Evolution of genes related to temperature adaptation in Drosophila melanogaster as revealed by QTL and population genetics analyses

The fixation of beneficial variants leaves genomic footprints characterized by a reduction of genetic variation at linked neutral sites and strong, localized allele frequency differentiation among subpopulations. In contrast, for phenotypic evolution the effect of adaptation on the genes controlling the trait is little understood. Theoretical work on polygenic selection suggests that fixations of beneficial alleles (causing selective sweeps) are less likely than small-to-moderate allele frequency shifts among subpopulations. This thesis encompasses three projects in which we have experimentally addressed the issue of selective sweeps vs. allele frequency shifts in the context of polygenic adaptation. We studied three X-linked QTL underlying variation in chill coma recovery time (CCRT), a proxy for cold tolerance, in Drosophila melanogaster from temperate (European) and tropical (African) environments. The analysis of these QTL was performed by means of selective sweep mapping and quantitative complementation tests coupled with expression assays. While the results of the selective sweep mapping approach identified a gene (CG4491) that is unlikely to be affecting CCRT, quantitative and gene expression analyses revealed two linked candidate genes (brk and CG1677) that appear to differ in their evolutionary histories. We found that the difference in expression of the gene brk between populations affects CCRT variation. Cold tolerant flies from the temperate zone have a lower expression of this gene than cold sensitive flies from the tropics. We found that a likely cause of this difference is variation in a cis-regulatory element in the brk 5’ enhancer region. Sequence variants in this element exhibit moderate frequency differences between populations from temperate and tropical environments, forming two latitudinal clines: one from the equator to the north and another one in opposite direction to the south. In contrast, the other gene within the same QTL (CG1677), which is linked to brk, showed no measurable effect on cold tolerance but is a likely target of strong positive selection leading to a selective sweep in the European population. These results are consistent with the aforementioned theoretical predictions about footprints of selection in polygenic adaptation. They are also proof of the conceptual bias incurred when identifying candidate genes within a QTL via selective sweep mapping, at least in naturally evolving populations. The challenge for the evolutionary genetics community in the coming years is to develop statistical tools that are as powerful and robust as those already available to map selective sweeps to identify sites in the genome where allele frequency shifts have occurred due to adaptive evolution at the phenotypic level. Finally, the last section of the results is a report of a new population genetics dataset. It consists of a collection of 80 inbred lines from a natural D. melanogaster population in Sweden and 19 full genome sequences derived from this sample. We hope this material will provide us with further insight into the processes underlying adaptation to novel and stressful environments