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Monday, June 5, 2017

Ancient human genomes from Southern Africa (Schlebusch et al. 2017 preprint)


Over at bioRxiv at this LINK. Emphasis is mine:

Abstract: Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|'hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) 'hot spot' for the evolution of our species.

Schlebusch et al., Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago, bioRxiv, Posted June 5, 2017, doi: https://doi.org/10.1101/145409

80 comments:

Nirjhar007 said...

Fascinating stuff .

Gioiello said...


A1b1,PF776/M11770 * FGC37883 * M11782/PK1+41 SNPs 125100 ybp, TMRCA CI 95% 131800 120400 ybp" class="age" formed 130700 ybp, TMRCA 126000 ybp BT M8968/PF207 * V187/PF1403 * M8961/PF201+464 SNPs 125100 ybp, TMRCA CI 95% 92500 83600 ybp" class="age"formed 130700 ybp, TMRCA 88000 ybp

A1b1/BT YFull 130700 years ago
Schlebusch et al. 260000 years ago

Samuel Andrews said...

I don't see what the origins of humanity have to do with 2,000 and 400 year old genomes from South Africa. A genetically divergent population in South Africa in recent times isn't evidence humanity originated in South Africa.

Ric Hern said...

@ Samuel Andrews

I think the key words here are "(not necessarily exclusive)"

Ric Hern said...

What is interesting is that there were speculated in the past that Khoi-Khoi people had some Cushetic or Nilotic admixture. What is also interesting is that Khoi people historically were also found in significant numbers in Zimbabwe until the +-1500s.Could this East African/Eurasian admixture have taken place during the formation of Great Zimbabwe(Zimbabwe Ruins)?

Could this be proof that Great Zimbabwe was built by Arabic Traders(Slaves and Ivory)?

mickeydodds1 said...

Good Lord!

Kryptonite for the politically correct brigade!

Gioiello said...

@ Samuel Andrews

"I don't see what the origins of humanity have to do with 2,000 and 400 year old genomes from South Africa. A genetically divergent population in South Africa in recent times isn't evidence humanity originated in South Africa".

Of course it has nothing to do, but may mean:
1) that Africans had introgression of Basal Eurasian, i.e. hg E isn't African in its origin
2) Shi Huang and colleagues merit to be studied very carefully
3) Click languages isn't "African" but derive from Afro-Asiatic which came from Eurasia/Middle East (as the great Italian linguist Alfredo Trombetti demonstrated more than a hundred years ago)
4) All the dates used against my theories are wrong. Perhaps YFull shouldn't be multiplied only for an 1.17 or 1.27 factor.

Kjontendor001 said...

Let's hit the serious issues : waz we kangz or not ?

P Piranha said...

The admixture from Cushitic-Nilotic groups is likely to be very ancient (as the authors find) and responsible for the introduction of pastoralism to the Khokhoi groups--a pastoral package around the Kalahari that is not contiguous with the savanna pastoral complex of North and East Africa. The Khoikhoi are not the same as the San, who are hunter gatherers.

Matt said...

Cool. Nice to see a paper that gets at the deeper questions of human population history using adna again. IRC the admixture estimates firm up what we already knew about admixture in recent Southern African populations, but increases with a new "floor" population and is ubiquitous in a Southern African population where D-stats would have said it was present, however it was a bit more unclear how to actually estimate %s.

Seems like it would have been preferable for them to model with Levant_N not LBK, but I suppose it is a coverage question.

Admixturegraph model is pretty nice:

Suggestive of an East African expansion through Africa and outside Africa, with the expanding East African population closer to Eurasians than Mota was.

Bantu-speaking population (West Africans) get 31% of their population from a human group who were outgroup to all African humans. Hard to say if this is likely to point to an East/South African origin of human anatomical modernity that then spread throughout Africa.

I think this graph would have been vastly improved by the addition of Neanderthals / Denisovans. No need to get into the weeds of intra-Eurasian structure, but this would help us understand how variant the "BasalHuman" that they have contributing to W Africa is, etc.

