A global perspective on genetic variation in modern Homo sapiens

Over the past few years our lab has assembled a collection of cell lines on over 30 populations including at least three populations from each of the major geographic regions of the world. To date we have a complete set of allele frequency data on 14 haplotyped loci (46 sites total, two to six sites per locus) and 9 single-site loci on 30 distinct populations with an average sample size n@50. This complete dataset of 23 independent loci on 30 distinct populations has now been analyzed for genetic distances, etc. The Fst values for the 55 individual sites across the 30 populations range from 0.04 to 0.41, with a mean of 0.16. The smallest value occurred at one site at the D4S 10 locus but the haplotypes for D4S 10 had an Fst =0.17. The largest value occurred for a single SNP in the ADH gene cluster. PCA analyses give four main clusters of populations corresponding to Africa, Europe and Southwest Asia, East Asia, and the Americas. In tree analyses, the Africa-Europe pair is separated by a long branch from the East Asia-Americas pair. Three populations do not fall clearly in any of these clusters: Nasioi Melanesians, Micronesians, and Yakut Siberians. The overall pattern is consistent with an out-of-Africa model; indeed, some of the haplotypes included-CD4, DRD2, DM, PAH-have been used on subsets of these populations to argue strongly for that model. The additional data at those and the other haplotyped loci continue to be consistent with the existence of a significant founder effect associated with the expansion out of Africa and accumulating drift and loss of variation from West to East across Eurasia and then from North to South in the Americas. Supported by NIH grants GM57672, AA09379, and NSF grant BCS-9912028.