A paper on skin pigmentation: San & Europeans share light skin alleles

I came across a recent paper published in Science in 2017 by Crawford et al., Loci associated with skin pigmentation identified in African populations, which holds some interesting facts about skin color genetics and when the dark and pale variants arose.

I have posted in the past about light skin pigmentation in Amerindians and Neanderthal skin color, but this post will look into light skin alleles shared by the San people of Africa and modern Europeans.

Skin color genes are ancient

When it comments on how skin pigmentation evolved in modern humans, the paper points out that there is a wide variability within Africa, from the most pale group (the San in southern Africa) to the East African people of the Nilo Saharian region, who aret the darkest. It correctly states that the genes causing both dark and light skin color evolved before our Homo sapiens species appeared around 300,000 years ago (300 ky).

Surprisingly, the paper finds that "the ancestral allele is associated with light pigmentation in about half of the predicted causal SNPs; Neandertal and Denisovan genome sequences, which diverged from modern human sequences 804 ka, contain the ancestral allele at all loci." So, our closest relatives in evolutionary terms carried this ancestral white-skinned allele with them. However, the paper tends to downplay this fact, and it says something which sounds the opposite: "These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years (My) after human ancestors lost most of their protective body hair" and then, like an afterthought mentions the paler tint of Neanderthals and Denisovans: "... although these ancestral hominins may have been moderately, rather than darkly, pigmented. Moreover, it appears that both light and dark pigmentation have continued to evolve over hominid history."

Shared genes between dark pigmented Africans and Australo-Melanesians

It mentions something I hadn't read before (I was always surprised by the similarity in the dark tint of pigmentation in Melanesians, Australian Aboriginal people, Andamenese islanders and Africans): they share a common genetic origin, and could be identical by descent (IBD). The paper says that "Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2, and HERC2 that are identical by descent from Africans. This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution."

It is indeed interesting to note that the bottleneck and founder effects and loss of diversity among the Out of Africa migration population managed to carry, intact, these alleles across Southern Asia, into Australia and Melanesia, while another group managed to carry the white, paler skin alleles.

A light pigmentation variant shared by San and Europeans

There is a variant at SNP rs1800404 within OCA2, that in its ancestral form (with a cytosine base or "C") is found in dark skinned East Asians, most Africans and Australians and Melanesians. The derived variant with a Thymine base or "T", is found in Europeans and the pruportedly most ancestral human beings, the San from southern Afirca! (found among these two groups in frequencies of over 70%). The split is ancient: " Coalescent analysis indicates that the TMRCA of all lineages is 1.7 Ma (95% CI, 1.5 to 2.0 Ma), and the TMRCA of lineages containing the derived (T) allele is 629 ka (95% CI, 426 to 848 ka)"

The tree shown above has two branches with the African one deeper (older) and shorter ones for most modern populations. Note the Oceanians and South Asians are on the African branch.

The allele shared by San and Europeans dates back approximately to the time Neanderthals and Denisovans split from the Modern human lineage.

Another region that acts upon skin color is HERC2, where SNP rs6497271 comes in an ancestral A variant (with an adenine base) providing dark pigmentation to Australo-Melanesians and Africans (identical in both groups, suggesting an identity by descent), and the derived base, (G) or guanine which is linked to lighter skin pigmentation and found in Europeans, and, yes, in the San people. This one is also old, dating back to "921 ka (95% CI, 703 ka to 1.2 Ma)".

If the dark "A" variant is IBD, the pale "G" one should also be IBD, and this one is possibly older than the Denisovan-Neanderthal / Human split as it is 921,000 years old.

The tree (above) show its distribution globally, with two branches the dark skin variant seems to have longer branches making it look more ancestral than the other, pale skin variants. I don't see the link between Africans and Australo-Melanesians in this tree, as mentioned by the authors.

How did Europeans and San people get to share this variant and the other OCA2 variant, while all the Africans living between both groups have the derived dark pigmentation variants? Note that there is 6,600 km (4,100 miles) between the southernmost tip of Europe in Greece and the San homeland in Botswana/Namibia.

We can imagine different alternatives to explain this: (1) A small population of modern humans split, one headed north into Europe, the other was displaced south into the southern tip of Africa. Between them, a mutation appeared, providing dark pigmentation for people living in the tropical regions of Africa, with benefits like UV protection, etc. (the paper hints that dark skin may have positive effects on other bodily functions: "...some of the pigmentation-associated variants identified here may be maintained because of pleiotropic effects on other aspects of human physiology."

Another option (2) is that pale pigmentation was prevalent among the archaic population that evolved into Neanderthal-Denisovan-Humans and moved with them across Eurasia but a later darker variant appeared in Africa and became predominant there, displacing the pale skin to the southern tip of Africa (San), and migrating out of Africa in a sub-population of modern humans that peopled South Asia and Australia-Melanesia (PNG, Aboriginals, Negrito, Andamanese people). Later overlaid by a wave of paler humans in Indonesia, Malaysia, Thailand and North India. Did the Europeans get pale skin from admixing with Neanderthals, and Asians from Denisovans?

(3) Prehaps ancient archaics had the darker pigmentation alleles, and a separate archaic group was lighter colored, the former remained in Africa (H. habilis), the latter moved into Eurasia (H. erectus?). Modern humans evolved in Asia, starting with Neanderthals and Denisovans, and back-migrated into Africa where admixture with archaics in Africa led to a darkening currently observed there. The san, part of the wave of migrants were displaced and isolated, retaining the original alleles. However, the dark skinned south Asians and Melanesians can't be accounted for with this model. Perhaps there was an Out of Africa migration along coastal South Asia into Melanesia? Or an ancient migration of superarchaics into Asia that mingled there with later populations?

In any case, I find it interesting that contemporary Europeans, who are deemed to be very recent, and the San people, supposedly the oldest intact group of humans, that split from the rest of us over 150,000 years ago, share the same light-skin pigmentation alleles. This oddity indicates that there is something amiss with our current idea of human origins and dispersal.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Archaics and recent humans in Africa: the evidence from stone tools

An article published in Nature in February 2025 (Ben Arous, E., Blinkhorn, J.A., Elliott, S. et al. Humans in Africa’s wet tropical forests 150 thousand years ago. Nature 640, 402–407 (2025). https://doi.org/10.1038/s41586-025-08613-y) found that the belief that humans didn't enter the African jungles until recently was mistaken. The paper found "late Middle Pleistocene material culture and a wet tropical forest in southern Côte d'Ivoire, a region of present-day rainforest... demonstrat[ing] that Africa's forests were not a major ecological barrier for H. sapiens as early as around 150 ka."

