Hitchhiking mapping

Functional innovations in natural populations are difficult to identify. Nevertheless, a recent spread of a favorable innovation leaves a characteristic pattern of variability around the genomic region coding for the innovation. Hitchhiking mapping aims to survey natural variation for a large proportion of the genome. By means of statistical tests it is possible to distinguish genomic regions coding for functional innovations from others. Using high throughput techniques (SNP microarrays and massive parallel sequencing) we are studying functional innovations in natural (D. melanogaster) and domestic populations (cattle).

Demography of Drosophila
In order to understand the partitioning of natural variation, it is important to have a solid understanding of the history of the populations. Hence, we are using microsatellites, nuclear and mtDNA sequences to reconstruct the history of D. melanogaster and D. simulans.

Intron evolution
Until very recently, introns were frequently considered to evolve under low functional constraints. Since then, it has become clear that introns contain important functional elements, resulting in a striking conservation, both in length and sequence. In this project, we are exploring to what extent introns could contribute to functional innovations. 

Evolution of Polycomb/trithorax genes
Previously, we showed that the cramped gene, which belongs to the group of polycomb genes, is involved in the adaptation of natural D. melanogaster populations. We showed that several amino acid substitutions occurred, which affected the sensitivity of the flies to temperature. In this project other genes interacting with cramped will be characterized for their contribution to adaptation of D. melanogaster populations to temperature.

Evolution of gene expression
Gene expression is one of the most accessible molecular phenotypes. Nevertheless, interspecific comparisons of the entire transcriptome have been limited to closely related species, as the existing microarrays were not suitable for the comparison of more diverged ones. We are taking advantage of the recent technological developments, which provide the possibility to study gene expression in extremely divergent species. Using these new tools, we study the evolution of gene expression in a set of Drosophila species, which covers more than 40 million years of divergence.