differentially expressed between the two populations might be targets of positive selection. Some of these encode proteins associated with insecticide resistance, food choice, lipid metabolism, and flight. These genes are good candidates for studying adaptive regulatory evolution that accompanied the out-of-Africa migration of D. melanogaster. To verify the accuracy of the microarray experiments, I performed quantitative Real-Time PCR (qPCR), which is another method to measure gene expression, on a subset of genes. I compared the fold-changes in gene expression between pairs of strains determined by the two methods. I also compared the pattern of expression variation in male and female flies. The qPCR approach supported the general accuracy of the microarray experiments, as the fold-changes measured by the two techniques were highly correlated. Expression differences among the strains tended to be similar for male and females. However, exceptions to this general pattern could be found by looking at the pairwise fold-changes for individual genes, some of which differed in expression pattern between males and females. I also investigated the molecular evolution and population genetics of the protein-encoding and upstream regulatory regions of genes that have potentially undergone adaptive evolution at the gene-regulatory level. These genes represent a subset of the genes that showed a significant difference in gene expression between the African and European populations. A set of control genes, which showed no significant difference in expression between the two populations, was also included in the analysis. Overall, I found evidence for both positive and purifying selection in the coding and non-coding regions. However, patterns of polymorphism and divergence did not differ significantly between the candidate genes and the control genes. One of the genes that showed an interesting pattern of expression in the microarray and qPCR experiments was subjected to further, more detailed population genetic analysis. This gene, CG9509, has twofold higher expression in the European strains than in the African strains. The coding and the upstream regions of this gene show evidence of recurrent positive selection since the split of D. melanogaster and its close relative, D. sechellia. A polymorphism survey of the CG9509 region uncovered a 1.2-kb segment, which included the putative CG9509 promoter that showed no polymorphism in the European population. The European population also has several fixed or nearly-fixed derived mutations in this region. These observations, coupled with statistical analysis, provide evidence for a selective sweep in the European population. The selective sweep was likely driven by local adaptation at the level of gene expression.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Gene expression, Gene regulation
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 5. Dezember 2008
• 1. Bericht­erstatter:in: Parsch, John