December 06, 2014

African Genome Variation project paper

A choice quote:
To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST = 0.027) may be a remnant of East African diversity pre-dating the Bantu expansion10.
I think this should be highlighted for a couple of reasons.

1. In too many papers to count, decreasing genetic diversity from East Africa was taken as evidence of an origin of H. sapiens in that locality and its expansion from there to Eurasia. This "East Africa=cradle of mankind" theory has, as far as I can tell, nothing really to stand on. Granted, the oldest anatomically modern human remains have been found in East Africa 200-150 thousand years ago. But, the fact that old sapiens have been found in East Africa and not elsewhere is easily explained by the excellent conditions for preservation (as opposed, e.g., deserts or rainforests of Africa or elsewhere), and by the extraordinary effort by palaeoanthropologists in that area. One also needs to overlook a century of physical anthropology that concluded that East Africa was a contact zone between Caucasoids and Sub-Saharan Africans. We now know that there is no deep lineage of humans in modern east Africans. Take out the Eurasian ancestry and only a paltry Fst=0.027 remains with other Sub-Saharan Africans, a fraction of the Fst between, say, Europeans and East Asians.

2. There has been enormous literature about phenotypic variation in Africans. The ultra-migrationism of old was replaced by ultra-selectionism that sought to explain every phenotypic marker of Eurasian admixture in Africa not as evidence of such admixture, but as a parallel process of evolution whereby some Africans tended to resemble some Eurasians not because of admixture but because of adaptation to similar environmental conditions.

This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6).
This study also confirms the presence of Eurasian admixture in the Yoruba
Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.

Nature (2014) doi:10.1038/nature13997

The African Genome Variation Project shapes medical genetics in Africa

Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, et al.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.



bellbeakerblogger said...

Dinekes: to your point #2.

A perfect example out this week regarding African specific allies for lactase persistence...

Hyper-evolution does not explain lactase persistence in people who only recently adopted pastoralism. All of the varients are probably Near East derived and came into being with the advent of the Middle Pastoral period.

bicicleur said...

cattle arrived in Africa 6-8000 years ago, probably from Anatolia, along with haplo T and R1b-V88.
cattle couldn't reach Central Africa because of infection by the tse-tse.
probably due to some climate change, there was a corridor free of tse-tse in eastern Africa, and so cattle reached South-Africa 2000 years ago, before the arrival of Bantu.

eurologist said...

But can one really simply mask Eurasian ancestry, or does that method not throw out the possibility, by design, that many of these SNPs are part of the original African diversity?

Grognard said...

Glad this study was made. You can just look on a PCA chart and tell this is the case.

It is wildly unpopular these days, but the truth is there was no out of africa, it's a fantasy made up with no evidence to back it up in archaeology.

We have tons of evidence of migrations into africa however. The only reason this myth continues is political propaganda.

HabariTess said...

As for your number 2 point, keep in mind that while the study claim that the variation could be due to the Eurasian admixture, they also claim that their is also evidence FOR local adaptation.

Also, this study did not include the South African Lemba people, who, frankly, blow that theory out of the water. Not only do the Lemba people have a substantial amount of (western) Eurasian genes(at fifty percent), they have it at a higher percentage than the Beja, Fulani,somali, and many Ethopian ethic groups whose appearance are always in question. The Lemba look NO different from their neighbors, which suggest that the centuries upon centuries of living and mixing with the local African population had altered their appearance to fit completely with the local populations. This could also suggest that the appearances of many Horn African populations is natural and not due to admixture, and the Eurasians who migrated to the Horn over a thousand years ago eventually took on the appearance of the local population.

It does not make sense for the Lemba to look so much like other Zimbabweans and have such a high percentage of Eurasian genes, than make the claim that the Horner Africans look the way they do due to admixture, especially when it is much less than the Lemba( Example, the Beja is said to be about 30% eurasian). "Local adaptation" is the most likeliest theory for African variation.

Mike B said...

"Some Africans tended to resemble some Eurasians not because of admixture but because of adaptation to similar environmental conditions."

Do you references to provide? I would be interested to have a look.

Thanks for your blog, which is a nice source of information.

Grizzlor said...

