December 22, 2009

New major study on African ancestry

This looks like a great continuation of the previous study on African structure from the Tishkoff lab. I will add the abstract when it's posted in the PNAS site.

From the press release, Genetic study clarifies African and African-American ancestry:
This newly acquired genetic data revealed a number of important advances, including:
  • The rich mosaic of African-American ancestry. Among the 365 African-Americans in the study, individuals had as little as 1 percent West African ancestry and as much as 99 percent. There are significant implications for pharmacogenomic studies and assessment of disease risk. It appears that the range of genetic ancestry captured under the term African-American is extremely diverse, suggesting that caution should be used in prescribing treatment based on differential guidelines for African-Americans.
  • A median proportion of European ancestry in African-Americans of 18.5 percent, with large variation among individuals.
  • The predominately African origin of X chromosomes of African-Americans. This is consistent with the pattern of gene flow where mothers were mostly of African ancestry while fathers were either of African or European ancestry.
  • A technique which can reliably distinguish African and European ancestry for any particular region of the genome in African-Americans. This could have implications for personalized ancestry reconstructions, personalized medicine and more effective drug treatments and could aid in developing more effective methods for mapping genetic risk factors for diseases common in African-Americans, such as hypertension, diabetes and prostate cancer.
  • The similarity of the West African component of African-American ancestry to the profile from non-Bantu Niger-Kordofanian speaking populations, which include the Igbo and Yoruba from Nigeria and the Brong from Ghana
  • A comparison of the West African segments of African-American genomes. This is wholly in line with historical documents showing that the Igbo and Yoruba are two of the 10 most frequent ethnicities in slave trade records; however, most African-Americans also have ancestry from Bantu-speaking populations in western Africa.
  • Population structure within the West African samples reflecting primarily language and secondarily geographical distance, echoing the Bantu expansion from a homeland in West Africa across much of sub-Saharan Africa around 4,000 years ago.
The paper is open access and is now online.

PNAS doi:10.1073/pnas.0909559107

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

Katarzyna Bryc et al.


Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Link (pdf)


eurologist said...

Seems interesting that the Xhosa fit so nicely on the north-south (PC2) axis, given the distance in space and time. Does that (and the west-east match on PC1) mean much of Africa's origin (outside the extreme north) is indeed described by the proposed two populations that may have first diverged, what, almost 200,000 years ago, or so?

Maju said...

I have been checking the supplemental material, specially because I wanted to see if they had deeper K-means clustering and how did it change the components' distribution.

I found that at fig. 2 and I feel that K=6 and maybe also K=7 are still very meaningful. Level 6 clustering alone makes marked differences between Xhosa and the other Bantus specially, while at lv 7 Fang also appear largely clustering on their own, while a further component (bright blue) appears as very important among Hausa and Brong. Maybe it's the sampling but there seems to be clear subdivisions among Bantus. In any case, I wanted to know what the growing "green" component meant among Bantus and it seems clearer at K=7: it hides three elements: a "Fang" component, a "Bamoun" component and a "Xhosa" component that may well be Khoisan in fact, as it's low in all other NK peoples).

At K=7 the K=5 Mada component (only showing up at that level) is re-absorbed by the Bulala one. So it's surely an artifact to some extent.

Anyhow the distinct clustering of Fulani specially at lower levels is quite curious. At the PC analysis Fulani seem from "another planet" so to say (but they never cluster with Caucasoids at all, so they are genuine ultra-Saharan ethnos in all aspects).

Kepler said...

Very interesting article.

Dienekes, do you know by chance how precise scientists can get about timing the mtDNA?

I mean: there is some rough knowledge of timing for branches among Y haplotypes, but: is there something about determining when a given mtDNA haplotype from Africa appeared?

I have L1c3 on my mother's side. The link to Africa must be from before 1810 and after 1528 if it was an African slave to the Americas OR it could be some centuries older if it was via someone from the canary Islands or continental Spain. The African haplotypes in Venezuela are the least common among our three main groups

I do know there are lots of "sub-Saharan" haplotypes that only appear in the Americas for the moment, partly because there has been so little research in Africa.

An African said...

The low self-esteem of whites rears its sad sorry head once again. Still at trying to claim all things African again.