At the University of Bern since 2001, I have been interested in the development of computational methods to understand evolutionary processes at the population and species level, for instance to study how past climatic and environmental changes have influenced the pattern of genetic diversity of a given species, or to detect evidence of local adaptations from genomic information.
With Nicolas Ray and Mathias Currat, we have been interested in better understanding the role of spatial processes on genetic evolution, mainly during range expansions. To this aim,we have been developing a spatially explicit framework (SPLATCHE) to simulate genetic and genomic data in a changing and heterogeneous environment, allowing for complex interactions and competition between neighboring populations. This approach has then been key to study the genetic surfing mechanism occuring when (bneutral) genetic variants occuring on the edge of a population spatial expansion spread and increase in frequency, looking like a selective sweep.
I have been also interested in developing better ways to estimate demogrpahic parameters and thus the past history of populations from genetic and genomic data.With Daniel Wegmann, we have been studying how one could use simulations under an Approximate Bayesian Computation (ABC) framework to to study complex evolutionary models. Then with Vitor Sousa, Isabelle Dupanloup, and Isabel Alvès, we have switch from ABC to composite-likelihood methods based on the Site Frequency Spectrum (SFS) to make inference from genomic data. We have therefore developed an efficient and robust methodlogy (fastsimcoal2) to estimate demographic parameters from genomic data, an approach that has been recently extended and made more flexible to allow for spatial and temporal heterogeneity with Nina Marchi.
Following on the consequences of genetic surfing, with Stephan Peischl, we have investigated the effect of spatial range expansion on non-neutral (functional) diversity, evidencing the buildup of a mutation load (an expansion load) due to inefficient purifying selection on wave fronts. We have been testing these theoretical predictions by studying the genomic diversity of populations having gone through recent range expansions like humans and bacteria. More recently, with Flávia Schlchta, we have been investigating the effect of genetic surfing on patterns of genomic diversity along chromosomes in neutral and functional regions of the genome, evidencing the imporance of recombination and selected variant dominance levels on these patterns.
With Joachim Burger, at the University of Mainz, and Daniel Wegmann, now at the University of Fribourg, we have started to study the genetic diversity of ancient individuals to better understand the origin of early Neolithic farmers having colonize Europe through the Danubian corridor, using extensively the fastsimcoal2 framework to estimate divergence times, past populations sizes, and admixture between and with hunter-gatherers. This (Evoledge) project is still going on to better infer the complex and detailed processes having occurred during this Neolithic expansion, the with the help of Nina Marchi. Sandra Oliveira, Stefan Struett, and Adamandia (Mado) Kapopoulou. This last project wil lkeep me busy at least for the first year of my retirement, so that I will not completely leave science.