Also wonder if they have truly fully accounted for West->East African agricultural expansion here though.

Doubt that Mota, in their model is actually unadmixed by the EAfrica2 nodes, given its late time in history, that the person was living in East Africa, and the ultimate ubiquity of EAfrica2 related admixture across Africa and Eurasia.... but I guess the point is that they don't have a more unadmixed ancestor to justify the extra admixture edge.

Karl_K said...

"I don't see what the origins of humanity have to do with 2,000 and 400 year old genomes from South Africa. A genetically divergent population in South Africa in recent times isn't evidence humanity originated in South Africa".

The 2000 year old genome is very important to this discussion, for comparison to modern Khoekhoe and San groups. If it shows that the modern groups have 9-22% non-SSA admixture, when previously considered to have close to zero, that affects calculations of Neanderthal admixture and divergence times, as well as estimates of SSA admixture into Eurasians.

If 2000 year old Modern Humans who diverged 260,000 years ago lived in South Africa, but there is no evidence of them being anywhere else until at most 200,000 years ago? That has everything to do with the location of origin and spread of Modern Humans.

Matt said...

I'm finding Pickerll's 2013 paper is a good one to update ourselves on if I'm forgetful / unclear of the previous conclusions - http://www.pnas.org/content/111/7/2632.full. (There are later ones that refine, but IRC this was the big one).

Note re: table 2 from Schlebusch, this is the estimate of Amhara admixture. Not an estimate of pure OOA ancestry. They are not saying populations have 9-22% of non-African ancestry but "9-22% genetic admixture from East African/Eurasian pastoralist groups".

For actual Eurasian / OOA admixture, assume the Admixturegraph is accurate: 0.14 EAfricaEurasian, with 0.31 OOA, therefore 0.14*0.31 = 0.0434, e.g. 4.34% OOA in Ju|'Hoansi.

Compares with Pickrell 2013 estimate of 1% OOA in Ju|’hoan_North and 0% in Ju|’hoan_South, therefore a 4% increase in estimated ancestry.

Matt said...

Quick graphic using the ancient proportions in Amhara from Lazaridis 2016 and the Amhara ancestry estimates from Schlebusch 2017 to estimate Levant_N / Levant_BA in African populations:

http://i.imgur.com/yk1VGYo.png

Remember, the reasons why they use the Amhara estimate is because the ancestry came from the East African population, and the main contributor node to East Africans (EAfrica2) is about exactly as divergent from the main trunk of Southern African ancestry (BasalSAfrica) as OOA is (but for the small edge of Neanderthal/Denisovan into OOA pops). (Hence why the models of OOA+BasalSAfrica are a massive fail, as they detail in the paper+supplement.)

Unknown said...

Does it mean Khoisan are surviving Homo Idaltu?

Karl_K said...

@ Unknown

"Does it mean Khoisan are surviving Homo Idaltu?"

It does not mean that. Without DNA, it is impossible to place Homo sapiens idaltu. They could have been a seperate branch, as the lines leading to several other Sub Saharan African populations had already split from each other by 160,000 years ago.

Chad Rohlfsen said...

All African will be shown to have Eurasian admixture as more ancients come. I wouldn't be surprised if everyone is over 5%.

postneo said...

It means they had a mostly unbroken lineage of 260 k years and became anatomically modern without much external input.

postneo said...

So they are one of the ancestral populations of humanity

Karl_K said...

@postneo

"So they are one of the ancestral populations of humanity"

No... they are a modern population that shares a common ancestral population with all other modern humans, and that population split at least 260,000 years ago.

postneo said...

Sure obviously they are not ancestral but they represent an unbroken amh lineage which contributed to row ancestry

Karl_K said...

@Chad

"All African will be shown to have Eurasian admixture as more ancients come. I wouldn't be surprised if everyone is over 5%."

Maybe not 'Eurasian' in the sense of coming from Eurasia, but definitely with admixture from Non-Sub-Saharan Afican populations.

