Genes that have been subject to recent positive selection are expected to leave a genome signature of loss of polymorphism around the selected locus (called "selective sweep"). This can potentially be used to do systematic genome screens for genes involved in recent adaptations. We are focussing on natural populations of the house mouse (Mus musculus) for identifying such genome signatures as well as studying underlying gene functions. Since mouse populations have expanded across the whole world in several waves, it is possible to compare populations at various levels of divergence, including very recently separated populations (a few hundred to a few thousand years), as well as longer separated ones (up to one million years).
Copy number variants are often defined as segments of DNA that are 1 kb or larger and present at a variable copy number in comparison to a reference genome. They can be insertions, deletions and duplications and can encompass one or more genes. They are very common in the genome and possibly constitute the biggest contribution of variation in genomic sequence among individuals: in mice and humans, CNVs affect up to 12% of the genome. Given the abundance, size and mutability of CNVs they might contribute to phenotypic variation, including rapid adaptations. We hypothesize that due to these features CNVs may be involved in early stages of population differentiation, and aim to understand the dynamics of copy number variation in the context of adaptations.
Adaptation works frequently via changes in morphology, but the underlying genetic processes are only poorly known. We are focussing on the mouse skull as a model system to approach the genetics of shape. We use morphological data based on computer tomogrphy and geometric morphometrics to quantify changes in shape components and various QTL and association mapping approaches to identify genetic components.
Gene mapping for complex or quantitative traits remains a challenging task. This is primarily because complex trait variation is caused by numerous quantitative trait loci (QTL), each of relatively small effect size that traditional genetic approaches struggle to isolate. Complex traits are particularly relevant for evolutionary adaptations, since most of them are based on quantitative characters that are likely to involve many genes. Hence, understanding the genetics of complex traits is also a prerogative for understanding the genetics of evolutionary processes. Bodyweight is an archetypal complex trait in mice. A plethora of resources including mapping crosses, recombinant inbred lines, and long-term selection lines have helped identify many bodyweight QTLs. But despite decades of intensive study, a fine-grained understanding of the genes underlying growth and/or bodyweight remains elusive. Increased bodyweight in house mice has been observed repeatedly and independently, both under long-term artificial selection in the laboratory, and in natural populations in the wild. Since most of these mice are primarily derived from the Western house mouse M. m. domesticus and share recent genetic ancestry, some part of the response to selection is likely to have a shared allelic basis. We applied “parallel selection mapping” to identify this component of shared loci underlying parallel increase in bodyweight across multiple long-term artificial selection experiments in mice.
Mate recognition and mate choice in house mice has long been thought to be driven by olfactory cues, either conveyed by MHC peptides or major urinary proteins. However, in the past years it has become clear that mice use also ultrasonic communication to convey mating signals.
Newly evolved genes are expected to have contributed to lineage-specific adaptations throughout evolution. It is now becoming clear that they can be born de novo from non-genic sequences. These processes have been poorly documented and analysed so far, especially in higher eukaryotic systems. Using a combination of comparative genomics and high throughput transcriptomics we aim to gain better knowledge of the properties of the newest genes in the mouse genome.