May 30, 2015

Out of Egypt or Out of Ethiopia?

I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.

For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.

For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.


AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Luca Pagani et al.

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

Link

18 comments:

Annie Mouse said...

I have previously commented that I thought "Out of Africa" was really "Out of sub-Saharan Africa" with North Africa being the destination. There have been suggestions of this in data from other studies and it makes geographic sense that folk would travel up the Nile. Nice to see this idea supported with more data.

Mark Moore (Moderator) said...

1) I don't have any confidence that they can really do what they think they can do (filter all of the noise from later admixture) and 2) I seriously doubt that the population there now has much if any left from whatever population might have been there 55,000 years ago. As you mention Europe had pretty much total replacement. Maybe even more recently than that. What percent of the population in Europe 40K years ago was a direct ancestor of anyone living in Europe today? The answer could be zero! I doubt it is more than 10%. Maybe some of the same genes got passed on, but from later populations that shared those genes. So why is it any different in northeast Africa?

eurologist said...

I also highly doubt the authors' method can be successfully applied, here. In addition to the reasons already mentioned, back migration into Egypt probably started ~55,000 ya, when the first UP people arrived in the Levant from (likely) ~Pakistan. Those people not only were quite removed from modern Europeans, but also appear to have admixed with ancestral population that somewhere survived in SW Asia. If North Africans admixed with this back-migrating population (very likely), but Ethiopians did not(or not as much), then Egyptians today would show a higher affinity to extant ooA populations for that reason - not because they magically retained a population history difference with Ethiopians between 130,000 - 105,000 (ooA) and 55,000 years ago.

Gaia's sister said...

Why talk of “migration”??? People -- listen up: it was an adaptive radiation! A migration is what birds and caribou do SEASONALLY. What the heck can people not use the correct terms for this?

Also, there was not a “complete replacement” of the hunter-gatherers by the farmers that came in form the near East. The answer is NOT zero. I know there is controversy, but it down to the way everything is hyped these days.. so you get this:
"Study: Europeans are of hunter ancestry” http://www.physorg.com/news8097.html
as well as this: “Europe's first farmers replaced their Stone Age hunter-gatherer forerunners”

Then we get this: "European hunter-gatherers and immigrant farmers lived side-by-side for more than 2,000 years”

Are we to believe there was not development of trade, no mutually beneficial interaction, even though this has been shown to be the case in numerous ethnographies about contemporary interactions??

What about this? European hunter-gatherers owned pigs as early as 4600 BC -- ScienceDaily

Sure, people admit that the period is poorly understood but they are ready to jump to all kinds of conclusion based on tiny amounts of data.

Marianne Luban said...

Here's some related news. Check out my blog to see how autosomal DNA apparently indicates that the mother of an ancient Egyptian queen of the 18th Dynasty was related to a pharaoh of the 20th Dynasty--and his queen! I need some feed back on this one. http://thetimetravelerreststop.blogspot.com/

Grognard said...

Even 2k years ago is not realistic to sort out without ancient DNA, let alone 50-250k years ago.

Jim said...

Gaia's sister:
A migration is what birds and caribou do SEASONALLY. What the heck can people not use the correct terms for this? "

First off, the term is also used for immigrants or emigrants who may return to their home country. That's why they are often called "migrants."

Second, why do you assume these people didn't migrate back and forth? Many documented forager societies relied on forms of seasonal or multi-year migration patterns. In fact it's the rare ones that don't. Why assume these people were any different?

Gaia's sister said...

Jim: you are quite right. I spoke in irritation.. and thank you for both your points, as they add a dimension to the story that is much needed.

However, I have to say,in my own defence, that my point of view was restricted (too narrowly, as you now point out) the language used in describing humans “leaving Africa”, which was truly an adaptive radiation on the part of a species expanding its range as its population increased.

Your comment exposed the other aspect: within that broader process of adaptive radiation, there was very likely internal back and forth movement of people - both qualifying as immigration and emigration (although not with the context of modern states and their borders) and return migration, as well as a general drift of personnel (and genes) in both directions as the expansion of the population progressed across Eurasia and beyond.

Gaia's sister said...

I did not assume this, I was just too narrow in my focus. I was irritated by the way the “leaving Africa” part is always framed.

You are quite right, though, for all along this process of adaptive radiation on the part of our species, there would likely have been movement, both individual and in larger groups, in both directions. the extensive networks and mobility over these networks, that we see in modern hunter-gatherers certainly suggest that membership in any local population would have existed within a larger framework that provided opportunities for constant drift of personnel (and genes) all along the various populations established along taken during the expansion.

eurologist said...

Gaia,

You are unfortunately incorrect. For human migration, it "is the movement by people from one place to another with the intention of settling temporarily or permanently in the new location." (wikipedia).

And conversely, "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal."

Awale said...

This new paper with new Beja, Sudanese Arab, Nubian and Sudanese Copt samples may interest you:

http://www.nature.com/srep/2015/150528/srep09996/full/srep09996.html

terryt said...

Turns out there is a new paper that, to me, absolutely proves the Sinai route rather than the Bab al Mandeb:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129839

The paper deals mainly with the evidence for a northern route for mt-DNA N through Eurasia but also covers many other very interesting aspects of such a movement.

"back migration into Egypt probably started ~55,000 ya, when the first UP people arrived in the Levant from (likely) ~Pakistan".

From much closer to Africa according to the above paper, and unlikely to have been from Pakistan.

terryt said...

"I was irritated by the way the 'leaving Africa' part is always framed".