The population structure within Africa must have been very deep for a very long time, with several distinct North, East, West, Central, and Southern populations. But there must have been several episodes of major admixture between many of those in the last 20,000 years.

Gioiello said...

Everything depends as to how we'll be able to understand which is the terminal SNPs of these A1b1b2, and it could be demonstrated also that Shi Huang and colleagues are right, because anyway this Y may not be 160000 years old, only the autosome, and, if their Y came from Eurasia, the autosome is even older.

Ric Hern said...

Isn't this East African/Eurasian admixture within the Khoi only after 1000 years ago ? Or did I read something wrong ?

Karl_K said...

@Ric

Yes, you are correct. BUT, that us because we are looking at a 2,000 year old genome.

If we had a 10,000 year old genome, it might well reveal that there had been considerable additional admixture between 9,000 and 3,000 years ago.

Synome said...

Is it possible that archaic admixture in the Ballito Bay samples is biasing the divergence times?

Ric Hern said...

@ Karl K

That 2000 year old genome does not show East African, Eurasian or Bantu admixture so which other population do you think was responsible for admixture before 2000 years ago ?

Karl_K said...

@Synome

Only if it does not exist in any sampled modern populations.

Karl_K said...

@Ric

You can only see differences. There could be 50% Bantu admixture, but how could you tell without unmixed samples? That is the beauty of ancient DNA! You need an unmixed reference.

Ric Hern said...

@ Karl K

Where do you think those Eurasian admixture came from within the last 1000 years since Bantu DNA dominates Southern Africa today and does not seem to be connected to the East-African/Eurasian contribution into Khoi ?

Derek said...

Can anybody use extended data figure 2 to gauge how long ago "Basal Humans" split off from the rest of us?

Ric Hern said...

@ Karl K

I'm going to tgrow a prediction out there and time will tell if I am right.

The Khoi people dominated Southern Africa before a 1000 years ago. Then came Arabian Slave Traders from Tanzania and established Great Zimbabwe (Zimbabwe Ruins). Then followed a Bantu expansion from the Great Lakes area(Zambia/Malawi)and the collapse of Great Zimbabwe on their way Southeast into Southern Mozambique Swaziland and Kwa-Zulu Natal.

Karl_K said...

@Ric

That's an excellent question. If it was pure 'Basal Eurasian' admixture, it would not affect Neanderthal levels, and be very difficult to detect.

Keep in mind that 'Basal Eurasian' is not any different (in this case) than the Never Left Africa population that led to the Out Of Africa migration.

Synome said...

@Karl_K

You mean in regards to Ballito Bay's divergence w/respect to all other pops. I suppose what I meant to ask is something broader. Could there be pervasive archaic admixture in Khoisan and other SSA populations biasing divergence estimates backwards that is somewhat masked by the Eurasian admixture biasing it forwards?

To know for sure we need African hominin DNA don't we?

Karl_K said...

@Synome

It would not be 'bias' if it occurred before the split with all other modern humans. But, yes, if they had admixture from a very divergent population 100,000 years ago... that could appear as a more divergent recent common ancestor.

As I said before, nothing can compete with actual ancient DNA. You can only make guesses without it.

JohnP said...

How accurate is this?
http://evoandproud.blogspot.com.br/2012/02/encounters-between-modern-humans-and.html
By Anthropologist Peter Frost.

Well, so, after the end of the Out of Africa events, while the population who went out mixed with the likes of Neanderthals, Denisovan and who know what else, the populations who stayed in Africa acquired, directly or indirectly, 13% Homo rhodesiensis and 2% Homo erectus admixture.
Haven't this new aDNA sequencing technology being used on ancient hominids yet? Or there are other preventing factors?

Gihanga Rwanda said...

@ Karl K and Ric Hern Great Zimbabwe and other complexes throughout southern Africa are the legacy of Bantu-speakers, not Khoe pastoralists or Arabian merchants. People like you are the reason why some people navigate to Afrocentrism.

JohnP said...