I found it interesting because of the different papers (see the list at the end of this post) suggesting archaic admixture into modern humans in Western Africa, which does indicate that modern African humans did enter the jungles in that region. But, in this paper, the authors mention stone tool assemblages which in my opinion seem rather "primitive", lacking the refined appearance you'd expect from tools made by human beings 150 kya. After all, our species is said to have developed in Africa 300 kya, and left it in two waves, one, around 100 kya which is believed to have failed, and the second one that peopled the World, 60 kya. So, why would they produce tools that look so primitive? See below, an image with the upper "Unit C" tools dated to 20-12 ky and the older "Unit D" dated to 55-150 kya.

Figure S4: Stone tools from Units C and D at Bete I and III from Lioubin and Guede, and photos taken of the remaining artefact collection at the Institut des Sciences Anthropologiques de Developpement (ISAD) in 2021. Unit C: A) ‘end-scraper’, B) ‘point’, C) ‘end-scraper à museau’, D) ‘double-ended carinated end-scraper’, E) ‘small handaxe’, F) ‘fragment of a bifacial foliate piece’, G) ‘point Levallois’, H) ‘combination tool’, I) ‘end-scraper with spine’, J) ‘short foliate biface’, and K-N) ‘cores’. Unit D: O) ‘side and end chopper’, P) ‘biface - trihedral’, Q) bifacial LCT (our term), R) ‘pick with double-flat cross-section of the body and centred quadrihedral distal point’, S) ‘pick with double-flat cross section of the body and centred trihedral distal point’, T–U) bifacial pieces (our term). A-N and O, P, R and S are from Lioubin and Guede. Suppl. Mat.

The more recent upper layer exhibits, according to the authors Levallois flakes and points, while the underlying and older stone artifacts are more massive and coarse-looking: "The assemblage in Unit D, featuring large tools alongside a small tool component, may support long-held views that the diverse heavy-duty tool assemblages seen in Central and West Africa are convergent adaptive solutions to tropical forest habitation."

Sangoan toolage

In the Supplementary Material, the authors mention two types of stone industries present in Pleistocene Africa, the Sangoan and the Lupemban. Sangoan, first discovered in Sangoa, Uganda "described as late Acheulian adaptations, transitional between the Acheulean and the MSA, or as belonging to the early MSA. They are generally characterised as featuring ‘rugged’ or ‘heavy-duty’ core tools, dominated by thick bifaces, picks, choppers, and core scrapers, referred to collectively as large cutting tools (LCTs)."

The literature describes them as a transition from Early Stone Age Acheulean tool technology to Middle Stone Age tools. To me, as an amateyr un the field, this spells tools made by less advanced hominins. Acheulean tools were the mark of H. erectus, and these crude Sangoan tools are common in Central Africa during the Upper Pleistocene, and coexist with Modern Humans in West Africa 150 kya? Strange overlapping of superarchaic hominins with modern H. sapiens.

The coarse and heavy build of Sangoan tools is believed to be due to their use in forested environment, for chopping or digging for edible roots and tubers. They have been found at Kalambo Falls in Zambia and dated to 500-300 kya. Clearly not the work of Homo sapiens, we appeared only 300 kya. In Simbi, Kenya their age is between 50-200 kya, indicating a survival of an ancient technology overlapping the appearance of modern humans and possibly, the survival of the archaics that made the Sangoan stone tools.

Lupemban

The Lupemban, on the other hand, named for a brook in Zaire, is different it displays careful crafting using Levallois core and flake technology, resulting in refined lanceolate, bifacial points. The oldest Lupemban tools are 266-132 kya. Overlapping with the more primitive Sangoan, as if two different groups of less, and more advanced hominins created them to exploit the forests and jungles (see this source for a comprehensive text on this industry).

Closing Comments

Rather than showing that modern humans were living in the West African jungles 150,000 years ago, the paper by J.A., Elliott, S. et al. seems to suggest an overlapping of different people in that area, namely archaics with early stone age Lupemban tools and modern humans with Sangoan ones.

Why would archaeologists ignore the signal provided by the Acheulean-like Sangoan tools and attribute them to modern humans living in a forested environment? In Eurasia, stone technologies, like the Mousterian are a clear indication of Neanderthal craft, why wouldn't the Sangoan be taken as a lithic technology developed by non-sapiens people? It seems to me that archaeologists focused on Africa have the obligation to defend the antiquity of Homo sapiens in that continent and ignore facts that indicate the opposite.

Below are some posts on the admixture of archaics and moderns within Africa: ↺

• May 2018: Archaic hominins admixed with Pygmies in Africa, citing: Psing Hsun Shieh et al, 2016. Summary: at least one introgression of archaics into pygmies ~9 kya.
• May 2018: More on archaic introgression into H. sapiens in Africa: the source of African's genetic diversity, citing: Hammer et al., 2011. Summary: modern Africans' DNA has a ~2% introgression that took place ~35 kya, from an archaic that split from our lineage 700 kya.ed DNA, ) that introgressed ~35 kya from an archaic population that split from the ancestors of anatomically modern humans ~700 kya
• May 2019: Archaic Ghost population admixed with Modern Humans in Africa, citing: Lorente-Galdos et al, 2019. Summary: a divergent ghost archaic population that split from the ancestors of modern humans 528 kya introgressed into Africans at the following frequencies:~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka.
• June 2019: Archaic humans admixed with modern humans in Africa, citing: S. Langley, Miga, Karpen, C. Langley, 2018. Summary:a distinct, old introgressed archaic lineage (~1.1 MYA) consistent with recent admixture with an extinct archaic in Africa.
• February 2026: On the Diversity of Africans, citing: Durvasula and Sankararaman, 2020. Summary: introgression into four West African populations, with frequencies of 2 to 19% from an archaic population that diverged before the split of Neanderthals and modern humans. It took plase 43 kya (95% HPD: 6 - 124 kya).
• February 2026: Diversity in Africa. Some explanations on why it is so diverse, citing: Skoglund et al., 2017, Jakobsson et al., 2025 and Padilla-Iglesias et al., 2025. Summary: deep stratification in Africa may come from admixture with an unknown archaic African group predating the divergence of Humans from Neandertals and Denisovans. Western Africans may have introgressed with archaics.
• April 2026: A New March 2026: Paper on Archaic introgressions in Humans, citing: Zhang, Biddanda, Johnson, O’Dushlaine, Moorja, (2026). Summary: two introgressions with super-archaics. (i) inside of Africa with a ghost population that diverged from ours over 500 kya it is found in all humans, Africans and non-Africans.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Denisovan and Neanderthal alleles in Africans at higher levels than in non-Africans

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!

