We usually hear that the modern humans, left Africa and, in Eurasia encountered their relatives, the Neanderthals and Denisovans, mating with them and sharing genes. This resulted in non-Africans having snips of genetic material from both ancient groups, with different levels depending on their geographic locations (Denisovan is higher in Oceanians, South eastern, and Eastern Asians, and Native Americans, while Neanderthal is higher among Europeans and Western Asians). Africans, on the other hand have almost zero introgression of Neanderthal genes (the little they have came from mixing with Eurasians who back-migrated into Africa after the OOA event), and zero Denisovan content. The Denisovans never made it back into Africa.
A paper I just read says the opposite! Africans have higher levels of Denisovan and Neanderthal genes than non-Africans.. This paper is ten-years-old (Povysil G, Hochreiter S. IBD Sharing between Africans, Neandertals, and Denisovans. Genome Biol Evol. 2016 Dec 1;8(12):3406-3416. doi: 10.1093/gbe/evw234. PMID: 28158547; PMCID: PMC5381509) and contradicts the history of migration and admixture mentioned further up. Let's see what this paper says and how it explains the higher level of Denisovan and Neanderthal genes in Africans.
p>First, the data, below is Table 1 from Povysil and Hoechretier, 2016. Unfortunately, the table does not include Native Americans! and therefore these are always underrepresented in research articles!
Ancient admixture within Africa?
The authors extracted Identical By Descent or IBD segments from genetic data of the 1000 Genomes Phase 3 dataset. They found two types of IBD segments that are shared between modern human beings and also with our ancestors, the Neanderthals and the Denisovans. These are the "longer" and the "shorter" segment types.
The long segments are those found in Eurasians, and the ones shared with Neanderthals and Denisovans are found at higher frequencies in Southern and Eastern Asians. Long segments seem to be related to admixture events outside of Africa.
The short segments, on the other hand, are shared by Africans, and for this reason, the authors believe that they represent ancient "events involving ancestors of humans and other ancient hominins within Africa."
The paper says that shorter segments are "presumably older than longer ones, the segments we extracted reveal events from the very distant past. We found short IBD segments that match the Neandertal and/or Denisovan genome and are shared mainly by Africans. These segments may either stem from a common ancestor with subsequent incomplete lineage sorting or more likely from an interbreeding of ancestors of humans and other ancient hominins within Africa."
They found a surprisingly high frequency of archaic short segments in the sexual X chromosome (that in men is inherited from their mothers, and in women, one part of their pair comes from their mothers, and the other from their fathers): "...chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa."
The logical explanation for this high frequency of archaic genes in Africans is that they met and bred with these people within Africa. But, this goes against the hypothesis that Africa had highly a structured population with many small, isolated groups, that only occasionally met, and that each of them harbored a high diversity which, when they finally blended, led to the current diversity encountered in Africa. The paper says the following:
"One interpretation of our results is that ancestors of humans and ancient hominins interbred within Africa. The hypothesis of ancient substructures in Africa with limited gene flow between subpopulations of hominins does not contradict this interbreeding. Neandertals and Denisovans could be more closely related to Africans than to out-of-Africa populations because of more interactions between their ancestors. In this case, since the ancestors of Africans and Neandertals/Denisovans were not clearly separated, this could be considered “admixture” rather than “interbreeding”.
So, the limited number of Denisovan or Neanderthal alleles in non-Africans would be the outcome of the bottleneck, and founder effect that took place as they left Africa, carrying a limited subset of the original Neanderthal and Denisovan genes.
The second explanation is similar, but is pushed further back in time. The shared genes are due to a common-origin of Neanderthals, Denisovans and Modern Humans:
"Another interpretation of the extensive IBD sharing between Africans and ancient genomes is that these shared IBD segments originate from a common ancestor of Neandertals/Denisovans and humans. They can only be found in modern Africans due to incomplete lineage sorting. According to this scenario, the detected IBD segments arose first in the population that existed prior to the ancient separation of Neandertals, Denisovans and modern humans, but were relatively rare. Consequently they survived in both archaic humans and in present-day Africans, while drifting to a very low frequency in non-Africans.
The authors analyze this hyptothesis and note that Africans carrying the Neanderthal-Denisovan genetic snippets either carry all of them (there are over 20 of these "rare variants") or none! This presents the improbable situation that all the other people (who carried intermediate ammounts of these alleles) died out leaving no descent. The paper suggests a way out: populations were separated.
"In our opinion, it is unlikely that, for thousands of IBD segments, only these extremes survived while all the intermediate cases died out completely. Consequently, we assume that the source population was separated from all the other populations for a long time and, therefore, acquired such a high number of mutations. We do not know, whether the separated population was already a Neandertal, a Denisovan, their ancestor, or a different hominin. We cannot rule out, that the IBD segments also existed in ancestors of modern Eurasians and were lost due to strong genetic drift. However, our results suggest an interbreeding within Africa that involved a population that was isolated for an extended period of time. This early interbreeding can still be detected via IBD segments that are shared between Africans and Neandertals and/or Denisovans.
The alternative that the African alleles are due to a back-to-Africa migration is discarded because Africans have exclusive alleles not found elsewhere and they are found in all Africans, suggesting a wide distribution.
This study also found a high level of "segments shared between South Asians and Neandertals and/or Denisovans than between other non-African populations and these ancient genomes." This, has been proven time and time again over the past ten years. Interestingly, the authors speculate about the reason for this prevalence of Denisovan genes and offer three explanations. All current papers focus on expanation #1, ignoring the other two, but we should not forget that there are other alternatives that explain the Denisovan introgression in Oceanians and Southeast Asians: "Recent investigations found that South Asians share a surprisingly high amount of DNA with the Denisovan genome (Sankararaman et al. 2016). In our analysis the amount is even higher. Possible explanations for this finding are as follows: (1) additional interbreeding events with ancestors of South Asians, (2) introduction of IBD segments from ancient genomes into other non-African populations via South Asians and not directly, and (3) combinations of bottlenecks, genetic drift, and different selective pressures."
Closing Remarks
Africans seem to have ancient lineages of Denisovan and Neanderthal alleles. An admixture that possibly took place in Africa, within the continent. How does this tally with current theories of an exclusive outside of Africa admixture? It is thought provoking to imagine introgression within Africa, because it alters the timelines of the admixture dates proposed in the different admixture papers (see my post with links to all my posts on admixture and introgressions).
It is a pity that this paper, like most papers, ignores data from Amerindians. Including them would probably uncover furhter research aveneues.
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