(A) Evolutionary relationship of modern human, Neanderthal, and chimpanzee. Divergence dates shown are estimated from genome sequence comparisons. A schematic of the single nucleotide changes detected in human–Neanderthal–chimpanzee comparisons is shown at right, ordered by the frequency at which they are likely to appear. Substitution classes and the ancient DNA artifacts particularly problematic for each are described in the legend. (B) Value of Neanderthal genome sequence for dating functionally relevant human-specific substitutions, using the HACNS1 enhancer as an example. (Top) HACNS1 is located in an intron of AGAP1 and downstream of GBX2 on human chromosome 2. (Bottom) The 13 human-specific substitutions implicated in the human-specific gain of function in this element. The enhancer expression patterns conferred by HACNS1 and the chimpanzee ortholog in E11.5 mouse embryos are shown on the right. In a human–Neanderthal genome comparison, single Neanderthal sequence reads (red arrows) will be tiled across this region. A single read spanning HACNS1 may identify which substitutions are unique to modern humans and which are shared between modern humans and Neanderthals. This analysis would also provide insight into the enhancer expression pattern of the Neanderthal HACNS1 ortholog.
