# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  "Ghost" Archaic introgression in African populations

## Angela

See:
Arun Durvasula,  View ORCID ProfileSriram Sankararaman
"Recovering signals of ghost archaic introgression in African populations"

https://www.biorxiv.org/content/10.1101/285734v2

"While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, *the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood.* Using *405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans*. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, *we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively.* Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations."

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## halfalp

So while humans got out of Africa, without this Archaic ancestry, there was another Homininae in Africa? If they are not referencing it, i guess North Africans dont have this archaic ancestry. Interesting stuff. Probably an Archaic Sapiens shifted from the Sapiens that left Africa. Jebel Irhoud, Idaltu, something else?

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## Jovialis

I look forward to when consumer genetic testing will be able to identify these currently unknown archaic hominids.

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## Moi-même

Mende in Sierra Leone, Liberia and Guinea; Yoruba from Nigeria to Côte-d'Ivoire...

From the fossil record, homo rhodesiensis seems too young, maybe homo antecessor or homo ergaster? Maybe a new homo species we haven't found trace of yet?

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## markod

I think equatorial West Africa might have been fully colonized by modern humans only quite late. If I had to guess the major constituents of modern West African ancestry would likely be Sudanese Wadi Halfa + archaic Iwo Elero, with varying degrees of Mbuti and North African admixtures. That would explain why Nilotics are inferred to share so much drift with West Eurasians in particular compared to Bantu populations. Archaic and Mbuti admixture pulls Bantu away. 

The rainforests could have provided shelter for surviving archaic groups.

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## Farstar

Interesting, I subscribe myself to this post.

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## bicicleur

if you check haplogroup A, western Africa has the highest diversity

I guess new subclades devellopped on the savanna in East-Africa, and west-Africa was a refuge for those who couldn't coop with the competition of new evolutions and the relative dense popultation

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## Ownstyler

> if you check haplogroup A, western Africa has the highest diversity
> 
> I guess new subclades devellopped on the savanna in East-Africa, and west-Africa was a refuge for those who couldn't coop with the competition of new evolutions and the relative dense popultation


You are assuming haplogroup A carriers are less able to compete, with no reason whatsoever.

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## Gnarl

> *Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans*.


19 percent !?! Thats an amount almost equal to an F2! The average between 2 and 19 % is 10,5. Thats pretty much a F3!

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## Angela

Razib Khan has chimed in...

See:
https://www.gnxp.com/WordPress/2019/...frican-genome/

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## bicicleur

> You are assuming haplogroup A carriers are less able to compete, with no reason whatsoever.


no, I'm not saying that
just that West-Africa is has the most of small very old subclades who are/were on the brink of extinction
West-Africa is the only place where they survived

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## holderlin

That is a TON of archaic in Mende. Wow. And that's old archaic too.

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## Punish Them 911

The Mende people, like most West Africans, don't really have any archaic physical features besides lower facial prognathism, which existed among early modern humans in the fossil record. Carleton Coon once wrote that there was no purer Sapiens man than a "Negro" [sic] -- a surprisingly candid observation for the 1930s. 


Stephen Jay Gould demonstrated that Negroid skulls were more "neotenous" and therefore more evolved than Caucasoid and Australian Aboriginal skulls. How could Black people be more evolved than whites with an 18% archaic introgression, if that population was truly "archaic?"


If the Mende have non-Sapiens ancestry, it must have come from a highly evolved population that had become its own version of Sapiens, which basically validates either the parallel polygenic evolution theory of human subspecies of Carleton Coon, or Milford Wolpoff's multispecific co-evolution theory, because that population definitely crossed over in to "Sapiens" (anatomically) before interbreeding with these Africans. 


Personally, I think it's just junk science like most of the "ancient DNA" crap going on nowadays, that will probably be turned over in no time.

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## markod

> The Mende people, like most West Africans, don't really have any archaic physical features besides lower facial prognathism, which existed among early modern humans in the fossil record. Carleton Coon once wrote that there was no purer Sapiens man than a "Negro" [sic] -- a surprisingly candid observation for the 1930s. 
> Stephen Jay Gould demonstrated that Negroid skulls were more "neotenous" and therefore more evolved than Caucasoid and Australian Aboriginal skulls. How could Black people be more evolved than whites with an 18% archaic introgression, if that population was truly "archaic?"
> If the Mende have non-Sapiens ancestry, it must have come from a highly evolved population that had become its own version of Sapiens, which basically validates either the parallel polygenic evolution theory of human subspecies of Carleton Coon, or Milford Wolpoff's multispecific co-evolution theory, because that population definitely crossed over in to "Sapiens" (anatomically) before interbreeding with these Africans. 
> Personally, I think it's just junk science like most of the "ancient DNA" crap going on nowadays, that will probably be turned over in no time.


It might be better to drop the Neanderthal supremacist doctrine, you're embarrassing yourself with those ever more convoluted conspiracy theories.

Think about it for a second before lashing out.