@Gihanga Rwanda
To be fair, in the Green Sahara period of ~8000BCE~3500BCE, there were people migrating southwards into SSA, bringing Cattle Herding, R1b V88 and the Chadic branch of the Afro-Asiatic languages.
So, what was the impact of those people there?

Gioiello said...

About what are we speaking about? As to YFull A1b1 and B-T formed 130700 years ago and separated without meeting anymore till recent times. CT would have formed 88000 years ago, after a bottlemneck of 42700 years. But if the descendants of B-T diverged 260000 years ago from the descendants of A1b1 (this A1b1b2 etc of South Africa), how would have lasted the bottleneck? Do you find all that reasonable? Isn't it more logical, as Shi Huang says, that the Y is more recent and come from elsewhere than Africa? About the languages spoken in Africa we have many proofs that they are recent and linked with Eurasian languages, that it is what German Dziebel has always said, demonstrating that African languages are less divergent than the Native American ones, and all this divergence between this aDNA in South Africa and all the rest could be due to introgression from unknown and divergent hominins rather than linked to te divergence of A1b1 from B-T.

Gioiello said...

@ JohnP
"@Gihanga Rwanda
To be fair, in the Green Sahara period of ~8000BCE~3500BCE, there were people migrating southwards into SSA, bringing Cattle Herding, R1b V88 and the Chadic branch of the Afro-Asiatic languages.
So, what was the impact of those people there?"

R-V88 came without any doubt from the "Italian Refugium" or anyway Western Europe. Read what I am writing since ten years and look at the YFull tree.

JohnP said...

>>So, what was the impact of those people there?<<
Quoting myself, because I felt the need to specify that I was referring here to the Khoe and Arabs, not to my Chadic example.

@Gioiello
I don't know about the origins, neither do I claim anything. But it went to SSA the way I described. I don't remember where, but I read it in an old paper now.

Gioiello said...

@ John P
@Gioiello
I don't know about the origins, neither do I claim anything. But it went to SSA the way I described. I don't remember where, but I read it in an old paper now".


The paper is Cruciani et al. 2010, but I wrote to him and Scozzari and he replied me that my hypothesis (then) was possible, but now it is demonstrated just from the data of Francalacci et al 2013 and 2015 and my analyses demonstrated that. Look at the YFull tree, or, better, my tree with all the Italian samples not in the tree. Unfortunately when a scholar, even though clever as Cruciani, writes something unproved only because there was the prejudice that R1b came from Middle East, everyone follows that, even though demonstrated wrong.

Gioiello said...

I could add that the African and Middle Easterner samples of R1b1-V88 aren't older than 7000 years as to YFull, but very likely are younger, because 7000 years ago is the date of formation, not of the split of the subclades. Italy and Western Europe have subclades separated 12000 years ago and all the intermediate subclades.

Ric Hern said...

@ Gihanga Rwanda

Is it okay if you are a Afrocentrist that excludes possible Khoi achievements ? That in effect does not make you a Afrocentrist but a Racist that discriminates against the Khoi people.

JohnP said...

@Gioiello
So there would be the need of a "reverse" migration from Italian EN Farmers again into the Middle East, and from there to North Africa, the Green Sahara and the Chad. Or they could have gone to North Africa first and then to the Middle East, West-North-Africa-Iberia and the Chad.
Now, this means these people spoke Afro-Asiatic?
The 12000-year is a gigantic wall here. Maybe the same population split at some time and one of them went to Italy and the other is a still undiscovered one that went to the Middle East?
The time range must have still been in the Neolithic, both because of the Green Sahara and the dramatic change that the Bronze Age would be.
I don't have any answers, I'll let you pros have the saying.

@Ric Hern
I think the point Gihanga Rwanda was trying to make is that, by "attacking" (in their view) other peoples (Africans and other specific tribes/nations) heritage and "perceived history" (like everything thought in school, almost always wrong), you only make them more of hard-liners and geared towards Afrocentrism.
Now, I find this stupid. People should take criticism, no matter the case. For instance, I'm Italian, and although I love my "Country" above all others and my "People" above all others, I also hate them both and criticize them all the time.

