Gene Expression

I referenced a paper in PNAS yesterday, and I thought it might be good to actually point to it today. There’s nothing that new in the paper. It confirms the finding that ~20% of the ancestry of African Americans is European, and, that African ancestry seems to be much more dominant when it comes to components of the genome presumably disproportionately contributed by females (2/3 of X chromosomes). In any case, the paper, Genome-wide patterns of population structure and admixture in West Africans and African Americans:

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study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

One of the value-adds from this paper is that the authors explored how African Americans related to disparate African populations. The historical records indicate that American slaves arrived disproportionately from the regions to the west of the Bight of Bonny. In other words, black Americans derive predominantly from the non-Bantu populations of West Africa, from Senegal down to Nigeria. This is in contrast to Brazil, where the black population was reputedly of more diverse origin, including many Bantu speakers from Angola as well as West Africans.

I reedited part of figure 1 to show which African groups are in the study and how they relate to each other genetically:

i-5594f4a37b1e374ae03490066df8be88-africangroups1.png

That the Fulani are atypical in this set of populations is not that surprising. They clearly have some Eurasian connections, including the a Eurasian version of the lactase persistence. The historical background behind this is also easy to pinpoint, the Almoravid domain spanned southern Spain to the Sahel, while more generally the Tuareg and Islamic orders helped mediate gene flow north and south of the Sahara.

But even without the Fulani there is still some genetic variation which maps onto to ethno-cultural clusters. Along one axis seems to be the “Bantu Expansion,” which scholars presume originated in eastern Nigeria. The second axis seems to point to a difference between West African & Bantu groups, and Nilo-Saharan groups. The differences are also evident in a FRAPPE derived plot. Again, K = # of putative ancestral groups:

i-49554b78ce2906bea1f908e470929381-africangroups2.png

Panel A opens up the floor to a lot of discussion on how the Hausa identity in particular emerged, and the historical processes which led to the current Fulani genetic relationships. The Fulani language belongs to the Niger-Congo group, along with the Yoruba, Igbo and all the Bantu dialects. The Hausa language is Afro-Asiatic, like Arabic and Hebrew. But more importantly, the genetic structure seems explicable in light of the PC charts.

This is important because of panel’s E & F. Note the lack of variance of the “blue” component of ancestry among African Americans, which resembles what you see among the Yoruba. So it seems that African American ancestry which is non-European is from groups like the Yoruba genetically, by and large. Also, K = 4 seems to suggest that African American European ancestry is mostly from the populations of northern Europe, which comports what the historical record, as southern European waves of immigration generally post-date the ethnogenesis of a black American identity.

Here’s a PC chart from figure 2 which shows how African Americans relate to the various groups above:

i-e1fe5d181884626a0938c2380af0bc63-africangroups4.png

The authors conclude:

several important points. First, patterns of genomic diversity within Africa are complex and reflect deep historical, cultural, and linguistic impacts on gene flow among populations. These patterns are discernible using high-density genotype data and allow us to differentiate closely related populations along linguistic and geographical axes, even with limited sample sizes from many of our populations. Second, admixture can be reconstructed for local genomic regions efficiently at a high density of genetic markers. For this study, we tailored the method to admixed populations with two ancestral source populations, but the approach is generalizable to multiple populations. Application of the method to genome-wide patterns of genomic variation in African Americans reveals the rich mosaic structure of admixture in this population. We find that we can distinguish African ancestry among West African populations to a large degree (e.g., Bantu from non-Bantu Niger-Kordofanian populations) but that some populations (e.g., Igbo, Yoruba, and, to a lesser extent, Brong) are so closely related genetically that their contribution to patterns of African ancestry in African Americans is not reliably distinguishable. We believe that increasing the density of markers and, more importantly, sequencing directly in these populations to identify ancestry informative markers may make this possible in the future.

Citation: Katarzyna Bryc, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean-Marie Bodo, Charles Wambebe, Sarah A. Tishkoff, and Carlos D. Bustamante, Genome-wide patterns of population structure and admixture in West Africans and African Americans, doi:10.1073/pnas.0909559107

Comments

  1. #1 toto
    December 23, 2009

    The hopeless counter-intuitivity of PCA, part n….

    On the 1st PCA plot, the Bantu gradient is almost invisible – all Bantu groups + Yoruba cluster together, but a Nilo-Saharan gradient stands out.

    Yet on the 2nd PCA plot, the Bantu gradient becomes the 1st principal component. The Nilo-Saharan gradient is still there, but as a 2nd PC.

    Is there some deep message related to some relationship between Peuls and Nilo-Saharans, or is it just statistical weirdness?

  2. #2 razib
    December 23, 2009

    toto, good point. it seems counterintuitive. but if the fulani are removed out of the data to generate the PC chart, you don’t necessarily know how the dimensions are going to come down. the second nilo-saharan component is probably different than the first since the fulani are no longer in the data set.

  3. #3 Crio
    December 24, 2009

    It would be interesting to see this kind of ancestry data with the subject’s IQ scores, to see what correlations emerge. I wonder why Jensen, Lynn, etc have not done such a study?

  4. #4 Oh
    December 27, 2009

    i wonder if they considered the distribution of Amero-Liberian bloodlines into that region. Many African groups have African-American bloodlines stemming back two centuries. Many of those families brought over European, and/or Native American bloodlines.

  5. #5 JonesHepkinz
    December 27, 2009

    What would be the relevance of researching correlations between this fascinating ethnicity data and IQ? How pathetically irrelevant. Jensen? Surely you jest. The current study is derived from scientific technology that would not have been available during Jensen’s reign of disinformation. Thank God.