The paper I linked to yesterday has some interesting comments regarding 'leaving Africa':

"From a mtDNA perspective, it was the wide radiation of macro-haplogroup L3 in Africa, during a mild climatic period, that prompted the African exit of modern humans to Eurasia [61]. At the beginning, this putative expansion was estimated around 89 ± 69 kya [107], but a later revised mtDNA time scale placed this radiation in an age window between 59 to 95 kya [1,27,49,61], comprising the last phase of a moist interglacial period and the outset of an arid glacial period. In addition, it has to be mentioned that, using a revised genome-wide mutation rate [108], the split between non-African and African populations was situated in a range of 90 to 130 kya. These ranges overlap with the presence of modern humans in the Levant, as attested by the fossil evidence retrieved from the Qafzeh and Skhul caves [109]. It also coincides with a wet climatic period that would facilitate a sub-Saharan Africa northward spread to the Mediterranean shores across the present-day Saharan desert, not only through the Nile Valley but also across Libya and the Maghreb [110–112]. In the same temporal window is the Aterian stone industry that extended overall in North Africa and the Sahara desert, from the Atlantic coast to the Nile Valley and outward into the Levant"

In other words they were able to expand through a wide region of very similar habitat, which makes complete sense.

terryt said...

Sorry. The Fregal (2015) paper actually has more to say on the OoA:

"This leaves the crossing of the Sinai Peninsula by land as the most plausible gate of exit. During this favorable climatic window, the Mediterranean Africa and the Levantine corridor presented a rather uniform environment that allowed the continuous dispersal into the Near East of small groups of modern humans with close familiar ties. These groups would carry basal L3* mtDNA lineages as their African counterparts. Only two of those lineages have survived till present day, giving the M and N macro-haplogroups that comprise all the non-African extant mitochondrial diversity".

eurologist said...

Terry,

Thanks for that link - great paper by open-minded authors.

I am still worried about the concept of AMHs coming ooA and deciding the next step is travelling 1,500 miles north where a short while later winter was 6 months long and it often froze at night during the summer. And even if they took local Levantine or Anatolian Neanderthal guides with them, those would have been clueless farther north than the Caucasus. I prefer to think that the northern route was south, but just south, of the Himalayas, crossing into China in northern Myanmar. From there, a northerly eastern route away from dense jungles would have been natural, and then a southern one once the Pacific Coast was reached.

"From much closer to Africa according to the above paper, and unlikely to have been from Pakistan."

The paper is a bit vague on the MIS3 ("UP revolution") expansion center, but in Fig. 1 it roughly coincides in part with my Northern Pakistan (upper Indus river valley) scenario. I don't see anything at all pointing to "closer to Africa" - but also note that I still distinguish between the UP expansion and a "basal Eurasian component" remnant that survived somewhere in SW Asia, or thereabouts.

terryt said...

"Thanks for that link - great paper by open-minded authors".

That's not what Maju thinks. He's spitting tacks. You might like to check him out. I have responded and so it is just before my comments:

http://eurogenes.blogspot.co.nz/2015/05/another-strange-paper-from-wellcome.html

"deciding the next step is travelling 1,500 miles north where a short while later winter was 6 months long and it often froze at night during the summer".

I don't think they 'deliberately' moved north. They expanded wherever they could. It is presumably quite a difficult journey to cross Iran to western South Asia although M seems to have done it.

"I prefer to think that the northern route was south, but just south, of the Himalayas, crossing into China in northern Myanmar".

I strongly suspect hat is exactly the route M took. It doesn't seem a s though M spread evenly across the Indian subcontinent. In fact the greatest diversity of basla M haplogroups is in China in northern Myanmar, including NE India, right down to Cambodia.

http://www.researchgate.net/profile/Bing_Su/publication/257753779_Analysis_of_mitochondrial_genome_diversity_identifies_new_and_ancient_maternal_lineages_in_Cambodian_aborigines/links/00b4952696afdcf9bd000000.pdf

"in Fig. 1 it roughly coincides in part with my Northern Pakistan (upper Indus river valley) scenario".

As I understand the paper they place the centre north of the Hindu Kush, not to their south. In fact between the Hindu Kush and the Altai

"note that I still distinguish between the UP expansion and a 'basal Eurasian component' remnant that survived somewhere in SW Asia, or thereabouts".

I think that is the absolutely correct position. The UP developed considerably after the OoA, and perhaps not until Y-DNA P had made it back from SE Asia.

Groggard said...

Gaia's Sister - Out of Africa has some specific requirements to have any validity because it relies only on where mtdna and y-dna are found today as evidence.

It says that people moved from one location, mutated slightly and stayed in place, that population mutated slightly and moved on. All through a series of founder effects where a slightly different population moves on. With no backwards input for some time. All from a sort of sudden human genesis/magic gene change.

Anyway, for a variety of reasons I don't think this is correct, such as evidence there was no sudden gene change and a million other things. And yes, the one way nature of it is a big part of that.

Unknown said...

Looking at the continent, it is safe to say that East Africa was the favoured out route to the Levant and hence, to the Eurasian landmass. It makes sense as Haplogroup E is seen in its original homeland (Somalia, Ethiopia, etc) then onto to Yemen and Saudi Arabia where it shows up in varied frequencies, where at some point, due to diet, environment, etc the chain broke off into the equivalent of a child haplogroup that emerged in its newfound locations (Middle East, Central Asia then to continental Europe over time and millenia.
It seemed that a haplogroup developed only with a long stay in a specific location then as that group took root and decided to move further away, this was/is reflect in the DNA makeup of the individual, family, group, village town and nation.