The HGDP panel includes 1063 individuals from seven continental groups classified into 51 populations, eight of which are located in Europe. Individuals are genotyped at a large number of biallelic markers (single nucleotide polymorphisms or SNPs). We removed individuals with less than 95 per cent complete genotypes, SNPs with less than 99 per cent complete genotpyes, or minor allele frequency less than 1 per cent. Finally, we allow for distinct subpopulation allele frequencies by adding normally distributed test statistics for Hardy Weinberg disequilibrium across tribes within subcontinents. SNPs with p-values less than 10−4 were removed. The POPRES database includes 2955 subjects of European ancestry. Demographic records include the individual's country of origin and that of his/her parents and grandparents. The sampling frequency varies strongly by region, including Swiss (1014), British and Irish (436), Italian (205), Portuguese and Spanish (252), French (108), north-west European (173), east-central European (75), south-eastern European (45), and other (647). Of the more than 650 000 markers typed on HGDP and 450 000 on POPRES, focusing on the fraction that were present on both platforms, we selected
