Fig. 1

Overlaps between functional regions of the human genome and the evolutionary model. a. Left, Venn diagram showing percentage of the human genome that overlaps with known non-coding functional annotations and conserved regions of the human genome. Right, scaled Venn diagram showing the proportion of conserved regions with respect to known functional annotations and gapped DNA representing telomeric and centromeric sequences (white). b. Graphic summary of our improved method. Left panel, the evolutionary ratio “ζ” is computed as the ratio of the substitution rate in a query (K_query) with respect to the substitution rate in a reference (K_reference) region. Queries can be obtained from functional annotations such as ATAC-seq or ChIP-seq peaks (red box), while reference alignments can either be taken by sampling local non-functional elements in the vicinity of the query or from a genome-wide random sampling of non-functional and putatively neutral regions of the genome (green boxes). Right panel, to test for positive selection in a query region on a foreground branch (red) of the tree, we fit, via maximum likelihood, both a null model and an alternative model to the alignments of the reference and query regions. In both models, on all branches, all sites in the reference region evolve neutrally. In both models, on the background branches, a fraction b1 > = 0 of sites in the query region evolve under purifying selection, at rate ζ₁ < 1 relative to sites in the reference region, and a fraction b2 = 1 - b1 of sites in the query region evolve neutrally, at relative rate ζ₂ = 1. In the null model, evolution on the foreground branch is the same as on the background branches, except a fraction Δ > = 0 of sites in the query region that evolve under purifying selection on the background branches may evolve neutrally on the foreground branch, that is, the model allows for relaxation of constraint on the foreground branch. In the alternative model, fractions Δ₁ > = 0 and Δ₂ > = 0 of sites in the query region that evolve under purifying selection and neutrally, respectively, on the background branches may evolve under positive selection on the foreground branch, at rate ζ₃ > 1. A likelihood-ratio test indicates whether the alternative model fits the alignments significantly better than the null model. As explained under “Materials and methods”, we conservatively approximate this test as a chi-squared test with one degree of freedom