Logo Logo
Help
Contact
Switch language to German
Adaptive gene regulatory polymorphisms in natural populations of Drosophila melanogaster
Adaptive gene regulatory polymorphisms in natural populations of Drosophila melanogaster
It has long been recognized that changes in gene regulation, specifically mutations in cis-regulatory elements that tend to be stable and additive, are important to adaptive processes and phenotypic evolution. Since cis-regulatory elements are found in the vicinity of the genes they regulate, the direct effect of changes in these sequences is typically limited to a particular gene that allows for refined, situation-specific control of gene expression but are not exclusive of downstream or trans-acting elements. This dissertation focuses on examining mechanisms responsible for maintaining adaptive cis-regulatory polymorphisms in two Drosophila melanogaster genes: fezzik (fiz) and Metallothionein A (MtnA) and their associated effect on gene expression and organismal phenotype. Previous experiments show that the 3’ untranslated region of MtnA contains an insertion/deletion (indel) polymorphism, wherein the deletion is rare or absent in the ancestral African range but its deletion frequency appears to follow a latitudinal cline in derived populations worldwide. By genotyping biannual collections of wild caught D. melanogaster across a 5-year period, I show that the deletion is maintained at a high frequency (~90%) in a single German population with no evidence for overdominant, seasonally fluctuating or sexually antagonistic selection. Expression analysis on pairs of nearly-isogenic lines and on data from a North American population indicated significant differences in expression associated to the indel. Furthermore, the data from this North American population showed that expression variation was only partially explained by the deletion and the effect on oxidative stress tolerance was significantly associated with menadione sodium bisulfite and not paraquat. Altogether these findings suggested a scenario in which MtnA expression and consequently oxidative stress tolerance is likely a polygenic adaptation that varies with genomic background. Indeed, the effect of the deletion allele on oxidative stress tolerance was dependent on the genomic background with some indication of sign epistasis. Transcriptomic analysis revealed that MtnA expression was induced by oxidative stress independent of the indel status, indicating a general role of this gene in stress tolerance as well as suggesting additional levels of context-dependent expression regulation. The transcriptional response to oxidative stress between lines with and without the deletion was mostly similar but interestingly, there were consistently larger numbers of differentially expressed genes associated with the deletion which is possibly related to regulatory cascades resulting from aberrant microRNA epigenetic regulation due to the loss of microRNA binding sites in the deleted region. In general, the response to MSB indicated the significance of functional categories such as general stress response, oxidative stress response, metabolism, apoptosis and autophagy. In particular among the differentially expressed genes with the largest fold-change in response to MSB-induced oxidative stress were several genes related to glutathione metabolism and biosynthesis, suggesting a strong association between this pathway and oxidative stress tolerance. Another instance of expression divergence between ancestral and cosmopolitan populations being associated with a regulatory polymorphism is represented by a single nucleotide polymorphism (SNP) located 67 base pairs upstream of the start codon, in the enhancer region of the gene fezzik, referred to here as “SNP67”. SNP67 has two variants segregating in natural populations of D. melanogaster: the ancestral “C” variant, and the derived “G” variant that is found outside of the ancestral range at intermediate frequencies and is associated with increased fiz expression. Previous studies suggest that this SNP was a recent target of balancing selection; therefore to determine the forces of selection maintaining this SNP in cosmopolitan populations we genotyped biannually collected wild-caught D. melanogaster from a single European (Munich, Germany) population. A model-based approach using allele and genotype frequency data of the SNP67 variants across seasons and sexes was employed. The model indicated that sexually antagonistic and temporally fluctuating selection may help maintain variation at this site, with the derived variant likely being female-beneficial but there was some uncertainty of dominance estimates in the model. Gene expression and body-size phenotypes that were dependent on genomic background and developmental stage indicated that variable dominance may play a role in the maintenance of this polymorphism. Lastly, we identified a novel sex-dependent association between fiz expression and starvation resistance that may suggest that this trait is a potential phenotypic target of selection. Interestingly our findings for the MtnA and fiz regulatory polymorphisms both indicated that the relationship between gene expression divergence and population-level genetic mechanisms underlying phenotypic evolution is potentially complicated by context-dependent factors such as genomic background or spatial and temporal differences. By integrating extensive experimental work to identify the mechanisms of selection in natural populations along with functional characterizations, a refined understanding of these adaptive regulatory polymorphisms was achieved.
Not available
Ramnarine, Timothy
2022
English
Universitätsbibliothek der Ludwig-Maximilians-Universität München
Ramnarine, Timothy (2022): Adaptive gene regulatory polymorphisms in natural populations of Drosophila melanogaster. Dissertation, LMU München: Faculty of Biology
[img]
Preview
PDF
Ramnarine_Timothy.pdf