Let me get this clear. Are Dienekes, and most users on this site, proponents of the "Out of Europe" model or just the Classic Multi-regionalism (modern races evolving from different homo-species druing millions of years of separation)? Just to have an idea what I'm dealing with.

Tobus said...

there was no out of africa, it's a fantasy made up with no evidence to back it up in archaeology.

Except for a myriad of African AMH fossils dating back ~200ky of course.

We have tons of evidence of migrations into africa however.

As this paper shows, Africa was already populated when these migrations happened.

Dr. Clyde Winters said...

@Grognard please post the archaeological evidence of a back migration into Africa. The archaeological evidences points to numerous African migrations into the Levant--not the otherway around

@bicicleur where is the evidence that hgs V88 and T entered Africa from Anataolia with Middle East farmers. The earliest African groups were cultivating millets, not wheat like Middle East people. Moreover, between 20-10kya the people of the Levant were probably sub-Saharan Africans.

Trenton W. Holliday, tested the hypothesis that if modern Africans had dispersed into the Levant from Africa, "tropically adapted hominids" would be represented in the archaeological history of the Levant, especially in relation to the Qafzeh-Skhul hominids.

This researcher found that the Qafzeh-Skhul hominids (20,000-10,000),were assigned to the Sub-Saharan population, along with the Natufians samples (4000 BP). Holliday also found African fauna in the area.
Below are a few quotes from the paper by Holliday they show that the population at this time were Negroid in Southwest Asia.

Holliday noted, "In this light, some of the more robust assignments (albeit not 95% of the Qafzeh-Skhul hominids to the sub-Saharan African sample (e.g., Qafzeh 8 at 85%, Skhul 4 at 71%) are remarkable indeed" (p. 62).

"The Qafzeh-Skhul hominids have sometimes been refered to as "Proto-CroMagnons" (e.g., Howell 1957; Vandermeersch 1996) because of their presumed similarity to the famous Aurignacian-associated hominids from Western Europe....Specifically [Brace], he notes that "in both the details of its dental and craniological size and from Qafzeh is an unlikely proto-Cro-Magnon, but it makes a fine model for the ancestors of modern sub-Saharan Africans"(p.63).

Holliday (2000) said, wrote "taken as a whole, the work of Tchernov seems to support the findings of the current research that the Qafzeh-Skhul hominids have their origins in Africa, while the Neanderthals are from cold to temperate biomes"(p.64).

Holliday (2000) noted that"The current study demonstrates African-like affinities in the body shape of the Qafzeh-Skhul hominids. This finding is consistent with craniofacial evidence (Brace 1996) and with zooarchaeological data indicating the presence of African fauna at Qafzeh (Rabinovich and Tchernov 1995; Tchernov 1988, 1992)" (p.64).\

Holiday, T. (2000). Evolution at the Crossroads: Modern Human Emergence in Western Asia, American Anthropologist,102(1) .

Given the archaeological evidence sub-Saharan Africans in the Middle East founded agriculture and cattle herding. Given the archaeological evdence hg R, was probably introduced into Eurasia by the Sub-Sahran Africans who maintained sub-Saharan flora and fauna in the Levan tetween 10-20kya.

Dobba Makale said...

Sorry for asking out of topic question, is it an established fact that African-Americans/blacks have denser bones than Caucasians and Asians?

Dobba Makale said...


Sorry for asking out of topic question. Is it true that Blacks (i.e Afro Caribbeans and African-Americans) have denser bone than Caucasians (i.e European-Americans)? Some studies have been conducted on bone mineral density among different races and they found Blacks (Afro Caribbeans and African-Americans) have the densest bone, with Afro Caribbean have even denser bone than African-American. But I doubt it because almost the majority of strongmen and powerlifters are of Caucasian origin, which mean they actually have the densest bone, much more than Blacks.


eurologist said...

"Let me get this clear. Are Dienekes, and most users on this site, proponents of the "Out of Europe" model or just the Classic Multi-regionalism"


AFAIK neither. There is just pretty good stone tool, some fossil, and also some genetic evidence ("Basal Eurasian" component) that ooA took place during the wet period ~105 - 125 thousand years ago, and not as recent as 60,000 ya (the then-hostile dry period makes that highly unlikely, anyway).

