Genomic diversity and composition evolve under diverse and complex constraints such as demography, selection, mutations, or genomic rearrangements. However, the influence of these evolutionary forces and their interactions remain to be fully understood. In that prospect, I will present two projects based on the human genome.

First, I will use a population genomics approach and show that purifying selection at linked sites (i.e. background selection) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. Their magnitude are largely determined by variation in recombination rate and base composition and previous reconstruction of human demography based on synonymous sites for instance are thus likely biased by these two mechanisms. However, when focusing on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), the effects of background selection and gBGC are minimal. I will advocate to use these neutral regions to reconstruct demographies.

Second, I will focus on a longer time scale by showing that recombination also affects patterns of substitution in the human genome and importantly within genes. Synonymous codon usage varies widely among human genes and in particular among genes involved in different functional categories. These differences are not constraint by tRNA abundance and translational selection but reflect differences in levels of meiotic expression. Expression during meiosis is linked to variation in recombination and therefore in gBGC. Overall, the gBGC model explains 70% of the variance in synonymous codon usage among genes while translational selection explains less than1%.