March 22, 2012

Projecting Sub-Saharan Africans on the European-East Asian axis

Continuing my exploration of Sub-Saharan origins, I projected African populations onto the Principal Components created by a set of European and East Asian populations. The set of SNPs was ascertained on a San individual, as before, and 112 European/110 East Asian individuals were used to avoid sample size issues.

Note that projecting populations onto PCs generated by other populations tends to make the projected populations regress to the mean somewhat. Overall, it appears that African populations are strongly shifted to the European side of the fist principal component.

There is a dearth of haplogroups of Sub-Saharan origin in Europe. Most of them occur as outliers, and in small percentages. Hence, the very strong shift of African populations towards Europeans cannot be ascribed to occasional African admixture in Europe.

Y-haplogroup E is the only major link between Africa and Europe, which is not also shared by Africa and East Asia. But, this haplogroup occurs at very small frequencies in all the included European populations, and at quite variable frequencies overall. As McEvoy et al. correctly observed, even Y-haplogroup E devoid European populations exhibit a closeness with Africans not shared by East Asians.

If admixture with Y-haplogroup E bearing males in Europe cannot account for the relative closeness of Africans to Europeans, what does? As I have mentioned in my review of McEvoy et al., there are two possibilities:

  • An Asian component not shared by Eurafricans is actually pulling East Asians away from Europeans and Africans. With the discovery of Denisovans and archaic-leaning Red Deer Cave people, this is a possibility that must be seriously entertained.
  • Y-haplogroup E bearers were originally closer to West than to East Eurasians. This is also quite likely, since the origins of haplogroup E are traced to East Africa from DE-bearing ancestors who may have well lived in Eurasia; Asia possesses both sister clades E and D, as well as both sister clades DE and CF one level-up. But, even if DE originated in East Africa itself, we must remember that the population there was originally different than many of the current inhabitants of the region, and may very well have been genetically closest to the emerging Proto-Caucasoids of the adjacent regions of Asia, rather than to the more distant human populations that would ultimately evolve into the East Asians of today.
I tend toward the second explanation -because of the relatively shallow divergence times between East Asians and Europeans, and the lack of any archaic Y-chromosomes/mtDNA. It is hard to imagine such a strong divergence being explained by a little archaic admixture in East Asia.

22 comments:

Lank said...

I wonder how this would look with other ascertainment panels. I don't know what the point is in basing this kind of PCA on SNPs ascertained on the San?

I'm still not convinced that West Eurasians are closer to Sub-Saharan Africans (excluding East Africans) than East Asians are. I don't think PCA and ADMIXTURE are the proper tools for deciding that either. Reich et al. (Table S6.2 in the Supplementary Information) didn't find any West Eurasian shift for the San or Yoruba, despite the slight shift of the Yoruba toward Neanderthals, relative to the San. The Neanderthal shift could be explained by ancestry from undifferentiated (DE or CT?) Eurasians in the Yoruba, or archaic admixture in the San from hominins more distant than the Neanderthal-AMH common ancestor.

Also, there are no West Eurasian Y-DNA and mtDNA lineages in native West Africans. If Y-DNA E1b1 was spread by an East African population with West Eurasian admixture, then it's strange that the Yoruba lack any mtDNA lineages associated with West Eurasians (which are found in modern East Africans). The only way that could be explained would be an extreme founder effect, which would probably mean little to no autosomal West Eurasian ancestry in the Yoruba.

Dienekes said...

The simplest explanation is that native East Africans and Caucasoids of the Near East were once genetically very close.

Which makes sense, given that they're next door neighbors and live closer to each other than Caucasoids are to East Asians, or East Africans are to people of the interior of Africa.

So, the expansion of these "Caucasoid-like"/"Proto-Aethiopid"/name-them-as-you-will people from East Africa probably accounts for the pattern. The genetic proximity between this group and Caucasoids could be due to the back-migration of YAP-bearers into Africa.

From the staging point in East Africa, these people swamped the continent with their Y-chromosomes, and -presumably- a good portion of their autosomal DNA, leaving a few A/B remnants behind.

German Dziebel said...

"there are two possibilities...I tend toward the second explanation"

Why not both? Plus if you include Amerindians, with their stronger connection to Neanderthals than Asians have and an ambiguous position vis-a-vis West and East Eurasians (preceding this split if we observe that Amerindians don't have Y-DNA DE or possessing both West and East Eurasian components as in mtDNA hg X vs. ABCD), won't it create a stronger pull away from the African-Caucasoid continuum?

