June 28, 2010

Genetic structure of Qatar (Hunter-Zinck et al. 2010)

(Last Update Jul 11)

On the left the position of the three groups on the global PCA (Supplementary Figure 1). What's interesting about this figure is that it is done on low-FST SNPs, which should make them more resilient to the effects of ascertainment bias, i.e., the fact that SNPs used in the Affymetrix chip were found to be polymorphic in different populations than those of Qatar, and, correspondingly, very informative Qatari SNPs may be missing from the chip. Nonetheless, the differentiation between the three groups follows closely what one gets from the full set that is in the paper.

UPDATE (Jul 11):

The split into three groups was verified by STRUCTURE analysis of the Qatari individuals. Qatar 1 (red), Qatar 2 (blue), Qatar 3 (green) are quite evident:

The authors then compared surnames with membership in the three Qatari clusters, uncovering that:
A Mantel test comparing Qatari subgroups and surname origins indicates highly significant (p = 0.0001) correlations across the three population groups in the frequency of these name classifications, with the Qatar1 population having mostly Arab surnames, the Qatar2 population having a large Persian component, and the Qatar3 population appearing to be the most diverse and having the largest African component (Figure 7).
I think that it is a good idea for future studies of national populations to perform similar analyses in order to determine their homogeneity or lack thereof. This is quite critical, as population-specific features in a heterogeneous population may be incorrectly inferred, depending on the exact "sample mix" of the tested individuals. In this study, for example, Qatar1 (Arab-dominated) individuals were the most consanguineous, but the level of their consanguinity would have been underestimated if they had not been identified as a distinct component of the Qatari population.

The American Journal of Human Genetics
doi:10.1016/j.ajhg.2010.05.018

Population Genetic Structure of the People of Qatar

Haley Hunter-Zinck et al.

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari.

Link

4 comments:

AdygheChabadi said...

"People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture."

"Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture."

That is not really a surprise since the Y-chromosome analysis said basically the same thing in a paper, by Cadenas et al. 2007.

onur said...

Asia?! Leaving aside Middle Easterners (West Asians), who are categorized in this study as a group separate from Asians, there are two major groups of Asians in the HGDP: 1) Central & South Asians 2) East Asians. These two major groups are genetically quite distinct from each other, so they should have been categorized as separate groups in this study to prevent confusion. Clearly the Asians closest to Europeans and Middle Easterners on the above PCA plot are Central & South Asians. Most of them are in fact much closer to Europeans and Middle Easterners than to East Asians.

onur said...

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture.

Do these three tribes correspond to the three purely genetically based Qatari groups of this study? And in what degree of correspondence?

Alice C. Linsley said...

My research on Abraham's people shows that 3-clan confederations were the common socio-political arrangement. Some who were regarded as cousin brides were actually patrilineal nieces.