After identifying haplotype blocks, they compared the average Fst for all SNPs in each block between populations.
Genes involved in skin pigmentation for which they find evidence of positive selection:RAB27A, DCT, EGFR, ATRN, MATP.
They also find that many of the areas under selection are in non-genic locations. They mention the example of the lactase gene is an example of the functional variant being in a regulatory region -- see this recent, interesting article in Science regarding the issue of the importance of genic vs. nongenic variation in evolutionary change (which this picture refers to).
Another interesting finding which they discuss is the small amount of overlap between loci that they find and the loci that other groups have found to be under recent positive selection.
Identification of local selective sweeps in human populations since the exodus from Africa
Åsa Johansson and Ulf Gyllensten,
Hereditas Volume 145, Issue 3, Pages 126-1372008
ABSTRACT: Selection on the human genome has been studied using comparative genomics and SNP architecture in the lineage leading to modern humans. In connection with the African exodus and colonization of other continents, human populations have adapted to a range of different environmental conditions. Using a new method that jointly analyses haplotype block length and allele frequency variation (FST) within and between populations, we have identified chromosomal regions that are candidates for having been affected by local selection. Based on 1.6 million SNPs typed in 71 individuals of African American, European American and Han Chinese descent, we have identified a number of genes and non-coding regions that are candidates for having been subjected to local positive selection during the last 100 000 years. Among these genes are those involved in skin pigmentation (SLC24A5) and diet adaptation (LCT). The list of genes implicated in these local selective sweeps overlap partly with those implicated in other studies of human populations using other methods, but show little overlap with those postulated to have been under selection in the 5–7 myr since the divergence of the ancestors of human and chimpanzee. Our analysis provides focal points in the genome for detailed studies of evolutionary events that have shaped human populations as they explored different regions of the world.