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## Tomenable

Iwo Eleru skull from Nigeria does not belong to an anatomically modern human, despite being very young:

https://www.bbc.com/news/science-environment-14947363

_"Reanalysis of the 13,000-year-old skull from a cave in West Africa reveals a skull more primitive-looking than its age suggests."_

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## eastara

This may have solved the mystery with haplogroup A00, which is only found in Western Africa around Cameroon. Since it was estimated to be around 270000y.o, older than Homo Sapience, some people thought it came from interbreeding with an extinct hominid. However, geneticists did not want to get involved in its scientific study, cautious not to be accused of racism. The A00 project for collecting DNA samples from Cameroon was crowd funded a few years ago.
*A00 (A00-AF6)*
_Mendez et al. (2013) announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00". It has an estimated age of around 270 kya,[older than estimates for the age of anatomically modern humans current at the time._
_A00 is also sometimes known as "Perry's Y-chromosome" (or simply "Perry's Y"). This previously unknown haplogroup was discovered in 2012, in the Y chromosome of an African-American man, who had submitted his DNA for commercial genealogical analysis.) The subsequent discovery of other males belonging to A00 led to the reclassification of Perry's Y as A00a (A-L1149)._
_Researchers later found A00 was possessed by 11 Mbo males of Western Cameroon (out of a sample of 174 (6.32%). Subsequent research suggested that the overall rate of A00 was even higher among the Mbo, i.e. 9.3% (8 of 86) were later found to fall within A00b (A-A4987)._
_Further research in 2015 indicates that the modern population with the highest concentration of A00 is the Bangwa (or Nweh), a Yemba-speaking group of Cameroon (fr:Bangoua (peuple)): 27 of 67 (40.3%) samples were positive for A00a (L1149). One Bangwa individual did not fit into either A00a or A00b._

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## markod

> Iwo Eleru skull from Nigeria does not belong to an anatomically modern human, despite being very young:
> 
> https://www.bbc.com/news/science-environment-14947363
> 
> _"Reanalysis of the 13,000-year-old skull from a cave in West Africa reveals a skull more primitive-looking than its age suggests."_


I wonder if he's admixed or pure archaic. There are no traces of sapiens in West Africa before the Neolithic afaik.

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## Megalophias

There are very few pre-Neolithic human remains from West Africa at all. Really, what is there apart from Iwo Eleru? Some fragmentary remains from Shum Laka, if you count Cameroon.

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## Moi-même

John Hawks talk about the subject last month in a Gibraltar conference. The relevant part start about 28:00.

https://www.youtube.com/watch?v=aa3258dAOxo

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## Angela

> John Hawks talk about the subject last month in a Gibraltar conference. The relevant part start about 28:00.
> 
> https://www.youtube.com/watch?v=aa3258dAOxo



Thanks, Moi-meme.

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## Angela

> John Hawks was one of those who went on a witch hunt against David Reich and other ancient DNA researchers. To Hell with him.


Well, he may still be right about the subject of this thread.

I was disappointed in him as well as far as the Reich story goes.

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## Ownstyler

Keep in mind that these are just simulated models. The numbers are not necessarily reliable. They are using 95% CI intervals, just like all the social sciences, which produce conflicting claims with equally deserving methodology. Their CI for admixture time goes from 0 to 125.000 ybp! The CI for archaic DNA inheritance is 2%-19%, as you all noted, a huge interval. In my experience, that is not a very good sign. If they set the CI at 99% it would have probably included 0. And remember that they did this a year ago, and since then the numbers have changed quite a bit.

In any case, the split they suggested for this archaic human lineage is around 625.000 ybp, quite far, but not that much further than the Sapiens-Neaderthal/Denisova split.

But disregarding the numbers, the main conclusion that some African population interbred with yet unknown archaic humans looks very plausible.

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## Angela

> Keep in mind that these are just simulated models. The numbers are not necessarily reliable. They are using 95% CI intervals, just like all the social sciences, which produce conflicting claims with equally deserving methodology. Their CI for admixture time goes from 0 to 125.000 ybp! The CI for archaic DNA inheritance is 2%-19%, as you all noted, a huge interval. In my experience, that is not a very good sign. If they set the CI at 99% it would have probably included 0. And remember that they did this a year ago, and since then the numbers have changed quite a bit.
> 
> In any case, the split they suggested for this archaic human lineage is around 625.000 ybp, quite far, but not that much further than the Sapiens-Neaderthal/Denisova split.
> 
> But disregarding the numbers, the main conclusion that some African population interbred with yet unknown archaic humans looks very plausible.


 Thanks for the analysis. Very clear.

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## Jovialis

> Mende in Sierra Leone, Liberia and Guinea; Yoruba from Nigeria to Côte-d'Ivoire...
> 
> From the fossil record, homo rhodesiensis seems too young, maybe homo antecessor or homo ergaster? Maybe a new homo species we haven't found trace of yet?


In the past it has been assumed that it is a sub-species of Homo Erectus.




> “Based on our analysis, the most plausible explanation for this extreme variation is archaic introgression — the introduction of genetic material from a ‘ghost’ species of ancient hominins,” Gokcumen says. “This unknown human relative could be a species that has been discovered, such as a subspecies of _Homo erectus, or an undiscovered hominin. We call it a ‘ghost’ species because we don’t have the fossils.”
> 
> _http://www.buffalo.edu/news/releases/2017/07/028.html

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## Farstar

Are there efforts to find fossils for the "ghosts"?

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## Angela

> Are there efforts to find fossils for the "ghosts"?


Absolutely. The problem is that with the climate in many areas of Africa, they degrade more quickly than in more northern, colder parts of the world.

Newer techniques are making it easier to get some dna from them, but I don't know if we'll ever have as much as from more northern areas.

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## halfalp

What about this?

https://www.researchgate.net/publica...metric_studies

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