Original caption: Note.—The column labeled “Chr.” gives the chromosome, and “Neandertal” and “Denisovan” group IBD segments matching the Neandertal and Denisovan genomes, respectively. “ALL” gives the total number of IBD segments matching the respective ancient genome, “EAS”, “SAS”, “EUR”, and “AFR” report the number of matching IBD segments shared exclusively by East Asians, South Asians, Europeans, and Africans, respectively, and the percentage compared to the total number of IBD segments matching the respective ancient genome.

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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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

High African diversity despite population bottlenecks. Why? (archaic admixture in Africa)

Higher diversity is normally associated with a effective populaton size, and that is why the Out of Africa migrants are said to have a lower diversity: they moved in a small group and this carried less diversity than the original population (a founder effect and a bottleneck for the migrants),

However, a paper published in Nature by Jakobsson et al., 2025 studied the evolution of modern humans using genetic information garnered from "ancient southern African genomes" and found that the African population size wasn't all that big. In fact it was the same size as the Out of Africa band!

Below I quote the relevant passage in the paper, my comments in brackets, and I highlighted some interesting parts of the text:

"Long-term large population size
... Heterozygosity (HO) for ancient southern Africans (mean across genomes; HO = 0.80 × 10−3) was similar to other ancient Africans, only surpassed by an ancient western African individual (HO = 0.93 × 10−3), indicating a large Holocene population size in southern Africa. A multiple sequentially coalescent approach shows that the effective population size (Ne) was large for several hundred thousand years, up to Ne ≈ 30,000 around 200 ka, similar to other African groups. The large Ne at ≥300 ka for all humans was potentially caused by population subdivision. [interesting! so small populations divided into many give the appearance of a large Ne when in fact it isn't] We note a decline in Ne for ancient southern Africans from around 100–50 ka, to Ne ≈ 10,000 by the Last Glacial Maximum (20 ka), similar to non-African groups and the ancient northern Africans [So at the time of the supposed Out of Africa Event 100,000 to 50,000 years ago southern & northern Africans and non-Africans had the same population size! So where is the OOA bottleneck?]
Runs of homozygosity (ROH, where greater numbers and total length of ROH segments indicate a smaller population size) show that the ancient southern Africans were at the upper tail of the distribution of modern-day Africans, but less extreme than most non-Africans—a pattern attributed to the out-of-Africa bottleneck. [homozygosity is attributed to small populations, and inbreeding, loss of diversity or heterozygosity. So the supposed most ancient humans, the South African San people have the highest ROH among Africans — but lower than non-Africans.] This indicates a smaller population size (relative to, for example, western African groups) in the relatively recent history of each individual, but still larger compared with non-Africans and ancient northern Africans. Most ancient southern Africans are shifted towards greater total segment ROH length without affecting the total number of ROH segments, in particular the Great Brak River (2,355–2,310 cal. bp) and the Matjes River 1 (7,845–7,690 cal. bp) individuals [this date is extremely recent! well after the OOA event]. This pattern indicates a smaller recent ancestral population size, possibly with elements of inbreeding, indicating isolation and fragmentation among ancient southern Africans during the Holocene. Ancient southern Africans south of the Limpopo River therefore consisted of a large, stable population for many millennia, with a modest decline since around 50 ka, and a possible fragmentation and further decline during the Holocene."

Admixture with archaics!

As usual the paper also points out that: "Population stratification between southern Africa (the region south of the Zambezi River) and the rest of Africa probably existed for at least 300 thousand years (kyr), perhaps up to a million years. Such deep stratification may result from admixture with an unknown archaic African group predating the divergence of Homo sapiens from Neandertals and Denisovans, and//or from isolation from other groups." The isolation would mean that an archaic form of humans didn't admix with the others and carried ancient, unshared alleles. The admixture option seems more plausible.

When discussing diversity, the authors note that: "Cumulatively, the genomes of the ancient southern Africans show that this group displays many Homo sapiens-specific variants (and variable positions) at amino acid-altering sites, also reflected among the modern-day San people. This observation cannot be explained solely by a large, stable southern African population, which retained derived variants to a greater extent compared with other groups. The ancient southern Africans were probably also isolated from other African groups for long periods. The derived variants unique to southern Africans may also signal low-to-modest gene flow from an unknown/unsampled group of genetically differentiated humans." Indeed, introgression from archaics.

Notice how reluctant mainstream scholars are. Instead of digging deeper into the archaic admixture hypothesis, they set it aside. In this case, the authors seem to agree with this option, but, politely wrote: "Irrespective of cause, the many variable amino acid-altering sites among the ancient southern Africans point towards a genetic model in which different protein variants can be combined to viable outcomes... The many Homo sapiens-specific variants found in southern African genomes point to a combinatorial genetic model of human evolution in which there are many possible combinations of genetic variants that lead to ‘genetically modern’ Homo sapiens." Yes, a combination brought about by mating with archaics within Africa.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

More papers on Denisovan introgression in PNG and superarchaic mix in Africans

Although it was published last June, a paper by Hsieh et al, is very interesting, and worthy of a post (free access to it her: A global map for introgressed structural variation and selection in humans. bioRxiv [Preprint]. 2025 Jun 24:2025.06.24.661368. doi: 10.1101/2025.06.24.661368. PMID: 40667000; PMCID: PMC12262424). It is not peer-reviewed so its conclusions should be taken with caution.

The paper looks into the introgression of archaics into modern people in Papua New Guinea and I highlight the following findings:

It Adds diversity

The authors state that "some archaic sequences likely contributed to human phenotypic variation" and that they were not necessarily bad for us (deleterious as other papers have suggested). Instead the paper proposes that "many introgressed loci in our genome show signatures of positive selection." They go on to add that Structural Variants or SVs, "such as insertions, deletions, and inversions, contribute disproportionately to human genetic diversity by affecting more genomic sequences than SNVs."

