Neandersovans mixed with Superarchaics as they entered Eurasia 700 kya

Six years ago I wrote a post (Denisovans interbred with Homo erectus) based on an article that suggested that Denisovans had admixed with a "ghost" population that had split from the line that links us and Denisovans, around 1 Millioni years ago. In my post I guessed that this ancestor was no other than Homo erectus.

A very recent paper (see full text: Neanderthal-Denisovan ancestors interbred with a distantly related hominin, Alan R. Rogers, Nathan S. Harris and Alan A. Achenbac. Science Advances 20 Feb 2020:Vol. 6, no. 8, eaay5483 DOI: 10.1126/sciadv.aay5483) came to that same conclusion after some interesting genetic analysis.

The Abstract of this paper says:

"... We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors—members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans."

The paper looks into the "large-brained hominins" living in Europe, that made Acheulean stone tools some 600,000 year. It calls them Neanderthal ancestors. They come from the "neandersovan" group, from which Neanderthals and Denisovans descend. And which split from our modern human lineage around 750 kya. The neandersovans left Africa and walked into Eurasia, which was not an empty territory. It had already been colonized some 1.85 Million years ago by other hominins, the "superarchaic" population.

Did they mix?

Yes, they did.

The authors consider that "If superarchaics separated from an African population, then this separation must have preceded the arrival of superarchaics in Eurasia. Nonetheless, our 1.8 to 2.2 Ma interval includes the 1.85 Ma date of the earliest Eurasian archaeological remains at Dmanisi. Thus, superarchaics may descend from the earliest human dispersal into Eurasia, as represented by the Dmanisi fossils. On the other hand, some authors prefer a higher mutation rate of 0.5 × 10−9 per year. Under this clock, the lower end of our confidence interval would be 1.6 Ma ago. Thus, our results are also consistent with the view that superarchaics entered Eurasia after the earliest remains at Dmanisi.".

So depending on the mutation rate adopted, they could have mixed with the descendants of the Dmanisi people from Georgia or from a later group. Dmanisi may be Homo habilis or Homo erectus.

The paper proposes that there were "... only three expansions of humans from Africa into Eurasia: an expansion of early Homo at about 1.9 Ma ago, an expansion of neandersovans at about 700 ka ago, and an expansion of modern humans at about 50 ka ago.". This first expansion led to the superarchaic population in Eurasia that mixed with the second wave of "neandersovans" 700 kya.

The scenario painted in the paper is the following: "Our results indicate that neandersovans interbred with superarchaics early in the middle Pleistocene, shortly after expanding into Eurasia. This is the earliest known admixture between hominin populations. Furthermore, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. According to our estimates, neandersovans and superarchaics had been separate for about 1.2 Ma. Later, when superarchaics exchanged genes with Denisovans, the two populations had been separate even longer. By comparison, the Neanderthals and Denisovans who interbred with modern humans had been separate less than 0.7 Ma.".

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

The complex Human tree in Africa...

A new paper published in Nature (Ancient West African foragers in the context of African population history, Mark Lipson, Isabelle Ribot, David Reich. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1) tells us about the admixture going on in Africa some thousands of years ago:

The paper's highlights are:

• They sequenced the DNA of four children from Shum Laka in Cameroon buried on two separate occasions (two of the children were buried 8,000 years ago, the other two, 3,000 years ago).
• One of them carried the oldest and most divergent Y chromosome haplogroup: A00
• Their model implies that these children belong to the fourth group that originated modern human lineages. There were three more groups: (i) from which modern Khoisan people descend from. (ii) Ancestral group to the East Africans. (iii) An exinct "ghost" population. These groups are some 250 ky old.

Science tells us more about the extinct group (iii): "Another two-thirds of children’s DNA came from an ancient "basal" source in West Africa, including some from a "long lost ghost population of modern humans that we didn’t know about before" says population geneticist David Reich of Harvard University, leader of the study."

