Joined: 07 Feb 2007 {Posts: 1876 } Location: Lookin DC Metro, Feelin Geneva
Posted: Tue 22 Dec 2009 15:55 Post subject: New Study on African American and West African Genes
Quote:
Contact: Jordan Reese
jreese@upenn.edu
267-934-9573
University of Pennsylvania
Genetic study clarifies African and African-American ancestry
Collaboration by University of Pennsylvania and Cornell University
IMAGE: This is a photo taken during data collection in Africa.
Click here for more information.
PHILADELPHIA –- People who identify as African-American may be as little as 1 percent West African or as much as 99 percent, just one finding of a large-scale, genome-wide study of African and African-American ancestry released today.
An international research team led by scientists from the University of Pennsylvania and Cornell University has collected and analyzed genotype data from 365 African-Americans, 203 people from 12 West African populations and 400 Europeans from 42 countries to provide a genome-wide perspective of African and African-American ancestry.
The data reveal genomic diversity among African and African-American populations far more complex than originally thought and reflect deep historical, cultural and linguistic impacts on gene flow among populations. The data also point to the ability of geneticists to reliably discern ancestry using such data. Scientists found, for example, that they could distinguish African and European ancestry at each region of the genome of self-identified-African Americans.
Sarah Tishkoff, a geneticist at Penn, and Carlos Bustamante, a computational biologist at Cornell, led the study to analyze 300,000 genetic markers from across the genome from West African, African-American and European-American populations to see whether they could reliably distinguish ancestry.
The team found that, while some West African populations are nearly indistinguishable, there are clear and discernible genetic differences among some groups, divided along linguistic and geographic lines.
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.
IMAGE: Sarah Tishkoff, professor in the departments of genetics and biology at University of Pennsylvania, is collecting samples in Africa.
Click here for more information.
"Africa, which is the homeland of all modern humans, contains more than 2,000 ethnolinguistic groups and harbors great genetic and phenotypic diversity; however, little is known about fine-scale population structure at a genome-wide level," said Tishkoff, professor in the departments of genetics and biology at Penn. "We were able to distinguish among closely related West African populations and showed that genetically inferred ancestry correlates strongly with geography and language, reflecting historic migration events in Africa.
"We were also able to show that there is little genetic differentiation among African-Americans in the African portion of their ancestry, reflecting the fact that most African-Americans have ancestry from several regions of western Africa. The greatest variation among African-Americans is in their proportion of European ancestry, which has important implications for the design of personalized medical treatments."
The study focused primarily on the genetic structure of West African populations, as previous genetic and historical studies suggested that the region was the source for most of the ancestry of present-day African-Americans. The results suggest that there are clear and discernible genetic differences among some of the West African populations, whereas others appear to be nearly indistinguishable, even when comparing more than 300,000 genetic markers. The researchers note that a larger sample size would likely reveal further substructure and diversity between these populations.
Analyzing patterns of population structure and individual ancestry in Africans and African-Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. Understanding ancestry not only provides insight into historical migration patterns, human origins and greater understanding of evolutionary forces, but also allows researchers to examine disease susceptibility and pharmacogenic response, and to develop personalized drugs and treatments, a frontier in public health.
There is also strong reason to believe that high-density genotype data from African and African-American populations may pinpoint more precisely the geographic origin of African ancestry in African-Americans, the researchers said. The study appears online in the Proceedings of the National Academy of Sciences.
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The study was funded by the National Institutes of Health, National Science Foundation, David and Lucile Packard and Burroughs Wellcome Foundation.
Research was conducted by lead author Katarzyna Bryca and Adam Autona of the Department of Biological Statistics and Computational Biology, Cornell; Matthew R. Nelson of GlaxoSmithKline; Jorge R. Oksenberg and Stephen L. Hauser of the Department of Neurology, University of California, San Francisco; Scott Williams of the Department of Molecular Physiology and Biophysics, Vanderbilt University; Alain Froment of the Unité Mixte de Recherche in Paris; Jean-Marie Bodo of the Ministére de la Recherche Scientifique et de l'Innovation in Cameroon; Charles Wambebe of the International Biomedical Research in Nigeria; and principal investigators Tishkoff and Bustamante.
The article says that the report was published in PNAS. But Pubmed says that it was published in Science. That is a shame because PNAS is free and in public domain, while Science is by subscription only and costs money. This means that we cannot download and post a PDF of the complete study (at least, not until someone with a kind heart and a Science subscription sends us a copy).
As to content:
It is interesting that the 18 percent mean of Euro DNA markers in A-As has been holding steady for about 8 years now, having replaced the prior estimate of 25 percent.