Mark B. said...

@Rick Hern

Regarding " Then came Arabian Slave Traders from Tanzania..."

I don't see how it matters to the genetic history of the human race whether Arabs explored the East African coast to buy slaves or to sell vacuum cleaners. Could you stick to the topic at hand? This subject is difficult enough to discuss without giving each ethnic/racial group its own naughtiness tag.

Gihanga Rwanda said...

@ Ric Hern and JohnP

The archeological and anthropological records is pretty straightforward, Mapungubwe and Zimbabwe etc. was a by product of the social complexity prompted by the arrival of Eastern Bantu speakers in the Zimbabwean plateau. I only have much love for Khoe speakers.

https://www.academia.edu/7500155/Mapungubwe_and_Great_Zimbabwe_The_origin_and_spread_of_social_complexity_in_southern_Africa

Gioiello said...

@ JohnP
"@Gioiello
So there would be the need of a "reverse" migration from Italian EN Farmers again into the Middle East, and from there to North Africa, the Green Sahara and the Chad. Or they could have gone to North Africa first and then to the Middle East, West-North-Africa-Iberia and the Chad.
Now, this means these people spoke Afro-Asiatic?
The 12000-year is a gigantic wall here. Maybe the same population split at some time and one of them went to Italy and the other is a still undiscovered one that went to the Middle East?
The time range must have still been in the Neolithic, both because of the Green Sahara and the dramatic change that the Bronze Age would be.
I don't have any answers, I'll let you pros have the saying.

For instance, I'm Italian, and although I love my "Country" above all others and my "People" above all others, I also hate them both and criticize them all the time".

That what you say happened, that R-V88 from Middle East came to Italy with EEF and then back migrated etc etc is just what the Levantinists are trying to make you all believe. Actually there has been found any R1b in Middle East, or Iran, except some recent subclades come from Samara and of the R-L23-Z2105 subclade, whereas Eastern Europe, but also Western one are plenty (don't forget that the oldest R1b1 found so far is in Italy: Villabruna 14000 years ago).
When you say that you are Italian like me, everythung is clear: there isn't a worst enemy of Italy and Italians tham Italians themselves, except me, of course.

Karl_K said...

@Gihanga

"@ Karl K and Ric Hern Great Zimbabwe and other complexes throughout southern Africa are the legacy of Bantu-speakers, not Khoe pastoralists or Arabian merchants. People like you are the reason why some people navigate to Afrocentrism."

People Like Me? WTF? I made zero mention to Great Zimbabwe, other complexes, or Arabian merchants!

It's People Like You!

Ric Hern said...

@ Mark B.

The Topic at hand mentions East-African/Eurasian admixture from a thousand years ago. So I believe myou discussion is valid.

@ Gihanga Rwanda

I mentioned possibilities. Nothing is written in Stone yet. A lot of sampling is still needed. However if the evidence eventually do not point to your theory will you accept the reality of it ? I already accepted that my forefathers from the Steppe were not the Great Monument Builders. However I am still proud to know that they adopted these knowledge and improved on it....

Gihanga Rwanda said...

@ Karl K

I must have misread your post, I sincerely apologize.

@ Ric Hern

Of course, I've had to adjust and shift long-held positions based on new data.

Karl_K said...

@Gihanga

No problemo. We all do that now and then!

Ric Hern said...

@ Gihanga

Yes that is what counts. Accept the past whatever it turned out to be and build on the future.

Mark Moore (Moderator) said...

If they are saying that the San split from the rest of mankind 260K years ago and only started mixing in the last 2K years, well I don't buy that. It doesn't seem reasonable that they would bounce around unadmixed for that length of time. Does anyone have a more parsimonious explanation? Maybe: The original members of the human race were much closer in time but the group also started with more significant genetic diversity?

batman said...