Denisovan and Neanderthal admixture in PNG

The authors noticed that "Unexpectedly, PNG individuals carry more Neanderthal sequences than Denisovan, contradicting the expected genome-wide estimates of ∼4% Denisovan and ∼2% Neanderthal ancestry" This is surprising, and they try to explain it as follows: "[caused by the differences between the sequenced Denisovan genome and the actual Denisovan population that interbred with the ancestors of the PNG as well as complex demographic histories in Oceania." Translated: We don't know why this happened!

MUC19

They observed the presence of a rare introgressed SV, the MUC19 segment: "... an introgressed variable number tandem repeat (VNTR) haplotype at the MUC19 locus with an uncertain archaic origin." I posted about MUC19 last March, because it is supposedly enriched among Amerindians, giving them adaptative advantages, and it is believed to have originated in Denisovans, and passed on to humans via Nenaderthals. These people in PNG have the variant. So it is not so uncommon as believed.

The timing of the introgression

The authors estimate that one of the SV introgressions, an insertion in chromosome 16 "diverged from the others about 596 thousand years ago (kya; range: 322–870 kya)" which is a rather wide range! and attribute it to Denisovans and that the actual "admixing" between Denisovans and the ancestors of the PNG people took place between 60 and 170 kya. Which is older than you would expect and consistent, in my opinion, with an early out of Africa event, or, perhaps a non-African modern human group mixing with Denisovans 170,000 years ago.

Centromeres

If you imagine a chromosome pair with its characteristic "✘" shape, the centromere is the place where the chromosome arms narrow down and meet. Since humans are diploid, we have 23 pairs of chromosomes (each with one paternal and one maternal chromosome) with a total of 46 individual chromosomes. Each chromosome of the pair links with the other one to form the typical "X" shape: "❱" to the left, and "❰" to the right join at the centromere (located at the apex of each single chromosome).

During cellular division (which I will oversimplify in this description) the cell sends fibers that attach to the centromere and and pulls the chromosomes apart, half going to one side, the other half going to the opposite side of the dividing cell. So centromeres play an important role in regulating the division of cells, and reproduction, where the sexual cells carry half the chromosome load compared to regular ones.

The paper goes on to look into centromeres, and reports that it found "11 centromeres likely derived from archaic hominins" and looks into them in detail.

The authors state, for instance, that the PNG people carry a centromere lineage (haplotype 2 chromosome 4) that is older than those found in other modern humans: "[it] diverged from the rest of the modern human lineages 489,447 – 507,131 years ago... also observed evidence for archaic origins for the chromosome 22 centromeres... The lineage that gave rise to the[m] ... diverged from other modern human lineages approximately 580,661 years ago (95% HPD interval: 469–694 kya... sugesting that these centromeres are likely introgressed from archaic hominins into the early ancestors of the PNG."

African divergence and superarchaic introgressions

An earlier paper by Langley et al., 2019 aldo studied the centromere region (they call them Cenhaps, large-scale haplotypes that span the centromere-proximal regions or CPRs in chromosomes). They reported that they found that Africans carry a very ancient, basal, diverged variant of a centromere not found outside of Africa in humans, and it predates the split of Neanderthal-Denisovans from the Modern human branch. The authors find that non-Africans carry another varaint closer to Neanderthals than Denisovans (proof of the admixture of OOA humans with Neanderthals). The superarchaic admixture in Africans comes from a 1.1 million-year-old hominin, and happened recently. The full text is the following:

"The most diverged, basal clade in the chr12 CPR is common in Africa, but, like the most diverged chrX cenhap, is not represented among the descendants of the out-of-Africa migrations (Bae et al., 2017). The great depth of the lineage of this cenhap is further supported by comparison to homologous archaic sequences (Green et al., 2010; Prüfer et al., 2014; Prüfer et al., 2017). Consistent with the hypothesis that this branch split off before that of Neanderthals/Denisovans, members of this cenhap share fewer matches with derived SNPs on the Neanderthal and Denisovan lineages (DM) and exhibit strikingly more ancestral non-matches (AN) than other chr12 cenhaps (see Figure 3b). This putatively archaic chr12 cenhap represents a large and obvious example of the potentially introgressed sequences within African populations inferred from model-based analyses of the distributions of sequence divergence (Hammer et al., 2011; Hsieh et al., 2016; Durvasula and Sankararaman, 2019). The small out-of-Africa cenhap nested within a mostly African subclade appears to be a typical Eurasian archaic introgression with higher affinity to Neanderthals (DM/(DN + DM)=0.91 and DM/(DM +AN)=0.90) than to Denisovans (Figure 3b). This bolsters the conclusion that the basal African cenhap represents a distinctly older archaic lineage. Unfortunately, there are too few coding bases in this region to support confident estimation of the TMRCAs of these ancient chr12 cenhaps. Based on the numbers of SNPs underlying the cenhaps, this basal cenhap is twice as diverged as the apparent introgressed Neanderthal cenhap, placing the TMRCA at ~1.1 MYA, assuming the Neanderthal TMRCA was 575KYA (Prüfer et al., 2017). While there is no direct evidence of recent introgression, the large genomic scale of the most diverged chr12 cenhap (relative to apparent exchanges in other cenhaps) is consistent with recent admixture with an extinct archaic in Africa
... Two examples are chromosome 8, containing an ancient cenhap limited to Africa with an estimated TMRCA of ~730 KYA, and chr10 that appears to harbor another clear Neanderthal cenhap introgression..."

Again, and this time from another source, we see proof of ancient surviving archaic hominins in Africa mating with Africans, recently, and in the process, adding to their diversity and divergence.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Mutation ratios and African admixture with archaics

In my previous post I mentioned the TCC→TTC mutation anomaly, which is higher among Europeans than Africans or East Asians.

Gao, Zhang, Przeworski, and Moorjani, 2022 reported that there were several other mutation discrepancies between these three popilations.

They also looked into mutation raties that differ in "old polymorphisms that predate the out-of-Africa migration" and suggest that this case is due to the different proportion that the ancient archaic ancestors contributed to modern African and non-African people. They also point out that age of reproduction (generation time) can't explain their observations and suggest that "other factors —genetic modifiers or environmental exposures— must have had a non-negligible impact on the human mutation landscape".

Aging fathers tend to pass on to their children more T→C mutations, and mothers contribute more C→G mutations.