Western Eurasians likely back-migrated into Africa multiple times since the UP.

German Dziebel said...


"Except for a myriad of African AMH fossils dating back ~200ky of course."

None of those fossils have usable DNA in them, the anatomical definition of AMH is fuzzy, and there're no signs of modern human behavior around them. So all this "evidence" is just a wash. It's only good for fans of sacred relics such as yourself.

Grey said...

I'd have thought the Bantu expansion itself might have erased a lot of the diversity that existed prior?

If so later migrations from Eurasia would seem a likely source of the current diversity.

(Although at the same time that wouldn't prove anything about the diversity that existed before the Bantu expansion.)

Tobus said...

@German: None of those fossils have...

But all of those fossils *do* actually exist - more than can be said for any of the alternate "Out Of My Arse" theories out there.

Annie Mouse said...


No idea of the original source but looks real.

Fits with this actual refereed paper.

Dobba Makale said...

@Annie Mouse

I have already read all the studies and researches done on the bone mineral density between different races including the link that you had given. But I still doubt it. So Blacks always have denser bones than Whites? Or is this just in general that Blacks have denser bones than Whites, Hispanics and Asians?

Mark Moore (Moderator) said...

@Dobba I distinctly remember reading a report some years ago where the researcher said that blacks tended to have a higher bone density than whites EXCEPT FOR RED HEADS. I can't find that study but aren't humans odd creatures?

German Dziebel said...


All those fossils do exist....

In your apocalyptic world, all the fossils were found by the year 2000. But fossils are not saints' relics carefully preserved for future generations. In my scientific world, we have thousands of years ahead of us to find fossils and just imagine how many denisovan like pinkies are strewn all over Eurasia and America. Nothing to build a theory on just 200 years into the onset of fossil hunting.

Dobba Makale said...

@Mark Moore (Moderator)

Of course humans are very odd lol. But I think the people with densest bone, regardless of their race, are powerlifters and weightlifters. And if you see them, most of them are Whites. Thoughts?

Bronze said...


No, your argument with the Lemba does not hold any water, just because one population has more foreign admixture than another does not mean it will look more admixed than the population with less admixture.

This is common sense just by looking at individual african americans and their genetic composition results, many of them who look more negroid/african actually has higher european admixture compared to others who can look very admixed while being mostly negroid in ancestry.

The phenotypical variation observed in modern african populations is without a doubt the result of euroasian admixture from ancient backmigrations, and not local adaption.

@Clyde Winters

Wrong, levantine populations from the neolithic and earlier, most certainly did not look sub-saharan african at all, they would have been genetically and phenotypically unrelated to sub-saharan populations. In fact the first humans who migrated out of africa during OOA did not look like modern africans/negroids.

And there is plenty of evidence confirming many back migrations into Africa where euroasian men mixed with local african women.

Dobba Makale said...


Many people portray Homo sapiens idaltu look like Negroid/African. You can see the images of reconstruction of Homo sapiens idaltu on the Google images. Some people also try to reconstruct the first European and they also tend to look like Negroid, once again we can see it on Google images. Do they really even look like Negroid?

Tobus said...

@German: In my scientific world, we have thousands of years ahead of us to find fossils and just imagine how many denisovan like pinkies are strewn all over Eurasia and America

I see the problem - when I say "evidence" I mean things that *actually exist*, not things that someone might *imagine* existing in some possible future.

Dobba Makale said...


Sorry once again for asking out of topic question. If the BMD (Bone mineral density) measurements of a group of Black men are 1.30 ± 0.12 and 1.25 ± 0.10, what is the bone density mineral of a single Black individual (man)? Thanks.

Grognard said...

@ Dr. Clyde - Hi Clyde, there's tons of migrations into africa. That doesn't prove there was no out of africa, but if there was it was probably going much further back.

Nubian complex is now shown to go from arabia into africa.

Berbers went into africa as well. Arabs after them. Before that mechtoids, about 20k years ago, who came from iberia. Aurignacian (neanderthal) culture also spread out from europe into north africa.