McVicker et al.1 used a different approach for detecting natural selection in the human genome than any that we discussed in lecture. Specifically, they
Used a hidden Markov model to identify genome segments that are highly conserved across placental mammals.2 Some of the segments are in exons, and some lie outside exons.
Compared the amount of nucleotide sequence diversity (within humans) and the amount of nucleotide sequence divergence (between humans and chimps, humans and macaques, and humans and dogs) at the 10 percent of sites closest to the conserved segments with the diversity and divergence at the 50 percent of sites that were farthest away.3
Compared sequence divergence along the branch leading to humans with divergence along the branch leading to chimps and the branch leading to macaques.
Here are figures taken from the paper that illustrate the main patterns.