The full supplementary materials from this study are not online yet [UPDATE (May 2): You can read my comments on the suppplement here]. This seems to be based on a presentation from ASHG 2008. As I explained in that post, because Europe was settled from the east, it is expected that genomic diversity (left) would be higher in SE Europe and lower in SW Europe. However, the opposite is true. This, coupled with the observation of a higher degree of haplotype sharing between SW Europe and the Yoruba HapMap sample, suggests that genomic diversity in the Iberian peninsula has been enriched directly from Africa.
The STRUCTURE analysis is not quite clear, but clusters centered in Europe, Mexico, South Asia, East Asia, and Yoruba appear. From the figure, it appears that a little bit of "South Asian" appears in Europe, which may represent either a Gypsy element, or the more general "light blue" element which appeared in Li et al. Figure B, shows variability of Mexicans, who are mainly a European-Amerindian mix. Figure B distinguishes between Japanese and Chinese. Figure D distinguishes between Dravidian and non-Dravidian South Asians.
The POPRES sample has been previously used in a study on geography and genetic structure in Europe.
Genome Research doi:10.1101/gr.088898.108
Global distribution of genomic diversity underscores rich complex history of continental human populations
Adam Auton et al.
Characterizing patterns of genetic variation within and among human populations is important for understanding human evolutionary history and for careful design of medical genetic studies. Here, we analyze patterns of variation across 443,434 SNPs genotyped in 3,845 individuals from four continental regions. This unique resource allows us to illuminate patterns of diversity in previously under studied populations at the genome-wide scale including Latin America, South Asia, and Southern Europe. Key insights afforded by our analysis include quantifying the degree of admixture in a large collection of individuals from Guadalajara, Mexico; identifying language and geography as key determinants of population structure within India; and elucidating a North-South gradient in haplotype diversity within Europe. We also present a novel method for identifying long-range tracts of homozygosity indicative of recent common ancestry. Application of our approach suggests great variation within and among populations in the extent of homozygosity suggesting both demographic history (such as population bottlenecks) and recent ancestry events (such as consanguinity) play an important role in patterning variation in large modern human populations.