A new (open access) paper in Cell, Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals, is making a big splash in the media. 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!
The idea of no Neandertal introgression south of the Sahara was always strange. It was only based on a prejudice, namely that all gene flow went out of Africa and Subsaharans, except obviously admixed East Africans, have no Eurasian admixture of significance at all.
This assumption alone is strange, considering how widespread notions of “we are all mixed” are in science and media, even in instances where it is not suitable at all and doesnt fit reality.
But in “black Africa” they tested with a baseline of zero gene flow! How could that have happened in the first place? Probably just because of the Out of Africa and anti-migrationist dogma or lack of better methods?
Anyway, this new analysis makes even more sense if taking the Shum Laka paper into account as well. Together these two studies present factual evidence for a big scale, fairly recent back migration from West Eurasians to virtually all of Africa. One big sweep.
Now a question I couldn’t answer by a quick read of the paper via mobile phone is the estimate. Do they give one? Whats your assessment?
Going after the Neandertal admixture, the Eurasian backflow should be estimated to 30-40 percent in Yoruba, wouldnt you say?
The percentage could be even higher if a assuming a more Basal Eurasian ancestral component which itself had just reduced Neandertal ancestry. This could bring the sweep to 50+ percent, which would correspond nicely with some models of the Shum Laka paper, just correcting the source of the more Eurasian shifted main component.
If you’re speaking of ancient (paleo) Eurasian backflow into Africa you have to ask why there’s almost no Eurasian mtDNA in Africa. There is Y DNA E which is very popular in Africa and which is probably of Eurasian origin. But, where’s the Eurasian mtDNA?
“The idea of no Neandertal introgression south of the Sahara was always strange. It was only based on a prejudice……in “black Africa” they tested with a baseline of zero gene flow! How could that have happened in the first place? Probably just because of the Out of Africa and anti-migrationist dogma or lack of better methods?”
It does make sense considering Neanderthals never lived in Africa. And considering the lack of Eurasian mtDNA in Africa. mtDNA was the first thing human population geneticists studied. When, they saw a deep split between AFrica & Eurasia, they went on assuming for good reason the two had been isolated forever.
U6 and M1 are both almost certainly back-migrated Eurasian mtDNAs, especially U6. Both lineages are old enough to be fellow travelers along with E in a back to Africa migration, in particular M1 since it splits directly from the root of M.
If you’re speaking of ancient (paleo) Eurasian backflow into Africa you have to ask why there’s almost no Eurasian mtDNA in Africa. There is Y DNA E which is very popular in Africa and which is probably of Eurasian origin. But, where’s the Eurasian mtDNA?
sex bias isn’t a new thing. if the E people were mobile pastoralists, which seems plausible, then loss of maternal lineages may make sense. you have groups as in chad which are overwhelmingly R1b but have only a bit of eurasian autosomal signal.
First of all there are low level Eurasian mtDNA haplotypes in West Africa. Secondly like Razib said sex bias is nothing new at all. Its being constantly underestimated.
Third: L3 in particular was not found in Shum Laka and won’t be found in any related people before the admixture event. It appeared from the North in the region, it won’t have moved through the jungle. So it was either picked up in East Africa and transferred through the Sahara, or it was even born North Eastern Africa, even Eurasia. That’s a solid 30-40 percent of mtDNA which is fairly new in the region. Whether its African or not, it won’t be from West Africa, that should be a given.
Compare with a recent mtDNA study on West Africans:
https://www.sciencedirect.com/science/article/pii/S1872497319302492
I found the study which pointed to the L3 origin in Eurasia from 2018. Like the recent results from Shum Laka and with IBDmix, this study argues for an Eurasian origin of L3:
“The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.”
https://www.ncbi.nlm.nih.gov/pubmed/29921229
This is in full agreement with the new paper and the IBDmix results which propose a major back-migration from Eurasia to Africa.
They also come up with the interesting idea of a secondary SEA demographic centre from which a second global distribution of modern H. s. started.
By correlating E with mtDNA, from the same paper:
“It appears that the E and L2/L3 expansions were strongest in western Sahel and western Guinea, where they replaced the majority of the oldest mtDNA (L0 and L1) and Y-chromosome (A and B) lineages (Table (Table2).2).”
and
“Class I, characterized by relatively low frequencies for both the L3 and E haplogroups, encompasses the majority of the Khoesan-speaking groups from South Africa, Namibia, and Angola and the Hadza from Tanzania, as well as several pygmy groups from Cameroon, Gabon, CAR and Congo, such as the Baka and the Babinga. In addition to having different geographic locations, these groups are differentiated by the frequencies of other haplogroups. Thus, samples from Khoesan-speaking groups harbor high frequencies of mtDNA L0d and L0k haplogroups and Y-chromosome A lineages, while the Central African pygmies are characterized by the highest frequencies of mtDNA L1c and Y-chromosome B-M60 lineages.”
They estimated that the proportion of Neanderthal ancestry in West Eurasia is not that different from what’s seen in East Eurasia. If true, the mysterious Basal Eurasians are getting more elusive and perhaps unnecessary.
The paper on trans-Saharan patrilineages (D’Atanasio et al, 2018), revealed that several E-M2 clades such as E-V4990 and E-V5001, are restricted to North Africa. In addtion, E-Z15939 is present at high frequencies among different Fulani groups. In all of the published studies where the Fulani samples from various communities have been analyzed, their autosomal DNA systematically reveals a North African (“Maghrebi”) component which is widely distributed and stable.
In your post from 2012, (“The Fulani have an old “Berber” (?) element”), you observed that the West Eurasian component of Fulanis that’s commonly observed in admixture analyses (Henn, 2012) is hardly ever found in its “pure” form in the present-day North African populations. Perhaps, suggesting that the “Maghrebi” component of Fulanis must be older – approximately 2000 years old.
Could it be indicative of similar West Eurasian back migration into Africa?
@Obs do you agree with the claim that the Shum Laka genetic study makes the term “Eurasian” or “SSA” obsolete?
There are people who claim that the Shum Laka study shows that ANA is on the same branch as Basal West African and that this paper concludes that the component that constituent the largest component of West Africans (Basal West African) is on the same level and radiated with Eurasian. So basically West Africans are in the same branch with Eurasians with Khoisan as an outgroup. These people argue that the “exclusivity” of the so-called Eurasians in Africa, got a heavy blow with the Shuma study since any “Eurasians” who back migrated back to Africa wouldn‘t have been “Special”. They just would have met African people who were not that different from them, people who later picked up other ancestries with time. Hence the terms like “Subsaharan African” and “Eurasian” are totally meaningless genetically, especially in Africa.