Karl,

"The 2000 year old genome is very important to this discussion, for comparison to modern Khoekhoe and San groups. If it shows that the modern groups have 9-22% non-SSA admixture, when previously considered to have close to zero, that affects calculations of Neanderthal admixture and divergence times, as well as estimates of SSA admixture into Eurasians."

That's all based on the somewhat loose assumption that a genetic ancestor to all the naked, speaking, tumb-gripping monkeys - as in "human beings" - to come out of Africa.

There's still no proof of that - and the latest discoveries within modern paleontology may place the origin of "man-kind" to earlier dates and other locations.

http://www.telegraph.co.uk/science/2017/05/22/europe-birthplace-mankind-not-africa-scientists-find/

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177127

https://en.wikipedia.org/wiki/Archaic_human_admixture_with_modern_humans

Post-glacial mixes, finally determining the present etnicities:
https://academic.oup.com/mbe/article/28/1/717/986081/Extended-Y-Chromosome-Investigation-Suggests

Ric Hern said...

@ JohnP

Thanks. Yes I agree.

Jaap said...

@gihanga rwanda
Yes, people were trading commodities in the past as they are doing so right now. People are 'achieving' big things all the time! What the choi achieved is something altogether different. They've 'lived the life of the stars' since time immemorial. I don't know how they do it! They must have their maniacs, and their psychopaths! How do they create a platform for their ambitions? I've no idea. How is it possible for a group of human beings to be so utterly non-aggressive, non-invasive? And to lead a life of such utter human dimensions to the full?

Samuel Andrews said...

@batman,

But early human like bones in Europe is really weak evidence for a human origin outside of Africa. High mtDNA/Y DNA diversity in Africa is actually really good evidence humanity originated there.

Anyways I agree with you that the OoA theory could be wrong. One thing we've learned from ancient European DNA is you can never be sure till someone takes DNA from old bones.

One thing we can be confident about is that humanity's early history is much more complex than the OoA theory predicts. It definitely isn't as simple as a single genetically unfirom group of first humans in Africa, one genetically uniform group of humans leaves Africa and sprouts all non-Africans.

Matt said...

@Sam: "But early human like bones in Europe is really weak evidence for a human origin outside of Africa. High mtDNA/Y DNA diversity in Africa is actually really good evidence humanity originated there."

I'm not really an expert but the recent Graecopithecus theory that batman links to is about a really, really deep ancestor of the whole Homo genus (millions of years ago). Pre-Homo Erectus, pre-Australopithecine. That stage of differentiation of our ancestors could well have taken place in Europe, but the differentiation and expansion of Homo Sapiens surely did not.

I'm not sure how solid it is (because the evidence is basically a few teeth and an analysis) but there's no contradiction in a European Miocene origin of this very basal genus and an African origin of Homo Sapiens (or even Homo).

High heterozygosity on autosome and clonal dna for present day tells us about the likelihood of a long term high population size in Africa, and therefore likely origin, of Homo Sapiens, but basically nothing about the origin of Homo.

IRC actually, the argument for the origin of an African origin of Homo (as opposed to Homo Sapiens) still hinges on the same kind of ideas it did back in the day when Darwin proposed it; the closest living ape ancestors live in Africa, and the fossil record both outside and within Africa is sparse enough that it is actually quite a challenge to say too much more. But on the other hand, the reason why there is some question today still is that climate change within Eurasia has been vast since that time, the populations of apes that did develop and live there millions of years ago (when there was a warm climate they were adapted to) were largely wiped out, and there are questions that the fossils we do have, can have more Homo like features than extant Great Ape African species / fossils ...

White Elephant said...

Hey, I was hoping a knowledgeable person could help clarify a few things for me.

This Schlebusch paper is very interesting, but taken in context with papers like:

*Yuan et al "Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA" (2017)

*"The Forgotten Continent" by Jane Qiu in Nature (July 2016)

I am feeling confused about modern human origins and the centrality of Africa. Ever since the discovery of the A00 lineage, the direction things seem to be going for TMRCA estimates for Y & mtDNA, autosomal is to be pushed back further and further to before any of our AMH fossils.

