Regulatory innovation. Each panel shows data for the frequency of regulatory innovations near genes in a different GO category (panel title). Colors indicate the five lineages studied. Each data point (colored circle) represents the relative frequency of regulatory innovations on a specific lineage (color) as determined by analysis using the reference genome for that lineage. The relative frequency (enrichment factor) for a specific GO category is defined as the frequency of innovations in genes of this GO category as compared to what would be expected by selecting genomic regions at random (denoted by the horizontal line at the relative frequency of 1.0). Each data point is an estimate from at least 2800 putative regulatory innovations. The time associated with each data point, indicated on the horizontal axis, is the midpoint of the branch of the phylogenetic tree on which these innovations are inferred to have occurred by comparative genome analysis (Fig. S3 and Tables S1 and S2). The horizontal axis is annotated with both geologic time periods as well as speciation events for the lineages analyzed.

Enrichment for regulatory regions originating near genes involved in hair development during the time hair originated in evolution. For each branch we plot the percentage of genes or regulatory elements created on that branch that are associated with hair development.

A comparative history of innovations in regulatory regions and genes. Each panel shows data for the frequency of regulatory innovations near genes in a different GO category (panel title) as well as the frequency of genic innovations for that GO category. Each data point for regulatory innovations (red circle) represents the percent of regulatory innovations appearing on a branch in the human lineage that are associated with a gene annotated with the given GO category. Each data point for protein-coding genes (red x) represents the percent of protein-coding genes appearing on a branch that are associated with the given GO category. The time associated with each data point is as described in Fig. 1.