Genetic Variation and Recent Positive Selection with 1 million SNPs

On the left Figure S4 shows PCA and frappe analysis for Eurasia. From the paper:

When just the Central/South Asia, Middle East, North Africa, and European groups are analyzed, PC1 (Fig. S4A) distinguishes the Mozabite (North Africa), Middle East, and Europe groups from the Central/South Asian groups, while PC2 separates the Mozabite and Middle East groups from the Europe groups, with no overlap among individuals from the different North Africa/Middle East/Europe groups. By contrast, there is overlap among individuals from the different Central/South Asia groups; in addition, the Makrani and Sindhi individuals identified in the worldwide analysis as having experienced recent sub-Saharan African admixture are clearly differentiated by PC2. The frappe analysis at K = 5 (Fig. S4B) indicates ancestry components corresponding to the Mozabite, Kalash, Hazara/Uygur, other Central/South Asia, and Europe groups. The three Middle East groups have varying amounts of the Europe, Mozabite, and Central/South Asia ancestry components. The three Italian groups are alone among European groups in having low amounts of the Mozabite ancestry component, possibly indicating gene flow across the Mediterranean. The Sardinians differ from continental European groups in lacking any Asian ancestry component, while the Russians and Adygei differ from other European groups in having appreciable amounts of the Hazara/Uygur and other Central/South Asia ancestry components, respectively, indicating more gene flow and/or ancestry with these groups (Fig. S4B).

Also from the paper, referring to Figure 3 and Figure S3:

Second, many of the subsequent statistically-significant PCs (Fig. 3 and Fig. S3) distinguish among various combinations of the sub-Saharan African groups (or among individuals within such groups), despite the fact that there are only six such groups in the analysis. This disproportionate impact of structure within sub-Saharan Africa on analyses of worldwide genetic diversity clearly emphasizes both the importance of such structure and the great need for further in-depth genetic characterization of sub-Saharan African populations [22]; we would hardly expect that these six groups encompass all of the genetic diversity in sub-Saharan Africa.

PLoS ONE doi:10.1371/journal.pone.0007888

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

David López Herráez et al.

Abstract

Background
Genome-wide scans of hundreds of thousands of single-nucleotide polymorphisms (SNPs) have resulted in the identification of new susceptibility variants to common diseases and are providing new insights into the genetic structure and relationships of human populations. Moreover, genome-wide data can be used to search for signals of recent positive selection, thereby providing new insights into the genetic adaptations that occurred as modern humans spread out of Africa and around the world.

Methodology
We genotyped approximately 500,000 SNPs in 255 individuals (5 individuals from each of 51 worldwide populations) from the Human Genome Diversity Panel (HGDP-CEPH). When merged with non-overlapping SNPs typed previously in 250 of these same individuals, the resulting data consist of over 950,000 SNPs. We then analyzed the genetic relationships and ancestry of individuals without assigning them to populations, and we also identified candidate regions of recent positive selection at both the population and regional (continental) level.

Conclusions
Our analyses both confirm and extend previous studies; in particular, we highlight the impact of various dispersals, and the role of substructure in Africa, on human genetic diversity. We also identified several novel candidate regions for recent positive selection, and a gene ontology (GO) analysis identified several GO groups that were significantly enriched for such candidate genes, including immunity and defense related genes, sensory perception genes, membrane proteins, signal receptors, lipid binding/metabolism genes, and genes involved in the nervous system. Among the novel candidate genes identified are two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature.

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