Shared evolutionary processes shape landscapes of genomic variation in the great apes.

For the past six decades population genetics, as a field, has struggled with trying to explain the precise balance of forces that shape patterns of variation in genomes. Here, we go beyond genetic diversity within a single species and study how diversity and divergence between closely related species change with time. We find strong correlations between landscapes of diversity and divergence in a well sampled set of great ape genomes. Through highly realistic, large-scale simulations we show that the observed great ape landscapes of diversity and divergence are too well correlated to be explained via strictly neutral processes alone. We describe how various processes such as shared ancestral variation, mutation rate variation, GC-biased gene conversion and selection could contribute to correlations. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in which 10% of fixations within those regions is driven by positive selection.