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In Dr. Daniel MacArthur’s post on Roots into the Future Blaine Bettinger left an interesting comment:

It will be interesting to see how 23andMe deals with the pool of people that respond to the 10,000 free kits. Doesn’t seem like they can pre-screen applicants, since African American heritage is sometimes more sociological than genetic (based on previous genetic studies, anyway). In other words, who’s to say who is an African American and who isn’t?

And how will they deal with the unscrupulous people who apply with the full knowledge that they have no recent African ancestry? Certainly they won’t be screen those people out, even with surveys or other methods.

My concerns probably won’t apply to the genetic association studies, since they can look for test-takers that have, for example, a certain % of African American ancestry, or can look for African American ancestry in the region of the genome where the association is believed to reside (after it’s predicted to exist).

However, my concerns will certainly apply to any conclusions they might make about African American genetic ancestry. For example, a conclusion such as “XX% of African Americans have less than XX% of African American DNA,” or “XX% of African Americans have European Y-DNA signatures.” These calculations will unfortunately be biased by the “unscrupulous”, even if they ask for surveys or other methods to deter bias. The best they might be able to do is “XX% of African Americans with 5% or more of African American DNA have European Y-DNA,” and conclusions that take the “unscrupulous” bias into account.


Naive nerd that I am I hadn’t even considered the possibility of fraud! In any case, after running the African Ancestry Project I have to be honest and admit that it’s weird but I have started to “profile” genotypes automatically. I guess that’s a fraught term to use with black Americans, but the honest truth is that I don’t pay much attention to the ancestry that people report to me in the emails. I just assign them IDs, do the format conversions, and run the algorithms. I then push the results online and let people interpret it how they want to interpret it. But with all that said the genetic profile of African Americans is pretty straightforward. My sample of ~130 individuals has around 100 African Americans, and they’re distinctive in having a mix of European and African ancestry. The individuals who are from Africa stick out like sore thumbs, and I immediately know that ID X has to be African. After 200+ years African Americans almost always have some European ancestry, even if it’s at a low fractional quantum.

One of the aspects of Blaine’s comments is the idea that those who attempt to sneak into this project might distort the distribution of ancestral components reported within the African American population. I don’t think this is an issue. This is one group which has been studied some, and the consensus is rather clear that it’s about ~20% white. Let’s look at some of the papers which report results that give us a sense of what’s going on.

First, Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X. The title says it all. ~15,000 African Americans in their total pool. Here’s the table with the statistics by population set (the ranges are standard deviations):

Let’s go graphical. Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans has a PCA which shows the two largest dimensions of variation in their combined data set, which includes East Asians, Europeans, and Yoruba from Nigeria, in addition to African Americans. After removing 11 individuals (outliers and related individuals), they found that of the remaining 89 the ancestral percentages were 21 percent European and 79 percent African. The range in European ancestry in these individuals was 1-62 percent with a standard deviation of 14 percent.

Finally, let’s look at a bar plot from the Genome-wide patterns of population structure and admixture in West Africans and African Americans. Their sample of African Americans was 365. The median proportion of European ancestry was 18.5%, with the 25th–75th percentiles being 11.6–27.7%. To the left you can observe the range in African Americans in terms of admixture. A very few people are overwhelmingly European, but most individuals are much closer to 20% European.

My point in reviewing all this is straightforward: even without screening Roots into the Future will be able to ascertain the likelihood of fraud and deception. The distribution of ancestry among African Americans as a whole is pretty well characterized. There’s some inter-regional variation, but if the project observed a secondary mode with ~100% non-African ancestry I think they can assume that these should be discarded from the project.

(Republished from Discover/GNXP by permission of author or representative)
 
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ResearchBlogging.org The populations of the African Diaspora have a particular interest in the new genomics, and its relationship to ancestry. Unlike other post-Columbian Diasporas they have sketchy, at best, knowledge of the regions from which their ancestors arrived. This probably explains the popularity of Roots and Henry Louis Gates Jr.’s various genealogical projects which have utilized cutting edge genomics. It may seem silly to hang one’s hat on one maternal lineage, but perhaps it seems silly if you are relatively assured of the broad outlines of your own genealogy. The fact that I am U2b is not very interesting to me, but I also happen to know that my maternal grandmother’s mother’s family were long resident in their region of Bengal (and, that her father was a migrant from northwest India). It would be a different matter if my ancestors had been enslaved and dispossessed of their heritage.

