Fine-scaled human genetic structure revealed by SNP microarrays

Abstract

We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

Genomic Evidence for an African Expansion of Anatomically Modern Humans by a Southern Route

“…We analyzed genetic diversity at more than 100,000 single-nucleotide polymorphisms (SNPs) in 86 individuals belonging to nine populations selected from two different public genomic data set (Reich et al 2009;Xing et al 2009). Seven of these populations were chosen along the putative "Southern route," mainly in the Indian subcontinent.…”

Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan

“…Its compact distribution of deeply divergent languages 4 provides a unique possibility to test gene-language co-evolution at a fine scale and to illuminate the genomic footprint of events such as migration and admixture on genetic variation. However, most previous genetic studies either did not perform dense sampling of the region, or were limited to autosomal Alu insertion, autosomal STR, Y-chromosomal, and mtDNA surveys [14][15][16][17][18][19][20][21][22][23][24][25] .…”

Genome-wide patterns of population structure and admixture in West Africans and African Americans

“…Nonetheless, recent studies of microsatellite and DNA sequence variation suggest a significant population structure exists within sub-Saharan Africa, with geography, language, and mode of subsistence (e.g., hunter-gatherer, pastoralist, agriculturalist) as potential key factors (2,12,13,19). Given that high-density genotype data have revealed discernible population structure within other continental populations (e.g., Europe, East Asia) and even among geographical regions within countries (e.g., Switzerland, Finland, United Kingdom) (20)(21)(22)(23)(24), there is strong reason to believe that high-density genotype data from African and African-American populations can elucidate patterns of genetic structure among these populations further.…”