They noticed different T→C/T→G mutations among archaic populations (over 28,800 generations ago) compared to more recent ones in all three populations. They were surprised by this difference: (YRI is Yoruba African, CEU is Caucasian and CHB is Chinese from Beijing):

"Unexpectedly, we detected significant differences between YRI and the other two populations, CEU and CHB, in the mutation spectra of polymorphisms that are estimated to long predate the OOA migration. Specifically, the T>C/T>G mutation ratio is elevated in the very old allele age bins compared to more recent bins for all populations, with a significantly higher ratio seen in YRI than in CEU and CHB. We showed that the inter-population differences cannot be explained by differential gene flow from sequenced archaic hominins —Neanderthals or Denisovans— into the ancestors of non-Africans and such introgression alone cannot explain the shift in the older bins in all modern human populations.
Instead, we found evidence that the signals come from extremely old variants that emerged prior to the split of modern humans and archaic hominins at least ∼550,000 years ago (Prüfer et al. 2014). This suggests that the observed differences between contemporary populations could have arisen from the complex demographic history of ancestral populations. Based on observed polymorphism patterns in contemporary African populations and using simulations, several recent studies have suggested that one or more ghost archaic populations may have introgressed into the ancestors of Africans and possibly into the common ancestors of all modern humans (Hammer et al. 2011; Ragsdale and Gravel 2019; Speidel et al. 2019; Durvasula and Sankararaman 2020). After the ancestors of non-Africans migrated out of Africa, the ghost archaic group(s) may have continued interbreeding with remaining populations in Africa, leading to higher ancestry in YRI. An alternative model is deep population structure in modern humans. Under this model, two or more long-lasting, weakly differentiated ancestral populations contributed differentially to contemporary human populations through continuous gene flow or multiple merger events (Ragsdale et al. 2022). In both models, a greater contribution from a group with a higher T>C/T>G ratio to the ancestors of African individuals would explain differences between YRI and non-African population samples as well as the elevated ratio in old variants for all three contemporary human populations. Our analysis further showed that the T>C/T>G signal comes from T>C mutations rather than T>G mutations, suggesting that one or more of the remote ancestral populations had a higher T>C mutation rate relative to their contemporaries as well as to modern humans."

Time and time again we have evidence of archaic introgression into Africans that has not been passed on to Eurasians. These contriuted to their heterozygosity, diversity, and different mutation rates. This renders many conclusions based on molecular clocks and differences in alleles obsolete. It makes the Africans look more divergent but in fact this may be the outcome of swapping bodily fluids after the OOA event.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

All the Introgression posts in one place

I decided to index the posts and the papers that I cited in them, to have in one single post, links to all of them. Over the years I posted about Neanderthal, Denisovan, Ghost, Super-Archaics, and unknown archaics introgressing (or not) with Modern Humans or with the ancestors of our lineage at different times (before the split with Neanderthals and Denisovans, or after that split), and also with humans injecting alleles into Neanderthals! Very confusing, and sometimes contradictory.

Our lewd ancestors and their dallies

What is the basis of these events? Politely termed admixture and introgression, the only way our ancestors could have exchanged genes is through sexual intercourse. They were sexually aggressive.

Research by Emma Nelson, Campbell Rolian, Lisa Cashmore, Susanne Shultz, 2010 (Digit ratios predict polygyny in early apes, Ardipithecus, Neanderthals and early modern humans but not in Australopithecus. Proceedings of the Royal Society B, 2010; DOI: 10.1098/rspb.2010.1740) reported that the finger bones of fossil ancestors (bones that are affected by sex hormones in the womb), can predict their levels of promiscuity and competitiveness (polygynous hominins! who had more than one mate). This study found that Ardipithecus ramidus, Neanderthals, and early anatomically modern human (like Qafzeh 9) were more polygynous than modern humans, while Australopiths had a lower polygyny. Strong sex drives that led to many mating events.

Below I list my posts with the corresponding citations, and the outline of the research in them.

• May 2018: Archaic hominins admixed with Pygmies in Africa, citing: Psing Hsun Shieh et al, 2016. Summary: at least one introgression of archaics into pygmies ~9 kya.
• May 2018: More on archaic introgression into H. sapiens in Africa: the source of African's genetic diversity, citing: Hammer et al., 2011. Summary: modern Africans' DNA has a ~2% introgression that took place ~35 kya, from an archaic that split from our lineage 700 kya.ed DNA, ) that introgressed ~35 kya from an archaic population that split from the ancestors of anatomically modern humans ~700 kya
• May 2019: Archaic Ghost population admixed with Modern Humans in Africa, citing: Lorente-Galdos et al, 2019. Summary: a divergent ghost archaic population that split from the ancestors of modern humans 528 kya introgressed into Africans at the following frequencies:~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka.
• September 2019: Super Archaic Hominin admixture with Denisovans, Neanderthals and Africans, citing: Hubisz, Williams, and Siepel, 2019. Summary: (i) 1% of Denisovan genes introgressed from super-archaic hominin that diverged from Human lineage 1 million years ago (MYA). (ii) 0.75% of Altai Neanderthal, and 0.70% of Vindija Neanderthal introgressed from super-archaic. (iii) Some of it passed from Denisovans to Humans. (iv) Detected super-archaic admix in Africans. (v) 3% of Neanderthal genes are an introgression from Anatomically Modern Humans ~200-300 kya.
• June 2019: Archaic humans admixed with modern humans in Africa, citing: S. Langley, Miga, Karpen, C. Langley, 2018. Summary:a distinct, old introgressed archaic lineage (~1.1 MYA) consistent with recent admixture with an extinct archaic in Africa.
• October 2025: Neanderthals and Denisovans in India?, citing: Kerdoncuff, Laurits Skov, Nick Patterson, et. al., 2024. Summary: Beside their introgressed Neanderthal and Denisovan ancestry, 0.37 to 0.48% of Indian ancestry is from another unknown archaic.
• October 2025: Archaic admixture in humans that is neither Denisovan or Neanderthal, citing: Tucci et al., 2018, Mondal, Bertranpetit & Lao, 2019. Summary: The first paper did not find any unknown archaic introgression in SE Asian pygmies, the second one did: a third introgression in all Asian and Oceaninans from an extinct population of the Neanderthal-Denisovan clade or a one that diverged early from Denisovans. First Neanderthals admixed with humans 1.3% frequency 69 kya, then Denisovans introgressed in Oceanians 1.6% frequency, 43 kya, and the unknwon archaic added 2.6% 51 kya. The archacic dates back to 304 kya. Teixeira and Cooper, 2019. Also support a third introgression with an extinct hominin (not Neanderthal or Denisovan), and finally Yuan et al., 2021 suggest that the most recent, of two, Out of Africa events may have mated with undiscovered archaics in South Asia or that ancestors of Neanderthals and Denisovans admixed with superarchaics.
• February 2026: On the Diversity of Africans, citing: Durvasula and Sankararaman, 2020. Summary: introgression into four West African populations, with frequencies of 2 to 19% from an archaic population that diverged before the split of Neanderthals and modern humans. It took plase 43 kya (95% HPD: 6 - 124 kya).