And even more interesting is that "...the Shum Laka individuals are most related to present day rainforest hunter-gatherers [pygmies] and not ancestors of Bantu-speakers is surprising given that Shum Laka was long considered by archeologist[s] as the site where Bantu-speaker culture [was] developing in situ," (from LiveScience)

These four children are therefore not related to the modern Africans living in Cameroon or to the Bantu speakers who spread out across Africa. Instead they are closer to the pygmies of Central Africa!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Neanderthal genes in Africans: a confirmed fact

Last October I posted about a paper that disclosed that Africans had a higher Neanderthal signature in their mtDNA than Asians or Europeans.

African lack of Neanderthal DNA (and mtDNA) is used as proof of the Out of Africa (OOA) event, because it is said that Neanderthals and Homo sapiens admixed outside of Africa after H. sapiens migrated from Africa on their OOA journey.

A recent paper cast a shadow of doubt on this assumption: they have found signals of Neanderthal DNA in Africans!

The paper is: Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals by Lu Chen, Aaron B. Wolf, Wenqing Fu, Liming Li, and Joshua M. Akey. Chen et al., 2020, Cell 180, 1–11 February 20, 2020 https://doi.org/10.1016/j.cell.2020.01.012.

It summarizes their research as follows:

"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"

The paper finds that some of the ancestors of modern Europeans back migrated into Africa after they had split from those who would later become East Asians.

They found 13 African-specific high-frequency Neanderthal haplotypes which are unique to Africans, and only found in Africa, and another 31< haplotypes shared with Europeans. Specific African genes means that selection preserved them because they gave those carrying them some immune benefits and also protection against UV radiation in sunlight.

So now we know that ALL humans have Neanderthal genes in their genome, including Africans.

This gene flow, which had not been recognized until now also caused biased estimations of Neanderthal admixture in Asians and Europeans: East Asians seemed to have 20% more Neanderthal DNA than Europeans, which was odd, considering that Neanderthals lived in western Eurasia so admixture there would have been higher than in the Far East.

But now it seems that roughly 0.3 to 0.5 % of African genome was inherited from Neanderthals (vs. 1.8% in Non-Africans).

So factoring in this African Neanderthal content, the East Asians ended up with only 8% more Neanderthal genes than Europeans.

The study found "[in] African populations, we identified approximately 17 Mb of putative Neanderthal sequence per individual"

Compare thiese 17Mb with what they found in Europeans and Asians:

"we found similar levels of Neanderthal ancestry in Europeans (51 Mb/individual), East Asians (55 Mb/individual), and South Asians (55 Mb/individual)"

So Africans have roughly one third of the Neanderthal admixture that non-Africans have! See the image below which shows exactly this (non-Africans in Blue, Africans in brown):

Neanderthal genetic admixture in humans. From Fig. 2 in Chen et al.

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Finally, around 94 percent of Neandertal DNA sequences found in Modern Africans is also shared with Non-Africans.

The paper explains the Neanderthal admixture into Africa as follows: "In summary, these data indicate that both pre-OOA human-to-Neanderthal gene flow and elevated historic backmigration contribute to the signal of Neanderthal ancestry detected in Africans.".

The first wave of humans to leave Africa between 250 and 150 kya, mixed with Neanderthals in Eurasia and passed on to them some archaic human genes. These were lost as this pre-OOA wave became extinct. The Neanderthals then mixed with the OOA wave and part of these admixed modern Humans returned to Africa bringing the genes with them.

Perhaps further studies -Science news reports an unpublished study that ratifies Chen et al. findings: "as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans."

I have written many posts about "into Africa events", but this one is the first paper to conclusively prove the presence of Neanderthal genes in modern Africans.

This will open the gates to more scrutiny on the origin of the higher "African" diversity when compared to the rest of humankind. This diversity is surely due to admixture with archaic populations and not only to bottlenecks caused by an OOA migration.

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall ©