05 May 2010

African-American Population Genetics

Ancestry estimates for 136 African-Americans based upon an examination of genes inherited from both parents. Blue is European in origin; the other colors represent different African subpopulations.

A recent paper looking at the genetic roots of African-Americans through genes inheritable from both parents largely confirms what prior genetic studies looking at paternal and maternally inherited traits and historical studies have shown: (1) the African genetic ancestors of modern African-American are overwhelmingly from a region, roughly speaking South of the Sahara desert, North of the Congo jungle, and West of the Nile Basin, or from Bantu peoples who migrated from there in historic times, and (2) most modern African-Americans have significant European descent although the percentage varies greatly from person to person.

The new study adds a couple of insights, however, that previous studies did not.

The West/Central African Roots of African-Americans

First, it quantifies the extent to which Africa-Americans share genetic roots with Africa's Pygmies and Khoisan, who are ethnically and genetically distinct from the West African populations we normally think of as "black." The average African-American has about 2.2% Pygmy ancestry (equivalent to one or two ancestors six generations ago), and 0.3% Khoisan ancestry (equivalent to one or two ancestors nine generations ago). Thus, African-Americans overwhelmingly have roots in one subset of African populations. This is in accord with previous studies that have found "minimal ancestry from North, East, Southeast, or South Africa."

This is very different from the South African "Colored" population, for example, in which the African component of genetic ancestry is overwhelmingly Khoisan (that population also has an even more pronounced share of European ancestry from parental, as opposed to maternal lines).

While Africa as a whole is very genetically diverse, the subset of Africa from which African-Americans overwhelmingly trace their ancestry is much less diverse.

African-Americans As A West/Central-African Melting Pot

Second, it shows that the African genetic heritage of African-Americans is highly admixed. Every single person in the 136 person study has some genetic ancestry from West Africa, Nigeria, non-West African Bantu populations, and has genes associated with descent from Pygmy populations or Khoisan populations or both.

The mix of African genetic heritages is generally speaking quite similar from one African-American individual to another and shows no biases within African-American populations. African-Americans have similar proportions of ancestry of the most Western African areas, Nigeria, and Bantu speaking populations historically from somewhere near the Nigeria-Cameroon area that migrated elsewhere on the continent during the Bantu expansion. These proportions are more heavily weighted towards Nigeria and populations derived from near there, and are less heavily weighted towards West Africa, by a factor of about three to one.

This is a good fit to historic records which show that "approximately 50% to 60%, derived from Central and Southern West Africa and the Bight of Biafra; approximately 10% from Western Africa; 25% to 35% from the West Coast in between (Windward Coast, Gold Coast, and Bight of Benin), and the remaining 5% from Southeast Africa."

If there were genetic subgroup distinctions in the populations that arrived from Africa, they have largely vanished in the hundreds of years (and dozens of generations) since then. Ethic distinctions among African groups have disappeared in African-American populations who now have an "unstructured" unified population so far as their African ancestry is concerned.

This is consistent with a long period with little immigration from Africa. According to the 2000 census, about 1% of African-Americans were foreign born in that year, with almost all of those immigrant populations being recent. In the 1960 census, about 0.2% of African-Americans were foreign born, and in 1910 about 0.05% of African-Americans were foreign born. In 1850 and in 1860, about 0.2% of African-American slaves were foreign born (i.e. about 80,000 people out of about 4 million) and a little more than 535 non-slaves who lived in the United States were born in Africa.

Probably fewer than 2% of African-Americans today have African ancestry from an ancestor who came to the United States less than 160 years ago, although some of them (e.g., President Obama and Malcolm Gladwell) are well known.

Estimates of European Descent Percentage

Third, it provides another data point for estimating the degree to which African-Americans are partially of European descent. The average amount of European descent in this study of genes inherited from both parents in 136 African-Americans from across the United States, was 21.9%, a standard deviation of 12.2% (thus about two-thirds of the individuals would have a European ancestry percentage of 10% to 33%), and a range of 0% to 72%.

Just one of the 136 African-Americans did not appear to have any genetic signs of European descent; eight has 45% or more European ancestry (eyeballing the table, about five of the 136 African-Americans had 50%-72% European ancestry).

This is generally in line with prior studies:

Numerous studies have estimated the rate of European admixture in African Americans; these studies have documented average admixture rates in the range of 10% to 20%, with some regional variation, but also with substantial variation among individuals. For example, the largest study of African Americans to date, based on autosomal short tandem repeat (STR) markers, found an average of 14% European ancestry with a standard deviation of approximately 10%, and a range of near 0 to 65%, whereas another study based on ancestry informative markers (AIMs) found an average of 17.7% European ancestry with a standard deviation of 15.0%. By using nine AIMs, Parra and colleagues found substantial variation of European ancestry proportions in African-American populations across the United States, ranging from just over 10% in a Philadelphia group to more than 20% in a New Orleans population. Similar levels (11% to 15%) of European ancestry also were reported by Tishkoff and co-workers, based on more than 1,000 nuclear microsatellite and insertion/deletion markers. . . .

Prior studies focusing on mtDNA and Y chromosomes have found a greater African and lesser European representation of mtDNA haplotypes compared with Y chromosome haplotypes in African Americans, suggesting a greater contribution of African matrilineal descent compared with patrilineal descent. For example, Kayser and colleagues estimated that 27.5% to 33.6% of Y chromosomes in African Americans are of European origin, compared with 9.0% to 15.4% of mtDNA haplotypes.

American and Asian Roots

This particular study did not attempt to identify the proportion of African-American descent that can be traced to Native Americans, although that proportion is non-zero (one recent estimate was of 3% maternal Native American ancestry, and 0.6% paternal Native American ancestry, while other genetic studies have put estimates of Native American ancestry component as high as 3% of total African-American ancestry based on ancestry indicative markers and more in areas with high Native American and Hispanic populations.

This study was also not designed to detect Indonesian or Asian ancestry, which was likely to be present in a significant share of the roughly 5% of slaves arriving in the Americas from Madagascar and Southeast Africa. The Madagascar side of Southeast African is atypical of the rest of Africa: "Malagasy peoples are a roughly 50:50 mix of two ancestral groups: Indonesians and East Africans." Some Indonesian ancestry (primarily from Borneo in the Malagasy population) would probably be confused for Native American ancestry in a genetic test that did not acknowledge the possibility of Indonesian ancestry.

A back of napkin estimate would expect that roughly 1% of African-American genetic ancestry would be from Indonesia and that this genetic heritage would be widely distributed in the African-American population. This happens to be a percentage that would neatly fit the discrepancy between the Native American ancestry predicted based upon paternal and maternal specific genetic markers and those based on ancestry indicative markers inherited from both parents, although the hypothesis that this explains the different is only a suggestive hypothesis.

One would also suspect some Asian ancestry in modern African populations via Afro-Caribbean immigration (which also probably have a larger share of Khoisan ancestry than African-American populations due to nature of the common slave trade routes from the 16th to 19th centuries).

Of course, some people who could be classified as African-American (e.g. Tiger Woods) have far more recent Asian ancestry than descendants of slaves from Madagascar.

American servicemen fathered tens of thousands or more children with mothers across Asia during periods of U.S. military presence in Asia from World War II onward (about 52,000 in the Philippines alone), some coming to the U.S. as part of intact families, and many more left behind. More than 8,000 those left behind eventually made their way to the United States. A significant subset of Amerasians in the United States, corresponding to the make up of the American military, have African-American paternity. Amerasians probably account for less than 0.01% of African-American ancestry in the United States, but descendants of U.S. servicemen probably account for quite a large share of all people of African-American ancestry outside the United States.

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