Continues below, after the picture with Hollywood's fantasy about love 1 million years ago (the actors look too tanned and clean don't they?).

One Million Years B.C. (1966), prehistoric love and survival, with Rachel Welch and John Richardson. Source

• February 2026: Diversity in Africa. Some explanations on why it is so diverse, citing: Skoglund et al., 2017, Jakobsson et al., 2025 and Padilla-Iglesias et al., 2025. Summary: deep stratification in Africa may come from admixture with an unknown archaic African group predating the divergence of Humans from Neandertals and Denisovans. Western Africans may have introgressed with archaics.
• February 2026: Did Humans admix with Neanderthals? Paper in Nature says NO, citing: Tournebize and Chikhi, 2025. Summary: There was no admixture between humans and Neanderthals, it is an artifact of mistaken models.
• April 2026: Human Ancestors Interbred with Two Distinct Populations of Superarchaics, citing: Rogers, Islam, Brand, and Webster, (2026). Summary: at least two distinct superarchaic populations admixed with us: one into archaic Eurasian populations (Denisovans and Neanderthal-Denisovan ancestors), an superarchaic that diverged earlier from the human lineage than did the second superarchaic, that admixed within Africa, contributing DNA to early modern humans.
• April 2026: A New March 2026: Paper on Archaic introgressions in Humans, citing: Zhang, Biddanda, Johnson, O’Dushlaine, Moorja, (2026). Summary: two introgressions with super-archaics. (i) inside of Africa with a ghost population that diverged from ours over 500 kya it is found in all humans, Africans and non-Africans. (ii) Superarchaic admixture at 0.3% frequency in Oceanians. This population diverged 1.77 Mya from humans. (iii) All non-Africans carry admixture with Neanderthals and Denisovans.
• April 2026: Another Paper on Introgressions (April 2026), citing: Nicholas W Collier, Simon Gravel, Aaron P Ragsdale. (2026). Summary: Through statistical models and genetic analysis of the autosomal DNA, the authors suggest a population structure and admixture, and population sizes for modern humans, Neanderthals, Denisovans, and super-archaics that mix to and fro over the past million years

Last Updated on April 18, 2026

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Human Ancestors Interbred with Two Distinct Populations of Superarchaics

As mentioned in a previouspost, there were many research article published last month. Today's post looks into one (not peer reviewed) published on March 23 in Biorxiv, that states that two different superarchaic populations admixed with the ancestors of modern humans, within Africa, and with the ancestors of both Denisovans and Neanderthals. Then, the Denisovans received another superarchaic introgression. The H. sapiens branch also mated with Neanderthals.

This is the article on, yes, another introgression: Alan R. Rogers, Md Touhidul Islam, Colin M. Brand, Timothy H. Webster, (2026). Human Ancestors Interbred with Two Distinct Populations of Distant Relatives. bioRxiv 2026.03.22.713509; doi: https://doi.org/10.64898/2026.03.22.713509

The paper's abstract reads: "Ancient DNA has shown that a distantly-related “superarchaic” population interbred first with the ancestors of Neanderthals and Denisovans and later with Denisovans themselves. Other work has shown that a superarchaic population interbred with the African ancestors of all modern humans. But it is not yet clear whether these events involved the same superarchaic population. Here, we use the distribution of derived alleles among populations to evaluate hypotheses about superarchaics and their relationship to other hominins of the Pleistocene and Holocene. We find evidence for at least two distinct superarchaic populations. The one contributing to archaic Eurasian populations (Denisovans and Neanderthal-Denisovan ancestors) diverged earlier from the human lineage than did the one contributing to early moderns in Africa. These findings reveal previously unrecognized structure among hominin populations of the Pleistocene."

Greek letters are episodes of gene flow; roman letters are populations: X, Africa; Y, Europe; N, Neanderthal; D, Denisovan; S, Superarchaic. Z is a superarchaic population that diverged more recently than S and contributed ancestry (ζ) to ancestral moderns. XY, ND, and XYND label ancestral populations.. Fig2 in Rogers, Islam, Brand and Webster, (2026).

The authors argue that some archaic lineage, which they don't identify, called Z shared genes (ζ) with the lineage of ancestors that, after the split of Neanderthals and Denisovans, lead to H. sapiens (XY). In a previous paper (Rogers, A. R., Harris, N. S. & Achenbach, A. A. (2020). Neanderthal-Denisovan Ancestors Interbred with a Distantly-Related Hominin. Science Advances 6, eaay5483.) they had suggested that a superarchaic popultion called S admixed (δ) with the branch that had split from the ancestors of modern humans, and lead to Neanderthals and Denisovans (ND). The S superarchaics later admixed (β) with Denisovans (D), while Neanderthals (N) received an archaic modern Human (XY) genetic input (γ). Neanderthals injected (α) genes into Eurasian modern humans (Y) but not into Africans (X).

This is the explanation provided by tha authors for these interactions:

"To make sense of this, we pointed out that the first wave of emigration out of Africa happened early in the Pleistocene, when Homo erectus spread across Eurasia. Later, during the Middle Pleistocene, humans evolved larger brains and began making Acheulean tools. Both of these innovations appear in Africa before Eurasia, suggesting a second wave of emigration out of Africa. We proposed that this second wave interbred with the Eurasian descendants of the first, during what we refer to as the δ episode of admixture. It seemed plausible that, before this contact, the two populations had remained largely isolated because of the difficulty of traveling between Africa and Eurasia. (At least during the Upper Pleistocene, human contact between these continents was largely restricted to relatively brief periods when the Sahara was humid.)
Now we have evidence of a second superarchaic population, Z, which diverged after the first and later interbred with the ancestors of modern humans. This contact presumably occurred in Africa, because it happened before moderns spread into Eurasia. We considered the possibility that this second superarchaic population was the same as the first—see model... Thus, there were two superarchaic populations, and it seems likely that the second (population Z) was African.
This is puzzling, because it implies that two African populations—population Z and the ancestors of moderns, Neanderthals, and Denisovans—remained essentially isolated across roughly a million years. What kept them apart? Africa has no mountain barriers as large as the Himalayas or the Alps. There are deserts, but these were not continuously arid. The results of Ragsdale et al. (see above) suggest that these populations may not have been isolated after all—perhaps there was a continuous trickle of gene flow between them. Yet somehow (as discussed above) population Z acquired many mutations that show up in modern humans but not in Neanderthals and Denisovans. If there was gene flow between these populations, it must have been weak."

