July 31, 2013

West Eurasian admixture in Khoe-San via East Africa

A new paper on the arXiv quantifies and dates the West Eurasian admixture in east Africa, and uncovers the presence of such admixture even in the Khoe-San of southern Africa. It appears that the admixture first occurred in East Africa about ~3ky ago, and reached southern Africa about ~1.5ky ago.

It is quite remarkable that different waves of migration converged into southern Africa from different directions: west African farmers and west Eurasian-admixed east African pastoralists. We should count ourselves lucky that the Khoe-San were discovered when they did: a few centuries more, and they too might have followed the fate of other populations finding themselves at the losing side of a technology differential, their culture lost, and their DNA preserved only as fragments in the gene pools of the more successful groups.

arXiv:1307.8014 [q-bio.PE]

Ancient west Eurasian ancestry in southern and eastern Africa

Joseph K. Pickrell et al.

The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter-gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger-Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to approximately 900-1,800 years ago, and show that it had the largest demographic impact in Khoisan populations that speak Khoe-Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to approximately 2,700 - 3,300 years ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa, and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.



eurologist said...

Just a few clarifying highlights from the original paper:

A major open question concerns the initial source
of the west Eurasian ancestry in eastern Africa. The estimated mean time of gene
ow in eastern Africa is
around 3,000 years ago, and the amount of gene
ow must have been quite extensive, as the west Eurasian
ancestry proportions reach 40-50% in some Ethiopian populations...

This observation can be interpreted in the context
of ancient DNA work in Europe, which has shown that, approximately 5,000 years ago, people genetically
closely related to modern southern Europeans were present as far north as Scandinavia [Keller et al., 2012;
Skoglund et al., 2012]. We thus nd it plausible that the people living in the Middle East today are not
representative of the people who were living the Middle East 3,000 years ago. Indeed, even in historical times,
there have been extensive population movements from and to the Middle East///

First, the gene
ow we observe is asymmetric: while some eastern African populations have
up to 50% west Eurasian ancestry, levels of sub-Saharan African ancestry in the Middle East and Europe
are considerably lower than this (maximum of 15% [Moorjani et al., 2011]) and do not appear to consist
of ancestry related to the Khoisan.

German Dziebel said...

With the wind are gone the nonsensical ideas that Khoisan genetic variation is a superset for the rest of modern humans and that non-Africans are a subset of Africans.

The dates are placeholders here. Since the "West Eurasian admixture" is so pervasive in South Africa, we may want to consider linking it to the Upper Paleolithic features of the Hofmeyer skull dated at 36,000 YBP, and not to the pastoralist spreads.

Grognard said...

All the arguments for subsets come from mt DNA diversity, anyway. When we look at number of variations we get a completely different story that says west europe has all the genetic variation. I think this is partly due to neanderthal admixture and partly because holy roman empire made it so lots of tiny nations and cities could remain independent, which didn't happen anywhere else on the planet - losers in wars got wiped out and in peace time cities got their ethnicites washed out of existence by mass immigration/migration from dominant cultures.

But you always have the question of what came from what to some extent. When we measure what's considered west eurasian we could be talking about an element that comes from middle east that went to both areas and likely originates in a third place. That is to say our definition of what is sub saharan, east african, middle eastern, west eurasian etc. all have to be based on a little conjecture. Especially what's middle eastern and north african today, which is certainly nothing like it was before the arab expansion.

But the article's conclusions are mainly what I am coming to believe believe is the case; Africa has in historic times, and maybe for a good half a million years, been a constant target of mass immigration not emigration.

Dr. Clyde Winters said...

I disagree. There is considerable evidence for African migration into Europe, not just a migration form the Levant.

The idea that Khoisan acquired Eurasian alleles via Semitic speakers from Ethiopia is pure conjecture--due to the lack of archaeological evidence for such a migration into East and South Africa. The first modern European reconstructed by forensic artist Richard Neves based on skull fragments resembled the Khoisan type. This supported the research of Marcellin Boule and Henri Vallois in Fossil Man, that indicated a Khoisan migration into Europe 35kya. Boule and Vallois based this conclusion on the skeletons, art and tool kits used by ancient South Africans and members of the Aurignacian and Solutrean cultures (see pp.318-319).

stevepolychronopoulis said...

All they need to do now is find that elusive "Oceanic" or "Melanesian"-like marker in Africans, and Out-of-Africa is pretty much done.....

eurologist said...

I apologize for the bad formatting above - for some reason it showed up fine in the comment window.

I am still puzzled by the "today's West Asians aren't those of 3,000 years ago" in the context of the proposed route (Southern Arabia) and language (Arabic-related Semitic). Aren't the latter exactly related to the people who subsequently become much more dominant in West Asia (and North Africa), as opposed to, say, a more Anatolian/ Northern Levantine population?

It would be useful to look at West Asian male haplogroups in East Africa down to South Africa to pin-point a source population.

Onur said...

3000 years ago is too late for the major West Asian admixture in East Africans, as the hypothetical transformation of West Asians from Southern European-like to pre-Arab-invasion West Asian-like, if occurred, must have occurred before 3000 ya. Historically fairly stable West Asian populations such as Armenians and Cypriots (they were tested in this study) are unlikely to have genetically changed much since at least the Iron Age times. Cypriots are especially important here, as they acquired their mainland Greek admixture with the Greek colonization and eventual Hellenization of Cyprus beginning from roughly 3000 ya. So Cypriots apparently became genetically more Southern European-like, not less, during the last 3000 years than before.

Creative said...

The theory of Prof. Dr. Norbert Nebes “Semitic studies” comes to mind. In a German on-line article from 2006 he mentions that he hypothesizes that proto-Sabaeans immigrated into South Arabia during the late Bronze Age from the Levant.

Strangely, also Prof. Jan Retsö “Semitic studies” theory comes to mind that ancient Arabs were originally an elite Religious based Warrior-Cult group.

Roy said...

From the Lemba perhaps?

eurologist said...

I could imagine that before the Bronze Age, there would have been quite some gradient between a more SE European-like population in W Anatolia and N Levant, and a more "Gedrosia-like" population towards Iran, Afghanistan, and Pakistan. So, e.g., a late Neolithic/ early Bronze Age expansion from Southern Mesopotamia (Persian Gulf) could have carried quite "westerly" people, by today's standards. Trade from the late Neolithic through the Bronze Age has been well-established between Mesopotamia and the S Arabian shores.

So, it is possible that today's SW Asians are a complex mix of such people, Africans, and later Bedouin-like arrivals. Still, looking at y-DNA signatures in E Africa, it seems everything must be hiding in J and especially E - nothing like G or R which is expected to be more typical for an early SE European but also Anatolian make-up. And that is going to be difficult to sort out, given later Islamic migrations.

Slumbery said...


I still think that the main West Asian migration in the Middle East happened before 5000 BP (included Egypt). I have one reason to believe so: such a big movement should show up in the archaeological materials of the(relatively) well documented and even literate classic civilisations.

Of course it is possible that there were millennia between their arrival to NE Africa and next stage of East African migration.