The impact of linked selection in chimpanzees: A comparative study

Levels of nucleotide diversity vary greatly across the genomes ofmost species owing tomultiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the relative importanceof these forces is the commonobservationof a strong positive correlation between nucleotide diversity andrecombination rate. While indeed observed in humans, the interpretation of this pattern has been difficult in the absence of high-quality polymorphism data and recombination maps in closely related species. Here,we characterize genetic features driving nucleotide diversity in Western chimpanzees using a recently generated whole genome polymorphism data set. Our results suggest that recombination rate is the primary predictor ofnucleotide variation with a strongly positive correlation. Inaddition, telomeric distance, regionalGC-content,and regional CpG-island content are strongly negatively correlated with variation. These results are compared with humans, with both similarities anddifferences interpreted inthe light of the estimated effectivepopulation sizes of the twospecies aswell as their strongly differing recent demographic histories.