Comments

This is an interesting hypothesis, that needs to be polished a little. It could also be expanded by imagining even later admixture events (μ) from Z into the African group X that added to its diversity during the past 50 ky. However, it does not break the Out of Africa paradigm as it suggests that after H. erectus left Africa heading into Eurasia (are they , humans in Africa developed Acehulean tools (typical of H. erectus) and left Africa in a 2nd migration. However, this does not seem to be reflected in the trees of the paper, so I am a bit confused.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Diversity in Africa. Some explanations on why it is so diverse

The contemporary San people in South Africa are usuallyt mentioned as the most basal group of humans, and the most diverse one, that split from all others ~150 ky ago (or more) and are the living proof of the richness in genetic diversity that was lost by those who trekked out of Africa.

By the way, this is the real post 1,000 ♥.

Human genetic diversity map (not sure how it was made). Source

About the image above. Interesting to see how Eastern China, Manchuria, Japan, Korea, Indochina, and Peru in South America are the least diverse! Also how African slave trade extended diversity into Brazil and European colonization into Eastern North America and parts of South America. The map is from reddit, though, so it has no references, source or hard data to back it. May be a fabrication.

However, a very recent paper published on line in Dec. 2025, in Nature, by Mattias Jakobsson et al., note that the alleles found in the modern San people are not only due to a large and stable population (large Ne), they also had an introgression from some other, unknown, group of genetically differentiated humans. The authors state that (yellow-bold highlighting is mine):

"Cumulatively, the genomes of the ancient southern Africans show that this group displays many Homo sapiens-specific variants (and variable positions) at amino acid-altering sites, also reflected among the modern-day San people. This observation cannot be explained solely by a large, stable southern African population, which retained derived variants to a greater extent compared with other groups. The ancient southern Africans were probably also isolated from other African groups for long periods. The derived variants unique to southern Africans may also signal low-to-modest gene flow from an unknown/unsampled group of genetically differentiated humans.
Genetic, anthropological and archaeological studies support an African origin of Homo sapiens, but the evolutionary process is debated based on fossils, archaeology and genetics, with Africa harbouring the greatest human genetic diversity, and southern and central African hunter-gatherer groups displaying some of the deepest diverging Homo sapiens lineages. Population stratification between southern Africa (the region south of the Zambezi River) and the rest of Africa probably existed for at least 300 thousand years (kyr), perhaps up to a million years. Such deep stratification may result from admixture with an unknown archaic African group predating the divergence of Homo sapiens from Neandertals and Denisovans, and/or from isolation from other groups.
Average population divergences between individuals representing the ancient southern African group (7 individuals with >7.2-fold genome coverage) to any other individual (ancient and modern-day western, eastern, central, northern Africans and non-Africans) were estimated to around 310–240 ka using a two-by-two site-frequency spectra approach (Supplementary Information 2.17 and Supplementary Data 15–31). Although the exact calibration of chronological population divergence-time estimates depends on model assumptions, mutation-rate assumptions and generation time, these estimates recapitulate findings in which the divergence between ancient southern Africans and all other groups captures the deepest population split-time at around 300 ka (see also Supplementary Fig. 11 for a comparison to modern-day Khoe-San individuals). This approximately 300 ka population-divergence-time estimate is not caused by a deeper partial archaic admixture event per se, but it does not negate such an event either (Supplementary Information 3.11 and Supplementary Figs. 12 and 13)."

This is something that I have mentioned several times in different posts: diversity in contemporary Africans is due to an introgression of highly divergent genes from super archaic hominins that took place recently.

The paper also attributes diversity to isolation and small subpopulations (more on this below).

Cecilia Padilla-Iglesias et al., (2025) in a paper published last May (Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution), explores the possibility of introgression and also how isolation, natural selection (adapting to local environmental challenges) and modest gene flow between separated populations shaped the contemporary highly diverse genetic makeup of Africans:

"Our results are consistent with findings that despite deep genetic divergences, there is evidence for intermittent episodes of gene-flow between all hunter-gatherer lineages. These episodes would have allowed on the one hand the emergence of adaptive cultural and phenotypic variants for local environments during periods of isolation, and on the other, the exchange of such variants during periods of connectivity. Crucially, our model highlights the vast diversity of environments in which the members of our species thrived throughout our evolutionary history, and thus, the adaptive potential of the human foraging niche.
The maintenance of viable population sizes and interconnectedness in the majority of African regions, following their initial settlement by hunter-gatherers, explains the evidence for low levels of historical inbreeding and high genetic diversity indicated by very few short runs homozygosity observed among contemporary and ancient African hunter-gatherers."

So isolation, selection, concentration of diverse alleles, and then exchange between groups shaped the current diversity, but what about archaic introgression? The paper addresses this issue too (MSA is Middle Stone Age):

"Our model reveals that West Africa, and in particular, the area around the Gulf of Guinea as well as Senegal is the region with the highest reconstructed population turnover in the continent and remains isolated for large periods of time throughout our evolutionary history, until the present. This is consistent with the finding of fossils showing very archaic features (and outside of contemporary human variation) as late as 11.2 kya (or 13 kya calibrated) in Iho Eleru, Nigeria, as well as the late persistence of MSA technologies in Saxomununya, Senegal, until a similar time well beyond their disappearance in Southern Africa, Eastern Africa and the Maghreb.
Genetic studies have shown that Southern African Stone Age hunter-gatherers (including those from our sample) despite representing the most diverged human genetic lineages, still share significantly more alleles with eastern Africans (including the present-day Dinka and Mota) than they do with present-day Western Africans (as represented by the Yoruba). These findings have been used alongside findings of some “archaic” morphological features and continued MSA industries in Western Africa in the Holocene to the presence of archaic lineages in the region that have left no direct descendants."