Furthermore, the accumulation of Chinese fossils has caused some to rethink the origin of Homo Heidelbergensis from being in Africa to being somewhere in the middle east, giving rise to the east asian archaics, Neanderthals, Denisovan, and then Heidelbergensis moving into Africa became Homo Sapiens.

So if there's reason to think Heidelbergensis may be non-African in origin, what necessitates that homo sapiens originate in Africa if our genetic origins predate the African fossils we find? Could those be homo sapiens that had crossed over from Yemen into Africa from Eurasian source population?

Is it just my own lack of understanding or does the Out of Africa framework looks considerably weaker in light of:

1. Substantial fossil evidence of continuous occupation by archaic humans/transitional forms in east Asia from 900,000-125,000 ya, some of which look damn near modern.

2. Plausible evidence that the source population for Homo Sapiens and Neanderthals being an Erectus descendant in the middle east.

3. The weirdness of the Yuan paper. I don't know how much credence to give this paper, but they claimed to have evidence that present-day human Y and mtDNA originated first in east asia and then hybridized with other hominids across Eurasia and Africa. Is this the non-peer reviewed work of nutjobs? I am being deceived by Chinese Nationalists propaganda masquerading as science?? Or is it paradigm-shifting science!?!?

Help me folks. Am I correct in seeing growing plausibility for de-centering Africa in the story of modern human origins, or not?

Ric Hern said...

@ White Elephant

I was thinking along the same lines as you. If the African "Adam" arose from a different archaic population than "Eve" and thousands of years appart when precisely did these two lines meet up to form "Modern Humans" ?

I get the distinct feeling that one of these days that Sapiens will become irrelevant and Modern Humans will be classified as different subspecies of Homo Heidelbergensis....

Ric Hern said...

And what did this other hominids that "Modern Adam" and "Modern Eve" had to mate with on their way to each other become ? Did they also become "Modern" ?

capra internetensis said...

@White Elephant

The Yuan paper is non-peer reviewed and their previous work based on the same genetic theory (and is *not* about humans) has not been published in reputable journals, as far as I have found. So while it's conceivable that it's revolutionary it's probably nonsense.

In the case of the mt and Y hg trees they literally just pre-set the roots to be where they wanted. They did not root the trees from the data, not even by their own methods.

German Dziebel said...

@capra

I should probably just turn on an automatic responder to your baseless claims. Shi Huang and team did not root the trees where they wanted. They (and I) rooted them based on rather simple criteria: most anciently attested, most widely spread and most frequent alleles. They are trying to avoid an out-of-Africa bias whereby the least frequent, unattested in aDNA and geographically restricted alleles are declared to be the oldest.

Peer-review is problematic in their case because they diverge with peers at a deep end - they are reviewing peers as much as peers are reviewing them.

Salden said...

I'm sure you deny the Holocaust and insist the Bible actually happened too.

White Elephant said...

@Ric Hern
I have had similar feelings about Homo Heidelbergensis. For a long time I clung to the idea of a single original source population of homo sapiens emerging in Africa 200-150ka in some particular region in eastern Africa, but it seems to me from a lot of what is being published is that AMH is probably the result of multiregional evolution within Africa (if OOA is true).

If it isn't, then somewhere in the middle east maybe? I believe Israelis found teeth in Qesem that are very close to modern humans from 400ka. I have a poor understanding of the ecology of Asia during this time period, but suppose this scenario:

1. Homo erectus migrates OOA
2. Erectus descendants give rise to various hominin in asia, europe, africa
3. AMH originate somewhere in SW Asia 300ka (Green Arabia at this time?)
4. Migrations into europe, east asia, africa, admixing with archaic humans they expanded

While Africa has the greatest overall genetic diversity, perhaps this is not a sign of being the most ancient homeland of AMH necessarily so much as it is a place that preserved the most from divergent populations that split in Middle Pleistocene.

The original SW Asian range of AMH would have been drastically altered by desertification, causing populations to leave, then with climatic changes, different groups move in there that are not reflective of the lands most ancient inhabitants.

