Archaic gene flow into African Populations

[EDsomali]

Results

Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbour populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.

Source

A few interesting notes about this paper.

1. It seems like a divergent DNA from something that split off the ancestors of humans 550kya contributed to west, central and southern African populations.
2. Dinka seems to have some pygmy ancestry, not sure if it's just them or a sign of mbuti admixture in all Nilo-Saharan ancestry.
3. AMH contributed ancestry to Neanderthals. When this is taken into account admixture from neanderthals for Europeans drops substantially to only 1.1% from 3.6%.

The situation is interesting for Niger-congo speakers.

They have = Ancestral East African- Ancestral North African- Divergent Homosapien admixture - Admixture from these hominids and potentially another ghost lineage (Though this might be the same as the former or something entirely different)

 

[EDsomali]

https://www.bbc.co.uk/news/science-environment-14947363

There are fossils found in Nigeria that appear to be different from the current populations.

I wonder if these were a mix of the divergent homo-sapien line and the archaic humans which Niger-congo peoples went on to conquer.

 

[Pitta]

Since khoisans are included in this would this mean that possibly ethiopians are affected by this, as I've read that they might have very slight admixture with them.Though it would be close to zero since even khoisans have low numbers ?

 

[911]

Dinka and other nilotes are the purest humans

 

[Apollo]

2. Dinka seems to have some pygmy ancestry, not sure if it's just them or a sign of mbuti admixture in all Nilo-Saharan ancestry.

I don't think Dinkas have real pygmy ancestry. Rather the Mbuti are related to the Dinka as they live in Northeastern Congo, not too far from South Sudan after all and evolved into pygmies.

 

[EDsomali]

Results
3. AMH contributed ancestry to Neanderthals. When this is taken into account admixture from neanderthals for Europeans drops substantially to only 1.1% from 3.6%.

I made a mistake.

They actually found increased levels of Neanderthal admixture when they took this into account.

 

[MI]

I know some of you like to joke around say West Africans have Homo Erectus DNA or something of the like but is that really it? I haven’t read much into the subject but here’s my take.

With the relatively recent discovery of Haplogroup A00 aka “Perry’s Y” found in an African American man named Albert Perry, the date of the human patrilineal ancestor of all modern humans was pushed further back than the appearance of Anatomically Modern Humans—meaning that the common Y-chromosomal ancestor of all modern humans likely wasn’t “human human” depending on your definition. This haplogroup has now also been found in several Mbo Bantu speakers, Bangwa Niger-Congo speakers & an ancient African Pygmy who lived circa 8000-3000ybp. It’s also been noted before that West Africans and Pygmies share deep ancestral genetic drift not shared with other populations.

https://www.pnas.org/content/105/5/1596.full

https://www.sciencedirect.com/science/article/pii/S0960982209005429


All other Y-DNA haplogroups today descend from A0-T(old Adam), which itself descends from A00(revised Adam). Isn’t it likely that a population although descended from the same source population as revised Adam, left West Africa thereby splitting from its sister population & contributing the majority of the ancestry of modern non-west Africans, whose descendants then later back-migrated into West Africa? This migration was accompanied by carriers of haplogroup E which is downstream from A0-T and A0-T itself and it’s derived sub-clades like A0 and A1.

Maybe the divergence of old Adam and revised Adam is caused by African multi-regionalism in regards to human origins, with old Adam picking up the genes of hominids in South Africa like the Florisbad man? There does seem to be a southerly migration.

I tried finding out what carriers of Basal A00 looked like and if they were Homo Sapiens but it turns out that’s very hard to answer since there’s a fossil gap in Africa (from 400–260 kya) around the time hominids like the carriers of A00 were alive and kicking.

 

[EDsomali]

https://www.somalispot.com/threads/archaic-gene-flow-into-african-populations.61451/

I made a thread about this ancestry.

 

[Nilotufian]

Heidelbergensis (an intermediate Homo lineage between Erectus and Sapiens) is most likely candidate, since Denisovan/Neanderthal ruled out & Erectus= 'too old'.

 

[MI]

Heidelbergensis (an intermediate Homo lineage between Erectus and Sapiens) is most likely candidate, since Denisovan/Neanderthal ruled out & Erectus= 'too old'.

I thought Heidelbergensis was ruled out as the ancestor of Sapiens and rather were an early form of Neanderthal?

 

[Nilotufian]

I thought Heidelbergensis was ruled out as the ancestor of Sapiens and rather were an early form of Neanderthal?

The archaic ancestry in West-Central Africans and Bantus cannot be from Neanderthals, since we have high quality genomes and yet Yoruba reject both as an appropriate admixture source.

 

[Apollo]

I thought Heidelbergensis was ruled out as the ancestor of Sapiens and rather were an early form of Neanderthal?

All of this stuff is based on statistical models rather than actual fossils.

They call it ''ghost populations''.

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

 

[MI]

The archaic ancestry in West-Central Africans and Bantus cannot be from Neanderthals, since we have high quality genomes and yet Yoruba reject both as an appropriate admixture source.

All of this stuff is based on statistical models rather than actual fossils.

They call it ''ghost populations''.

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

Yup, I’m familiar with the concept of a ghost population. But they’ve actually tested some of the genome of fossils believed to be Homo Heidelbergensis in Spain. They seem to suggest that Heidelbergensis is not the common ancestor to Sapiens but to Neanderthals and possibly Denisovans with the common ancestor to all three possibly being Homo antecessor.

https://www.researchgate.net/public...iddle_Pleistocene_Sima_de_los_Huesos_hominins

https://www.nature.com/news/oldest-ancient-human-dna-details-dawn-of-neanderthals-1.19557

But my original question was is it possible that the unknown archaic ancestry in some SSA populations is actually from the same population as hg A00? I know we don’t have any fossils of this hominid but I’m only asking in the hypothetical unless there’s some piece of information I’m missing that disqualifies it.

 

[Dr._Michael_H]

https://www.bbc.co.uk/news/science-environment-14947363

There are fossils found in Nigeria that appear to be different from the current populations.

I wonder if these were a mix of the divergent homo-sapien line and the archaic humans which Niger-congo peoples went on to conquer.

The fossils at Iwo Eleru are “Great Ape Proto Negroes”. They maintain the “Simian Shelf” like the fossils at Jebel Sahaba. They are not “Modern Humans”. The Niger Congo Bantu sub Saharan negroes are an admixture between CT M168 yDNA haplogroup via DE and an archaic hominin, probably homo erectus or homo Heidelbergensis. The oldest known AMH negro skeleton is dated to 6400 BP, also found in Nigeria. Yoruba show admixture with Eurasians dated to about 12,000 years ago. They also have neanderthal DNA carried to them by Eurasians.