1MB

Abstract

It has long been recognized that changes in gene regulation, specifically mutations in cis-regulatory elements that tend to be stable and additive, are important to adaptive processes and phenotypic evolution. Since cis-regulatory elements are found in the vicinity of the genes they regulate, the direct effect of changes in these sequences is typically limited to a particular gene that allows for refined, situation-specific control of gene expression but are not exclusive of downstream or trans-acting elements. This dissertation focuses on examining mechanisms responsible for maintaining adaptive cis-regulatory polymorphisms in two Drosophila melanogaster genes: fezzik (fiz) and Metallothionein A (MtnA) and their associated effect on gene expression and organismal phenotype. Previous experiments show that the 3’ untranslated region of MtnA contains an insertion/deletion (indel) polymorphism, wherein the deletion is rare or absent in the ancestral African range but its deletion frequency appears to follow a latitudinal cline in derived populations worldwide. By genotyping biannual collections of wild caught D. melanogaster across a 5-year period, I show that the deletion is maintained at a high frequency (~90%) in a single German population with no evidence for overdominant, seasonally fluctuating or sexually antagonistic selection. Expression analysis on pairs of nearly-isogenic lines and on data from a North American population indicated significant differences in expression associated to the indel. Furthermore, the data from this North American population showed that expression variation was only partially explained by the deletion and the effect on oxidative stress tolerance was significantly associated with menadione sodium bisulfite and not paraquat. Altogether these findings suggested a scenario in which MtnA expression and consequently oxidative stress tolerance is likely a polygenic adaptation that varies with genomic background. Indeed, the effect of the deletion allele on oxidative stress tolerance was dependent on the genomic background with some indication of sign epistasis. Transcriptomic analysis revealed that MtnA expression was induced by oxidative stress independent of the indel status, indicating a general role of this gene in stress tolerance as well as suggesting additional levels of context-dependent expression regulation. The transcriptional response to oxidative stress between lines with and without the deletion was mostly similar but interestingly, there were consistently larger numbers of differentially expressed genes associated with the deletion which is possibly related to regulatory cascades resulting from aberrant microRNA epigenetic regulation due to the loss of microRNA binding sites in the deleted region. In general, the response to MSB indicated the significance of functional categories such as general stress response, oxidative stress response, metabolism, apoptosis and autophagy. In particular among the differentially expressed genes with the largest fold-change in response to MSB-induced oxidative stress were several genes related to glutathione metabolism and biosynthesis, suggesting a strong association between this pathway and oxidative stress tolerance. Another instance of expression divergence between ancestral and cosmopolitan populations being associated with a regulatory polymorphism is represented by a single nucleotide polymorphism (SNP) located 67 base pairs upstream of the start codon, in the enhancer region of the gene fezzik, referred to here as “SNP67”. SNP67 has two variants segregating in natural populations of D. melanogaster: the ancestral “C” variant, and the derived “G” variant that is found outside of the ancestral range at intermediate frequencies and is associated with increased fiz expression. Previous studies suggest that this SNP was a recent target of balancing selection; therefore to determine the forces of selection maintaining this SNP in cosmopolitan populations we genotyped biannually collected wild-caught D. melanogaster from a single European (Munich, Germany) population. A model-based approach using allele and genotype frequency data of the SNP67 variants across seasons and sexes was employed. The model indicated that sexually antagonistic and temporally fluctuating selection may help maintain variation at this site, with the derived variant likely being female-beneficial but there was some uncertainty of dominance estimates in the model. Gene expression and body-size phenotypes that were dependent on genomic background and developmental stage indicated that variable dominance may play a role in the maintenance of this polymorphism. Lastly, we identified a novel sex-dependent association between fiz expression and starvation resistance that may suggest that this trait is a potential phenotypic target of selection. Interestingly our findings for the MtnA and fiz regulatory polymorphisms both indicated that the relationship between gene expression divergence and population-level genetic mechanisms underlying phenotypic evolution is potentially complicated by context-dependent factors such as genomic background or spatial and temporal differences. By integrating extensive experimental work to identify the mechanisms of selection in natural populations along with functional characterizations, a refined understanding of these adaptive regulatory polymorphisms was achieved.