Understanding the molecular basis for phenotypic differences between humans and 
other primates remains an outstanding challenge. Mutations in non-coding 
regulatory DNA that alter gene expression have been hypothesized as a key driver 
of these phenotypic differences. This has been supported by differential gene 
expression analyses in general, but not by the identification of specific 
regulatory elements responsible for changes in transcription and phenotype. To 
identify the genetic source of regulatory differences, we mapped DNaseI 
hypersensitive (DHS) sites, which mark all types of active gene regulatory 
elements, genome-wide in the same cell type isolated from human, chimpanzee, and 
macaque. Most DHS sites were conserved among all three species, as expected 
based on their central role in regulating transcription. However, we found 
evidence that several hundred DHS sites were gained or lost on the lineages 
leading to modern human and chimpanzee. Species-specific DHS site gains are 
enriched near differentially expressed genes, are positively correlated with 
increased transcription, show evidence of branch-specific positive selection, 
and overlap with active chromatin marks. Species-specific sequence differences 
in transcription factor motifs found within these DHS sites are linked with 
species-specific changes in chromatin accessibility. Together, these indicate 
that the regulatory elements identified here are genetic contributors to 
transcriptional and phenotypic differences among primate species.