Lank said...

You need to be more specific. Obsolete physical anthropology terms don't allow me to understand what you mean. Which mtDNA lineages do you propose were spread by this hypothetical East African population?

You've previously stated that you don't believe the results of your experiments can be explained by African structure, pre-OOA. So I can only assume you believe the early E carriers carried M and/or N. The lack of these lineages in West Africa is truly peculiar if they were common in the population that spread E1b1 to West Africa.

Suppose that L3 is of Eurasian origin, as you seem to believe for some unknown reason, and that E* males migrating into Africa were accompanied by L3(xM,N) females. East Asians are mtDNA M and N, just like West Eurasians. There's no reason why West Eurasians should be more similar to early L3(xM,N) populations than any other Eurasians.

Dienekes said...

I believe L3 is of Eurasian origin, not for "some unknown reason", but because there were modern humans in Eurasia before 100,000 years ago, spread in a wide area, and they could not have conceivably been replaced by an (archaeologically wholly invisible) expansion OoA c. 70,000 years ago.

So I can only assume you believe the early E carriers carried M and/or N.

I don't see why they would. They probably carried some of the East African L3 types that were spread around by them apparently into other parts of Africa.

The lack of these lineages in West Africa is truly peculiar if they were common in the population that spread E1b1 to West Africa.

And, so is -entirely symmetrically- the lack of East African mtDNA in Eurasia, if E was spread by people who had L3(xM,N) lineages originally.

In fact, there is no mtDNA counterpart to haplogroup E; it can be found on top of quite different mtDNA gene pools from South Africa to Europe, and I see no real reason to think that whatever event its success corresponds to involved a lot of female migration.

apostateimpressions said...

Is it possible that the slight 'African' admixture identified in southern West Eurasian populations is in fact a relic of the proto-Eurafricans? Perhaps ADMIXTURE identified the component as African because there has been less evolution in Africa over the last 100,000 years, given the environmental circumstances, and the signal is now stronger there.

Dienekes said...

@apostateimpressions,

1. There's no 'African' admixture in "southern West Eurasian populations" identified here
2. There's no ADMIXTURE here

Either you posted in the wrong post, or you need to re-read it.

Lank said...

I don't see why they would. They probably carried some of the East African L3 types that were spread around by them apparently into other parts of Africa.

I don't see how ancestry from an early Eurasian population carrying mtDNA L3(xM,N) could result in the specifically West Eurasian affinity you suggest exists.

And, so is -entirely symmetrically- the lack of East African mtDNA in Eurasia, if E was spread by people who had L3(xM,N) lineages originally.

Y-DNA E in Europe is recently derived from E1b1b1 Africans. The mtDNA they brought along has nothing to do with the mtDNA of the early E carriers, who preceded them by tens of thousands of years.

The mtDNA spread by E1b1b1 carriers in Eurasia was probably a mixture, as the East African gene pool was no longer simply L3(xM,N) at the time. Y-DNA E was not particularly successful in Eurasia during its initial migration into the Middle East. Subsequent genetic drift in Europe during the Neolithic, most obviously in the Balkans, is the reason for the rarity of mtDNA and autosomal affinities that can be attributed to the first E1b1b1 carriers in Europe.

In fact, there is no mtDNA counterpart to haplogroup E; it can be found on top of quite different mtDNA gene pools from South Africa to Europe, and I see no real reason to think that whatever event its success corresponds to involved a lot of female migration.

I believe it did. I agree with you that the expansion of E1b1 within Africa was probably accompanied by L3 females. There were apparently two waves of L3 expansion into West Africa; one has been dated to 35-40 kya, and the other to 8-10 kya. The expansion of mtDNA L3 and Y-DNA E-M2 into South-Central Africa is quite recent, a result of the Bantu expansion. Finding mtDNA L3 in hunter-gatherers isn't difficult because E-M2 Bantus didn't bring any females with them, but because of sex-biased gene flow.

apostateimpressions said...

D, I was just suggesting that the findings of this thread could help us to interpret the findings of another thread. Sorry if the threads are not convertible.

Onur said...

