To compare landscapes of diversity and divergence along chromosomes, we computed the Spearman correlation between the landscapes across windows within a chromosome. Because of computational constraints, we focus on chromosome 12. Chromosome 12 is one of the smallest chromosomes in the great apes, there are no major inversions, and it has good variation in exon density and recombination rate. The choice was made blindly before looking at the data, but we found it behaves similarly to other chromosomes (see Figure S6 through Figure S27).
We expected landscapes of two closely related species to be more correlated than the landscapes of two distantly related species. Thus, the correlation between any two landscapes of diversity and divergence is expected to depend on distances between them in the phylogenetic tree. We decided to plot our correlations against distance (in generations) between the most common recent ancestor (MRCA) of each landscape. In comparing two landscapes of diversity, this amounts to the total distance between the two tips in the species tree. For instance, the phylogenetic distance dT between diversity in humans and diversity in bonobos is the sum of the lengths of the human, pan and bonobo branches in the species tree (Figure 1). In comparing a landscape of diversity to a landscape of divergence, this amounts to the distance between the species of the landscape of diversity and the MRCA of the two species involved in the divergence. For example, dT for the landscapes of diversity in humans and divergence between Sumatran orangutans and eastern gorillas would be the distance between the humans tip and the great apes internal node. dT for the landscapes of divergence between the orangutans and divergence between the gorillas would be the distance between the orangutan and gorilla internal nodes. Some divergences may share branches in the tree, but these are excluded from our main figures; see subsection 4.1 and Figure S2.