John Parsch - Evolutionary and Functional Genomics
We study the evolution of genes and gene regulation, working mainly with the fruit fly Drosophila melanogaster and other closely-related species. A major goal is determining the type and strength of selection affecting the evolution of genes of different functional and expression classes. We are also interested in how levels of gene expression respond to changes in the abiotic (e.g. climate) and biotic (e.g. pathogen) environment. Finally, we are performing functional experiments to determine how selection and constraints on gene expression shape the distribution of genes throughout the genome.
Individual projects include:
- The evolution of sex-biased genes and sex-biased gene expression
- Gene expression variation in natural populations of D. melanogaster
- Functional analysis of gene regulation
These projects are supported by grants from the German Research Foundation (DFG)
Sex-biased genes are those that are expressed predominantly or exclusively in one sex. They are abundant in the Drosophila genome (thousands of genes) and show interesting patterns of molecular evolution. In particular, genes with male-biased expression tend to show rapid rates of evolution between species. Our work focuses on the evolutionary forces responsible for this rapid evolution. In general, we have found that male-biased genes experience more frequent adaptive evolution, with a high proportion of amino acid divergence between species being attributable to positive selection.
We are using transcriptomic approaches (microarrays and RNA-seq) to identify genes that vary in expression level within and between natural populations of D. melanogaster. For example, we compare expression between flies from Europe and flies from Africa. Genes that differ significantly in expression level between populations are candidates for those that have undergone adaptive regulatory evolution in response to environmental change. We are carrying out population genetic and functional analyses of such candidate genes to elucidate the genetic and evolutionary causes of the observed expression differences.
We are using transgenic reporter genes to study factors that influence gene expression in D. melanogaster. We have used this approach to test for X chromosome inactivation in the Drosophila male germline, to test the effects of cis-regulatory sequence variants on levels of gene expression, and to test the effects of changes in synonymous codon usage on gene expression.