  6. #6 truthandjusticeforall
    December 27, 2009

    I concur with JonesHepkinz what is the point and how is the relative to the status of African in the Diaspora? Will this change the racist views of African-Americans, will it stop injustice and racist activity? I feel that these studies only validate our existence over the millineum’s before European existence. Yes, today, many African’s are mixed, but that is because of the 600 years of the Trans-Atlantic Slave Trade. Still, what isn’t being studied should be studied, for example, why do Europeans feel that they are superior to African-American’s and African’s in general of all the populous in the world. Seems that they take a liking to us African’s that they want to destroy us genetically, why? Any brain studies on this subject? I only say this because they like to use studies like the above-mentioned studies to state their egoic theory that they are smarter than African-American’s, which we know that is not the case, nor has it ever been. However, still they like to amuse themselves with their lies…

  7. #7 Diamondz
    December 27, 2009

    Really I am at the tender age of 13, and I’ve always known that every single race originated from Africans.It saddens me that only a small amount of people have figured this out.But even with scientists proving this fact, that can put an end to so many prejudices, there is still racism against the beginning race of mankind.I ask you will racism ever cease?Or will this horrible trait among our dim-witted brotheren continue to edure?I hope that in my lifetime this disease of the mind will end.But as long as people with minds filled with prejudice are on this green Earth my dream will only be that a dream.

  8. #8 Ishefa
    December 27, 2009

    Here is one recent article of an African-American women who found her African ancestors not in Nigeria but Niger and discovered them to be Hausa (from Mali) and Fulani.

    http://mamiwatahealers.wordpress.com/ancestral-journey/

  9. #9 patrick
    December 27, 2009

    The Americo-Liberians to my knowledge mostly intermarried among themselves rather than with native Africans, at least until recent times.

  10. #10 B.B.
    December 27, 2009

    JonesHepkinz says:
    Jensen? Surely you jest. The current study is derived from scientific technology that would not have been available during Jensen’s reign of disinformation.

    Jensen’s reign hasn’t ended yet. He is still publishing articles in peer-reviewed journals.

  11. #11 B.B.
    December 27, 2009

    B.B.
    He is still publishing articles in peer-reviewed journals.

    Slight correction: The hyperlink goes to articles written by another AR Jensen, at the University of Washington. I thought they were from the same guy because the article were about assessment of technical skills (i.e psychometric research). Nonetheless, Arthur R. Jensen has published work in journals as late as 2008, and wrote his latest book in 2006.

  12. #12 Mr. Payne
    December 28, 2009

    So,I am curious as a white man where do we come from if Africans where here first, what are we genitally modified from the Africans DNA or something?

  13. #13 Surely they jest
    December 28, 2009

    So,I am curious as a white man where do we come from if Africans where[sic] here first, what are we genitally modified from the Africans DNA or something?

    It’s called evolution. A neat little science concept you should become familiar with!

  14. #14 RossM
    December 28, 2009

    I wonder how keen your correspondent Crio would be to examine why north Asians (Japanese in particular) have, on average, much higher IQs than white north Americans?

  15. #15 RNAzipper
    December 28, 2009

    “It would be interesting to see this kind of ancestry data with the subject’s IQ scores, to see what correlations emerge. I wonder why Jensen, Lynn, etc have not done such a study?”

    Here we go again, back to IQ. I contend that those so obsessed with Sub-Sahran IQ’s are surely trying to mask an inadequacy in European make-up, namely genetic disorders such as Tay-Sachs, ALS, Down Syndrome, etc., that are prevalent in Europeans and seen at a much lesser rate in Africans. How come no one talks about these things and instead are obsessed with trying to prove blacks to be brainless animals? No one is calling Europeans deformed mutants with bad genes so what is the point?

    Jensen and his ilk need to look at how many AFRICAN doctors, scientists, engineers there are compared to AA’s who have a higher rate of white ancestry. How come Africans are the most educated immigrant group in the US? These are more important tests to do instead of perpetuating beleifs that society itself are showing to fall flat.

  16. #16 osmanlı iksiri
    December 29, 2009

    Really I am at the tender age of 13, and I’ve always known that every single race originated from Africans.

  17. #17 Crio
    December 29, 2009

    RossM,
    I’m very “keen” on it. Any layperson with any familiarity in psychometrics know that Asians and Jews have the highest IQ’s. The data speaks for itself.
    Just what kind of person do you think I am, anyway? Why would I not be “keen” on it?

    RNA zipper,
    this article might shed some light on possible reasons for the prevalence of certain genetic brain disorders in some populations: http://www.latimes.com/news/nationworld/nation/la-sci-jewish-iq18-2009apr18,0,2228388.story

    Also, within any population, there are those who get lucky genetically to become much brighter than their coethnics. I would think such exceptional cognitive specimens would be much more likely to leave impovershed, violent, dysfunctional societies [like those found all over the continent of Africa] as immigrants. Good for them.

    Why, one may ask, are these sorts of discussions productive? What good can come of it? Well, for starters, by acknowledging human biodiversity, we can prevent social travesties inflicted on our society by blank slate egalitarians. Like this: http://www.eastbayexpress.com/ebx/berkeley-high-may-cut-out-science-labs/Content?oid=1536705

  18. #18 RNAzipper
    December 29, 2009

    Crio

    Thanks, but I also encourage you to study the violent and dysfunctional nature of colonial brutality and Nazi psychosis as well. Please study the dysfunction of Caucasion serial killers and pedophiles who travel the globe looking for underage children. While you are at it, please research the high rates of psychological disorders in Europen Americans and how they are twice as high as those Africans living in “violent and dysfunctional societies.” Maybe, then we could truely lay the foudation for an egalitarean society. I would love to peer-review it.

    Best of Luck.

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