Detection of positive selection by means of linkage disequilibrium analysis on highly diverged genes between humans and chimpanzees

Linkage disequilibrium (LD) is the result of the several phenomena that have shaped our genome, such as speciation processes and species-specific adaptations, besides other genomic and populational factors, particularly selection and recombination. In the present project, we will analyze the genetic footprint of selection in the haplotype structure of genes with high divergence in the lineage leading to humans after the split from the chimpanzee lineage, and we will interpret the LD patterns in human populations representing human global genetic variation. The divergence accumulated in the human lineage does not allow by itself to pinpoint the effects of recent positive selection linked to the unique adapative traits that define our species, given that the split from the chimpanzee lineage took place 5 to 7 milion years ago, while the origin of our species dates back to 150,000 years ago. Nonetheless, the LD patterns may indeed reflect this recent positive selection. Thus, we propose to choose some 40 genes for their high divergence between human and chimpanzees and type around 20 SNPs per genic region in a thousand human samples representing the global genetic diversity. The strategy to detect selection will be based on the extent of LD, as selection tends to increase LD in frequent alleles or haplotypes.