Neanderthal admixture in Africans (into Africa? or back to Africa?)

Time and time again you read that only non-Africans carry Neanderthal DNA because it was the wave of humans leaving Africa in an Out-of-Africa migration that encountered the Neanderthals in Eurasia and mated with them, mixing our and their genes. Africans who remained in the cradle of mankind, didn't admix and therefore carry no Neanderthal DNA.

A paper published in 2018 (Neandertal signatures in modern human mitochondrial genome haplogroups?, Renata C. Ferreira, Camila R. Rodrigues, James R. Broach,Marcelo R. S. Briones, BioRxiv, 18/Sep/2018. doi: https://doi.org/10.1101/190363) puts this idea upside down: the authors state that "...contrary to what is observed in the nuclear genome, African mitochondrial haplogoups have more potential Neandertal signatures than Asian and European haplogroups.".

Let's look into this surprising and contradictory finding.

The authors repeat the current orthodox view of an admixture outside of Africa:

"Intercrosses between Neandertals and ancient Homo sapiens lineages, or archaic Anatomically Modern Humans (AMH) who migrated from Africa into the Middle East and Europe in the last 50,000 years might explain the presence of Neandertal signatures in extant human genomes (Prüfer et al., 2014; Simonti et al., 2016). The spatio-temporal overlap of Neandertals and AMH is estimated to be approximately 22,000 years since the first AMH arrived in Europe around 50,000 years ago..."

Neanderthal mtDNA is liniked to certain diseases in modern humans, and the study found evidence of this too, and this included Africans: "Four of these disease associated N-SNVs were observed in African haplogroups (L0, L1, L2, L3, 10 L4, L5 and L6)", N-SNVs stands for Neanderthal SNVs. and the haplogroups they mention are considered the oldest and most basal ones. So how did the Neanderthal DNA admix with these "basal" haplogroups?

The autors explain this as follows: "A back to Africa hypothesis has been proposed in which humans from Eurasia returned to Africa and impacted a wide range of sub-Saharan populations (Henn et al., 2012). Our data suggest that Neandertal signatures might be present in all major African haplogroups which supports the “Back to Africa” contribution to the modern mitochondrial African pool."

They also conclude that modern human males introgressed with female Neanderthals more frequently in the Africans than in the Europeans (where the opposite took place: modern women were impregnated by Neanderthal men):

"Our data is compatible with a scenario in which the AMH-Neandertal crosses occur in Europeans, East Asians and African lines of descent. However, in the African haplogroups the crosses between AMH males and Neandertal females would have a higher frequency than in European lines of descent, where the reverse crosses would be predominant. Based on the comparison of Neandertal signatures in nuclear and mitochondrial genome haplogroups we hypothesize that the African lines of descent would have a higher female Neandertal contribution whereas European lines of descent would have higher male Neandertal contribution."

It is interesting to point out that Africans, Eurasians and Neanderthals share the N-SNV 16,278, which "is found in African haplogroups 34 (L0, L1, L2, L5 and L6) and two Eurasian haplogroups (X3, U2c and P2) and in all Neandertal sequences..."

What is also interesting is the link between Amerindians, Eurasians and the Altai Neanderthals, hinting at an admixture in Siberia : "... N-SNV 16.298 is found only in Eurasian-Native American 36 haplogroups (V1, V2, M8, C1, C4, C7 and Z1) and only in the Altai Neandertal."

The heat map (Fig. 4) in the paper shows a surprisingly strong introgression of Neanderthal genes in Africans, compared to Europeans, Asians, people from Oceania and Amerindians:

You would expect this admixign to have happened in non-Africans, instead it took place with Africans.

Could this enrichement of African DNA be caused by an actual into-Africa migration? One where modern humans -of Eurasian origin- with Neanderthal admixture entered Africa, and admixed there with the locals?

The gradient displayed in the image above, from a low (Oceania - Americas) to mid (East and western Asia - Europe) to high (Africa) Neanderthal genetic content clearly marks a migration path through Neanderthal territory (central Eurasia) into Africa.

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