Dieneke,

In your previous experiment Sub-Saharans fell along a cline towards Europeans while Europeans formed a tight group (except the obviously Mongoloid admixed ones like Russians and Adyghe). But in this experiment the reverse is the case, so, for instance, non-Sardinian Italians show up closer to Sub-Saharans than French are, who in turn show up closer to Sub-Saharans than Orcadians are. Do you know what made the difference (I ask this to you because as of now you should be quite experienced at making and interpreting PCA analyses)?

Maju said...

On one side, this test would appear to support your view of Africa-WEA special affinity but, on the other side, it contradicts your previously stated idea (Coon's?) of "Negroids" being a mixture of West Eurasians and Pygmies, because here Pygmies are at the same relative location as other Africans.

It's very inconclusive. There's something to ascertain but I still think that the answer is not so simple and that it has more to do with more or less continuous contact (at low levels which leave almost no trace) between Africa and West Eurasia, contact that East Asia has lacked.

Onur said...

Geographical proximity of West Eurasia and Africa pretty much explains these results. Unfortunately, the details of the contact between West Eurasia and Africa are lacking to a large extent, at least for now. But one thing is clear: Caucasoids, Mongoloids and Negroids are genetically (and not just physically) well differentiated from each other to constitute distinct races (admixture between races and contact zones between them do not refute the existence of races, even subspecies have such qualities).

Unknown said...

Using SNPs ascertained from San probably isn't the best route to go, but anyways moving on:


>>>>>I believe L3 is of Eurasian origin, not for "some unknown reason", but because there were modern humans in Eurasia before 100,000 years ago, spread in a wide area, and they could not have conceivably been replaced by an (archaeologically wholly invisible) expansion OoA c. 70,000 years ago.

I don't see how this supports a Eurasian origin for L3 and given the fact that the ages for haplogroup M and N are even much younger and the huge diversity of L3 lineages within African itself don't make any strong case for an Eurasian L3 origin.

Dienekes said...

>> Using SNPs ascertained from San probably isn't the best route to go, but anyways moving on:

Why not? Which is the best route to go?

>> given the fact that the ages for haplogroup M and N are even much younger

They are not "much younger", their ages are actually statistically indistinguishable with the oldest African lineage

http://dienekes.blogspot.com/2011/11/age-of-mtdna-haplogroup-l3-about-70.html

Onur said...

Dieneke, what are the variation percentages of the first two principal components of your this and previous PCA anlyses?

bmdriver said...

Amazing always read how South asia is completely avoided because those results WOULD affect the picture


Africa, to central asia, west asia, and from their to EAST asia, but NO south asia.

lol

and the reason because they are an admixture, and they think no one else is!..or it could it be, it blurs the line of what West asia really means.

Onur said...

bmdriver,

South Asians are both genetically and physically well differentiated from West Asians (the significant ASI ancestry in South Asians makes South Asians very different from Caucasoids), while West Asians are part of the same racial continuum with Europeans.

eurologist said...

In your previous experiment Sub-Saharans fell along a cline towards Europeans while Europeans formed a tight group... But in this experiment the reverse is the case, so, for instance, non-Sardinian Italians show up closer to Sub-Saharans than French are, who in turn show up closer to Sub-Saharans than Orcadians are.

Onur,

This is a projection of Africans onto the PC1/2 space between Europeans and East Asians - so you would expect them to form a tight cluster around the mean. Instead, they are closer to all Europeans in PC1. The drift of Europeans in PC2 away from the mean could be randomly larger in one or the other direction (based on the population history), so I would not over-interpret Africa's position along PC2, as long as it is relatively close to the mean - which it is.

Dienekes said...

Africans showed evidence of gene flow from (Sardinian, Basque) in a previous experiment, so that's consistent with their position in this plot (PC2), which is about halfway between Sardinians/Basques, a little on the Sardinian side.

Unknown said...

Yoruba and Bantu Kenyans have no mixture from Basques and Sardinians, the birden of proof is on you. Their position is best explained by serial founders within Africa. As I said before, San Pygmies are not founders of modern day Bantus and West Africans, at least not recently though there has been recent interaction and mixture between the two, a case can be made for vs some hypothetical mixture from Sardinians and Basques who have been shown to be outliers from Europeans.

DH said...

Very interesting topic..i may be a little off topic but is there any chance in the future of this science that Y dna from ancient skeletons can possibly be extracted & studied?

thanks

Jean Altime said...

AHHH So We Sub Saharan Africans DO have Genetics cousins (Europeans and Middle Easterners) Thanks!

Just like Northern Europeans are gentically close to Native Americans.