Slumbery said...

Ric Hern

But do we have any reason to assume that modern human mtDNA and YDNA originated from different populations? The time difference does not tell us about that, because YDNA success is much more uneven that mtDNA success. The population where the younger one lived could very well already have the older lineage by its own time even if there is a huge time gap.

Salden said...

Stop babbling your Chinese Nationalism.

Ric Hern said...

@ Slumbery

How many generations of inbreeding can be tolerated within a small population before genetic meltdown ?

Ric Hern said...

@White Elephant

I agree. There is still too many questions to be answered and they just keep on multiplying with new discoveries made.

Samuel Andrews said...

@Everyone,

Do you think the ancient Roman Middle Eastern "gladiator" from Britain was Egyptian? I know he was similar to Jordan_EBA aswell as the ancient Egyptians. But he also clearly had some Sub Saharan African ancestry unlike Jordan_EBA. So wouldn't Egypt make sense considering the ancient Egyptians did have a dose of Sub Saharan ancestry?

Ric Hern said...

@ Slumbery

Did Modernity originate within the Male or Female line ?

Tobus said...

@White Elephant:

There's a pretty decent write up here: http://www.nature.com/news/how-china-is-rewriting-the-book-on-human-origins-1.20231.. I think at the end of the day the DNA is incontrovertible - whatever transitional/semi-modern species existed outside of Africa, they were either exinct, or made so, by the OOA expansion. Yuan et. al. can cherry pick sites and try to frame an alternative tree, but really there is only one logical way that the Y- and mt-DNA trees can be constructed (ie with minimal back mutations), and they both suggest a recent origin in Africa.

Karl_K said...

@Tobus

"there is only one logical way that the Y- and mt-DNA trees can be constructed (ie with minimal back mutations), and they both suggest a recent origin in Africa."

This is exactly true.

Obviously there were 'humans' in Europe and Asia before this. I consider Neanderthals and Denisovans to be human. Where was the the geographic location of the ancestral population split? We don't know that exactly.

But as for the bulk of the shared modern human ancestry, 100% of Y and mtDNA have a 'recent' origin in Africa, and >90% of autosomal ancestry does as well.

As for the AOO Y chromosome, remember when we talk about the origin of a mammalian species, that we are always talking about populations, not individuals.

If the population that became Modern Humans had a bottleneck of even 100 people, there is still a lot of room to carry over several haplogrouos that diverged much earlier than the time of speciation. Also, look at the Neanderthal and Denisovan haplogroups in comparison, they are extremely divergent from Modern Humans.

Slumbery said...

Ric Hern: depends on how small we are talking about. If not really small, then infinite.
Also it could be the same population. My exact point was that time difference does not automatically mean unrelated populations. This of course still allows mixture from others.

German Dziebel said...

@Tobus

"Yuan et. al. can cherry pick sites and try to frame an alternative tree, but really there is only one logical way that the Y- and mt-DNA trees can be constructed (ie with minimal back mutations), and they both suggest a recent origin in Africa."

Don't spam the string, Tobus. Next thing you'll be talking about peanuts in a bag as proof for an out-of-Africa origin of modern humans.

Minimal back mutations? Counting from which outgroup sequence? Neanderthals? Well, they are an African-by-origin species. You confuse circular logic with logic.

A lot of mtDNA sites have recurrent mutations. What makes you think that macrohaplogroup-defining sites are not hypervariable? 489 has just been shown to have a transversion on hg X sequences in Croatia.

capra internetensis said...

Don't feed the troll.

German Dziebel said...

@Capra

You fundamentally misunderstand science, lack scientific credentials but still attempt to provide advise and guidance regarding scientific matters to lay people. This doesn't look good.

White Elephant said...

@Ric Hern

Speaking of questions multiplying with each new discovery...

https://www.nature.com/nature/journal/v546/n7657/full/nature22335.html

What a week.

Salden said...

They couldn't get the needed DNA for comparing with modern populations.

Ric Hern said...

Thanks White Elephant.