A new paper in PLoS ONE surveys the paternal (NYR), maternal (mtDNA), and autsomal (using 175 ancestrally informative markers), heritage of a range of African origin populations from across the Americans. Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas:

Our analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label.

There isn’t anything too surprising here. Blacks from Brazil have much more ancestry from the former Portuguese colonies of Angola and Mozambique. As we should expect. Because the New World African Diaspora dates to only the past 350-150 years even mtDNA should be a good snapshot of the genetic variation. And, because of the ability to construct clean genealogies due to lack of recombination, mtDNA can be even more informative than total genome surveys in terms of elucidating fine-grained geographical patterns. The map below illustrates the mtDNA results well:


But I was more interested in some patterns comparing the various African and European identified populations. In the figure which I stitched together below you have maternal ancestry on the left, paternal in the middle, and total genome ancestry to the right. The first panel has self-identified blacks from various nations, and the second has self-identified whites from Brazil and Philadelphia, USA. These results need to be taken with a grain of salt, because the samples from each nation need not necessarily be representative of the ethnicity for that whole nation (e.g., blacks in coastal Georgia have far less white ancestry than those in urban northern cities). But they give a rough picture of the differences and similarities.

Here the numbers with margins of error as well:


Self-identified black Self-identified white
African error European error Native error African error European error Native error
Brazil mtDNA 85 3 1 1 14 3 31 6 38 5 31 5
NRY 51 4 47 4 2 2 0 1 97 2 2 2
AIMs 58 30 12 20 64 17
USA mtDNA 93 1 5 1 2 1 6 5 92 7 2 1
NRY 77 2 25 2 0 0 2 1 97 2 1 1
AIMs 83 1.6 15 2 2 1 2 2 95 3 3 3

Similarities: a strong bias toward more male European ancestors, and more female African and Native ancestresses. This is what you’d expect. But look at the Brazil black sample. The disjunction between nearly total lack of female European ancestry and a substantial proportion of male European ancestry is rather striking. I think this is partly a function of the strong male bias of the Portuguese settler community. A process of “whitening” of the original mulatto and mestizo population of the colony probably occurred with each successive generation of male immigrants, who married into the hybrid communities and shifted the total genome content, though not the maternal background. The biggest difference of course is the much more clear and distinct difference between the races in the USA as opposed to Brazil. A minority of Brazilians identify as black, while a plural majority identify as white (the remainder are “brown” or mixed-race). And yet Brazilian blacks are ancestrally much whiter than American blacks, while Brazil whites are ancestrally much less white than American whites. Additionally, while Brazil perceives itself as a mulatto nation, there is a substantial Amerindian substrate which spans the black, white, and brown, populations.

Finally, going back to the main theme of the paper, African population structure, one of the main rationales is for purposes of medical research where stratification of ancestry within an aggregate pool may lead to spurious associations. In other words, mixing blacks with ancestry from Angola with those from ancestry from Nigeria may result in false positives in GWAS due to differences in predispositions of traits between these populations, which also track their genetic differences. The authors bring up the fact that African populations are the most genetically diverse in the world. But let me resurrect a comment from geneticist Nick Patterson:

I want to comment on Africa’s genetic diversity. There is a great deal of genetic diversity within many African populations. For instance more diversity within Yoruba than within Europe. But many African populations are quite similar. For instance divergence between Kikuyu (Kenya) and Yoruba (Nigeria) is just a little more than (Spain, Holland). This is of course caused by the Bantu expansion as Razib explained.

In other words, the great African genetic diversity is more a function of the intra-population variance, than inter-population variance. This sort of work is important for reasons of intellectual interest, but may not be quite so important for GWAS.

Citation: Stefflova K, Dulik MC, Barnholtz-Sloan JS, Pai AA, & Walker AH (2011). Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas PLoS ONE : 10.1371/journal.pone.0014495

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"