Previous inferences about demographic history and the role of local adaptation in shaping human genetic variation made from genome wide genotype data4, 38, 39 have been limited by the partial and complex ascertainment of SNPs on genotype arrays. While data from the 1000 Genome Project pilots are neither fully comprehensive nor fully free of ascertainment bias (issues include low power for rare variants, noise in allele frequency estimates, some false positives, non-random data collection across samples, platforms and populations, and the use of imputed genotypes), they can be used to address key questions about the extent of differentiation among populations, the presence of highly differentiated variants and the ability to fine map signals of local adaptation.