I would love to see their scatter diagram or histogram of A-A DNA admixture. I wonder if their measured distribution changes the conclusions of prior studies. The last few studies (by Collins-Schramm, Kittles, and Parra) showed that about 5 percent of the self-identified A-A population lacked any Afro markers at all.
Outstanding! It is in PNAS after all. It has simply not been added to the online indexes yet. The new web page gives the PNAS catalog number. I have retrieved the full-text original study and posted in into this site's archives, from where all members may now download it.
Mary Lee and I are presently leaving to visit our grandkids for Christmas, so I do not have time to catalog the study into our own index right now. I shall do so within the next couple of days, however. (if William does not beat me to it.) Thanks again, DH.
To me, the most interesting and informative figures in the paper are these four. They show the genomes (all 23 pairs of chromosomes) of four "typical" African-Americans. They reveal in the starkest fashion that "African-American" is an umbrella label that includes people of radically different genetic ancestry. In each figure: Red depicts stretches of DNA with Euro markers only. Blue shows DNA with nothing but sub-Saharan Afro markers. And green shows DNA where Euro and Afro markers are intermingled.
Almost pure Afro
The figure above shows the genome of a person of overwhelmingly pure African (or Geechee/Gullah) ancestry. It is mostly solid blue (meaning purely Afro markers) but with a few traces of green (meaning a long-ago blend of Euro and Afro markers). This suggests someone from Africa or the Sea Islands who has a distant ancestor who was mixed.
Afro plus Mixed
The above figure shows the genome of a person with about half pure African (or Geechee/Gullah) ancestry (blue), half long-ago mixed ancestry (green), and traces of pure Euro (red). It is what you would expect to see in the first-generation offpring of an African (or Geechee/Gullah) married to a typical mixed African-American with a White g-g-grandparent.
Euro plus Mixed
The above figure shows the genome of a person with about half pure Euro ancestry (red), and half long-ago mixed ancestry (green). It is what you would expect to see in a Coloured Creole, Puerto Rican, Melungeon, or Redbone.
Almost pure Euro
Finally, the above figure above shows the genome of a person of overwhelmingly pure Euro ancestry. It is mostly solid red (meaning purely Euro markers) but with tiny specks of green (meaning a long-ago trace of mixed Euro and Afro markers). This is either a typical White American, or one of the 5 percent of ethnically self-identified African Americans who have little or no detectable SSA markers.
In short, the figures show more clearly than mere words that "African American" denotes a widely diverse ethnic community, and not a distinct genetic population.
Almost pure Afro
The figure above shows the genome of a person of overwhelmingly pure African (or Geechee/Gullah) ancestry. It is mostly solid blue (meaning purely Afro markers) but with a few traces of green (meaning a long-ago blend of Euro and Afro markers). This suggests someone from Africa or the Sea Islands who has a distant ancestor who was mixed.
Almost pure Euro
Finally, the above figure above shows the genome of a person of overwhelmingly pure Euro ancestry. It is mostly solid red (meaning purely Euro markers) but with tiny specks of green (meaning a long-ago trace of mixed Euro and Afro markers). This is either a typical White American, or one of the 5 percent of ethnically self-identified African Americans who have little or no detectable SSA markers.
I would assume that an "Almost Pure Euro" genome would be the polar opposite of an "Almost Pure Afro" genome. But looking at the two genomes that is not the case. The "Almost Pure Euro" genome does look the part but the "Almost Pure Afro" genome has more of a definite majority of SSA markers but with an impossible to ignore amount of Euro/ Afro intermingled markers on the diagram. So would it be more accurate to label the "Almost Pure Afro" genome something less solid to reflect the small yet substantial amount of Euro/Afro intermingled markers?
I say this because I assume that my own genome diagram would be a polar opposite to that of the "Almost Pure Euro" genome since I have more than 96% SSA (due to a great deal of Geechee/Gullah ancestry).
The "Almost Pure Euro" genome does look the part but the "Almost Pure Afro" genome has more of a definite majority of SSA markers but with an impossible to ignore amount of Euro/ Afro intermingled markers on the diagram. So would it be more accurate to label the "Almost Pure Afro" genome something less solid to reflect the small yet substantial amount of Euro/Afro intermingled markers?
Yes, I agree. Actually, I was the one who applied the label "almost pure Afro" to that figure. The original authors called it "recent admixture" precisely because of all the green. But it was the bluest figure that they published, so I used it to show one extreme. As you say, your own genome would be solid blue with perhaps a barely noticeable fleck of green.
Another interesting point that the article made, by the way, is that "West African" itself can be a slippery term. The Fulani are inhabitants of West Africa and yet they are genetic outliers in all of the scatter diagrams. As has been noted in other threads in this forum, the unique appearance of the Fulani often causes them to be seen as "different" even by the surrounding peoples in their own lands. According to this article, their genes also depict them as a relatively isolated self-contained population.
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