Evidence of abundant purifying selection in humans for recently acquired regulatory functions

Abstract

Although only 5% of the human genome is conserved across mammals, a substantially larger portion is biochemically active, raising the question of whether the additional elements evolve neutrally or confer a lineage-specific fitness advantage. To address this question, we integrate human variation information from the 1000 Genomes Project and activity data from the ENCODE Project. A broad range of transcribed and regulatory nonconserved elements show decreased human diversity, suggesting lineage-specific purifying selection. Conversely, conserved elements lacking activity show increased human diversity, suggesting that some recently became nonfunctional. Regulatory elements under human constraint in nonconserved regions were found near color vision and nerve-growth genes, consistent with purifying selection for recently evolved functions. Our results suggest continued turnover in regulatory regions, with at least an additional 4% of the human genome subject to lineage-specific constraint.

Fig. 1

(A) Only a small fraction (purple) of biochemically-active regions (red) overlaps conserved elements (blue). (B) Active regions (red) show reduced heterozygosity relative to inactive regions outside conserved elements (white), suggesting lineage-specific purifying selection (black arrow). Conserved elements that lack activity (blue) show increased human heterozygosity relative to active conserved regions (purple), suggesting recent loss of selective constraint (white arrow). (C–D) Comparison of mean heterozygosity for ENCODE-annotated elements (red) vs. non-ENCODE elements (black) and active chromatin (green) vs. inactive (blue) shows a consistent reduction at varying genetic distances from exons (C) and varying expected background selection (D), confirming the heterozygosity reduction is due to purifying selection. Shaded regions represent a 95% confidence interval on the mean heterozygosity assuming independence between bases.

Fig. 2

Mean frequency of derived alleles (vertical bar) relative to samples of similar size (distribution) from the specified background for previous annotations (grey), ENCODE (blue) and chromatin states (red). Sizes of regions are shown.

Fig. 3

Average heterozygosity for bound regulatory motif instances (x-axis) and non-bound regulatory motif instances (y-axis), evaluated in non-conserved regions of the genome to estimate lineage-specific constraint. Shown are all transcription factors with at least 30 kb of bound instances (red points). Numbers in parentheses indicate number of bound and number of non-bound instances, respectively.

Fig. 4

Estimated proportion of bases under constraint (PUC) in human using SNP density (x-axis) and DAF (y-axis), across previously-annotated elements (squares) and newly-annotated ENCODE elements (circles), in both conserved (blue) and non-conserved (black) regions. Error bars denote 95% confidence intervals on the estimates. Each metric was linearly scaled between 0% for non-ENCODE non-conserved regions and 100% for conserved non-degenerate coding positions in each background selection bin separately (Fig. S8)