# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Neanderthal Dna in Africa

## Angela

See:
https://www.cell.com/cell/fulltext/S...ecsectitle0080

Basically, the authors believe it's higher than we thought.

"*Highlights*•IBDmix detects archaic ancestry without using a modern human reference population•African individuals have a stronger Neanderthal ancestry signal than previously thought•Evidence of back-to-Africa migrations contributing to Neanderthal ancestry in Africans•Variation in non-African Neanderthal ancestry has been overestimated

*Summary*Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.

*Graphical Abstract*



Razib Khan's piece on it:

https://www.gnxp.com/WordPress/2020/...medium=twitter

"Whether you believe this paper on its own is conditional on how deeply you can grok the methods. Honestly I don’t know if I trust myself to render any judgment until I’ve replicated the whole analysis pipeline. Intuition doesn’t come from a priori.That being said, in light of other factors and our general understanding of hominin gene flow this is a highly plausible result. They conclude that “A model that combines both of these events, elevated back migration and human-to-Neanderthal gene flow, matches the empirical data best across all features.” Gene flow from neo-African modern humans into Neanderthals seems very likely. Similarly, it is quite possible that there was widespread Eurasian back migration into Africa. But, that back migration was _West Eurasian._
_The “problem” with the older models is that it simply assumed that groups such as the Yoruba had no Neanderthal ancestry, presupposing a particular model of paleoanthropological gene flow where Africa is purely a source, rather than also a sink. Assume nothing!"_

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## Ygorcs

So what do you think is the most likely explanation? Neanderthals moving into Africa (they were in the Levant for millennia after millennia after all)? Modern Humans moving into West Asia and later coming back after an unsuccessful colonization attempt? Both things in different time periods?

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## Angela

> So what do you think is the most likely explanation? Neanderthals moving into Africa (they were in the Levant for millennia after millennia after all)? Modern Humans moving into West Asia and later coming back after an unsuccessful colonization attempt? Both things in different time periods?


I think the authors are going for both scenarios, don't you? 

Whether the Neanderthals moved into Africa or not I don't know. Perhaps there's room for a scenario where the Neo-African went into Neanderthals involved some movement by Neo-Africans into the Levant. It depends whether there have been any Neanderthal signs in Africa, say, Egypt at all, although given the conditions it may have happened and we just haven't found the evidence.

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## bicicleur

> I think the authors are going for both scenarios, don't you? 
> 
> Whether the Neanderthals moved into Africa or not I don't know. Perhaps there's room for a scenario where the Neo-African went into Neanderthals involved some movement by Neo-Africans into the Levant. It depends whether there have been any Neanderthal signs in Africa, say, Egypt at all, although given the conditions it may have happened and we just haven't found the evidence.


modern humans were found 185 ka in the Levant, and even 210 ka in Greece now
and Neanderthals were found in the same area

yes, modern humans went back and forth in and out of Africa since 210 ka
as David Reich pointed out in his book, it is even conceivable that modern humans were not born in Africa, but in Eurasia

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## Gnarl

> So what do you think is the most likely explanation? Neanderthals moving into Africa (they were in the Levant for millennia after millennia after all)? Modern Humans moving into West Asia and later coming back after an unsuccessful colonization attempt? Both things in different time periods?


From my reading they are saying its back migration from Western Eurasia.

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## Palermo Trapani

Gnarl: I read the paper as well and yes I agree it is Western Eurasian. Chen et al (2020) also document that the differences in Neanderthal admixture in Europeans and Asians is not as high as previously documented. As Angela noted in post #1, most of the prior research has assumed a source population in Sub-Saharan Africa (e.g., San) as having zero Neanderthal admixture since they did not directly breed with them. In a recent article in the Scientist (See link below) Prof. Tony Capra of Vanderbilt stated that the assumption of zero admixture in modern Sub-Saharan Africans failed to consider that Europeans with Neanderthal and Sapien admixture could have migrated back to Sub-Saharan Africa, which this study documents did happen and has also according to Professor Akey of Princenton resulted in an overestimation of Neanderthal DNA across the board for all modern Human populations. See linked article for source and further discussion. 

https://www.the-scientist.com/news-o...-thought-67033

Another recent article published in the American Journal of Human Genetics finds evidence of at least once archaic admixture in sub-Saharan Africa (earlier papers have documented this as well) but they don't seem to say it is Neanderthal. The abstract which I have linked is publicly available, but the full paper is not.

https://www.cell.com/ajhg/fulltext/S0002-9297(19)30426-4

Lorente-Galdos (2019) and Hammer et al (2011) are 2 earlier studies that document archaic admixture in sub-Saharan African populations of 4-6%, and 2%, respectively. Those are both publicly available can can be easily accessed. Signature Neanderthal admixture has already been documented in Modern North African populations by Sanchez-Quinto et al (2012) and that the Signature Neanderthal admixture in North Africans was not due to recent migrations of peoples from the Near East or Europe. So this study is consistent with the earlier back migration into Africa but this earlier paper was not able to detect the Neanderthal signal in sub-Saharan Africans that Chen et al (2020) did.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047765


Given all this Neanderthal admixture found now in all modern populations, I wonder what the role of Neanderthals with respect to the Jebel Irhoud fossil in Morroco dating back to 300,000 years ago. Spain was obviously a hotbed of Neanderthal territory given the fossil finds there. Was Jebel Irhoud and early example of Neanderthal and Sapien admixture?

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## Gnarl

Archaic humans seemed less mobile than the current lot. A pattern seems to have been that they would displace a more archaic population and then settle in to differentiate over time, like the Neanderthals and various Denisovan populations. Given this I am inclined to assume that Archaic admixture in Africa not directly traceable to Neanderthals involved African Archaics. Homo Idaltu, Heidelbergensis, and yet unsampled populations.

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## real expert

David Reich seems skeptical about the study's conclusions/suggestions regarding (greater than thought) Eurasian/neanderthal admixture in modern Africans.
 

https://theentrepreneurfund.com/nean...n-from-africa/

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## ThirdTerm

> Another recent article published in the American Journal of Human Genetics finds evidence of at least once archaic admixture in sub-Saharan Africa (earlier papers have documented this as well) but they don't seem to say it is Neanderthal. The abstract which I have linked is publicly available, but the full paper is not.


A new paper on ghost archaic ancestry in the Yoruba and Mende populations is out. They owe up to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans, which means that the ghost archaic population is much older than Neanderthals or Denisovans. The identity of the archaic hominin is still in question but Homo heidelbergensis is one possibility, ancestral to both Neanderthals and Denisovans.




> Abstract
> While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before 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. 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 West African populations.
> https://advances.sciencemag.org/content/6/7/eaax5097

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## bicicleur

> A new paper on ghost archaic ancestry in the Yoruba and Mende populations is out. They owe up to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans, which means that the ghost archaic population is much older than Neanderthals or Denisovans. The identity of the archaic hominin is still in question but Homo heidelbergensis is one possibility, ancestral to both Neanderthals and Denisovans.


https://www.eupedia.com/forum/thread...mans-in-Africa

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