Survival of very old lithic technology from the MSA coupled to archaic cranial features until very recently (11-13 kya) suggests the presence of archaic hominins who surely mated with, and left their genetic imprint in, modern humans in Africa. However, the need to downplay archaic introgression as a source of diversity (God knows why!) leads the researchers to suggest another mechanism (which I didn't quite grasp), yet, they must include the admixture option (highlight, by me):

"However, another possibility leading to this pattern is that the cline of connected groups across the Eastern part of the continent (connecting Eastern and Southern Africa) was not nearly as connected to Western Africa. Our demographic reconstructions show reduced levels of East-West migration compared with East-South migration for the vast majority of evolutionary history. This, together with the fact that we were able to predict the morphological distance between the Iho Eleru specimen and the rest of cranial specimens in our sample, shows that the second scenario is sufficient to explain the observed patterns, though we do not exclude the possibility of small amounts of introgression."

Pontus Skoglund et al., (2017) note the archaic admixture, they found: "... Evidence for a divergent human lineage contributing to western Africans... The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. "

The authors then mention the hypothesis: "there has been ancient structure in the ancestry of present-day Africans... One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages" This means, archaic, or super-archaic hominins liv

Yet, when confronted with taking a stance, the authors opt for a conventional explanation: "Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals." Meaning they mixed with more recent humans, not those that predate our split with Neanderthals some 600 ky ago.

J. H. Relethford (mentioned in a recent post), wrote an article, published in Nature back in 2008, in which he discussed the "regional diversity" issue very rationally, and offering explanations for the diversity in Africa and how it is a demographic rather than a phylogenetic matter:

"The genetic evidence: regional differences in genetic diversity
Not all living human populations show the same average level of genetic variability, and these differences in present-day diversity can provide us with inferences about our evolutionary history. DNA markers typically show higher levels of genetic diversity (heterozygosity and nucleotide diversity) in sub-Saharan African populations. This observation has been made for mtDNA (Cann et al., 1987), nuclear microsatellite DNA (Relethford and Jorde, 1999) and Alu insertion markers (Watkins et al., 2001). The same observation has been made on measures of variation from phenotypic traits; within-group variances are highest in sub-Saharan African populations for both craniometric measures (Relethford and Harpending, 1994; Manica et al., 2007) and skin color (Relethford, 2000).
Why would one geographic region consistently show higher levels of genetic and phenotypic diversity? One possibility is greater time depth for the accumulation of mutations. The longer a population has been in existence, the greater the number of mutations that will accumulate. Under an African origin model, mutations would accumulate longer in Africa, as any populations dispersing out of Africa would likely be small, and the subsequent founder effect would effectively ‘reset’ the accumulation of mutations in the non-African populations. Thus, a model of an initial African origin followed by dispersals out of Africa at a later point in time would generate the regional differences in genetic and phenotypic diversity that we see today. If correct, the observation of higher African diversity supports the other genetic (and fossil) evidence for an African origin for modern humans, but does not distinguish between an African origin with replacement and an African origin with admixture outside of Africa except to say that if there was any admixture it was not of sufficient magnitude to erase the genetic signature of an African origin.
Furthermore, the fact that the model of accumulated mutations is compatible with the observed genetic data does not mean that it is correct if there are other reasonable interpretations that are also compatible. In the case of genetic diversity, another possible explanation is regional differences in population size, because expected diversity is proportionally related to effective population size. Smaller populations experience more genetic drift and are therefore lower levels of diversity. If the long-term effective population size of Africa were larger throughout most of recent human evolution, then diversity would be greater in Africa than elsewhere, again consistent with our observations of present-day variation. Analyses of craniometric data and microsatellite DNA support this hypothesis (Relethford and Harpending, 1994; Relethford and Jorde, 1999). A larger African population is also consistent with archeological and ecological inferences (Relethford, 2001b; Eller et al., 2004). If higher levels of genetic diversity in sub-Saharan Africa are due to a larger long-term effective population size, then the observation of higher diversity does not provide any resolution about the modern human origins debate. All of the models proposed to date can easily accommodate a larger African population. In this case, genetic data may be telling us more about the demographic, rather than phylogenetic, history of our species."

Again, the higher Ne size and its impact on diversity. If we add introgression and, as mentioned further up, and also isolation in separate groups that evolve due to natural selection, and then admix with each other, it is easy to see what has shaped the diversity of modern Africans.

Nevertheless, Mark Lipson et al., (2022) published in Nature about the effect of many subpopulations: "Furthermore, small subpopulations with limited gene flow could result in low ancestral effective population sizes even if the region’s total population is high. Preservation of genetic diversity through the existence of many subpopulations over long time scales could also be a contributor to the high levels of genetic diversity observed in most present-day sub-Saharan African groups." This questions the need for a high Ne!

Fred W Allendorf, Ola Hössjer, and Nils Ryman (2025) expressed it as follows: "Fragmentation into many, small subpopulations with periods of infrequent gene flow, preserves allelic variation at the expense of heterozygosity. In contrast, fragmentation into a few, large populations maintains heterozygosity at the expense of allelic variation."

The original African pre-Homo sapiens populations were small groups of hominins with little admixing which meant that they had their own unique alleles, but, being small, had lower heterozygosity. When they came together, the outcome was a larger population with higher allele diversity and the sum of all the separate heterozygosities resulting in the current African high diversity.

And, finally the backflow from Eurasia! It contributed genes that may later have been lost as humans marched across the Old World, but were reintroduced into Africa at an early date, enriching the diversity there. A paper by Christopher B. Cole, Sha Joe Zhu, Iain Mathieson, Kay Prüufer, Gerton Lunter in the Covid pandemic year of 2020, boldly stated that "We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated."

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Neanderthals in Africa?

Continuing with my series of posts on the diversity and higher heterozygosity of contemporary Africans, which may be due to many factors: post-OOA admixture within Africa with diverse archaic hominins leading to a higher Ne. A higher mutation rate due to this higher Ne, and to adapting to the environmental challenges of Africa. Higher mutation rate driven by higher heterozygosity. All of which lead to a higher diversity in contemporary Africans (note that we have no ancient DNA sequences from H. sapiens in Africa as we do for Neanderthals in Eurasia, and H. sapiens in Eurasia, Oceania, and America.

There is also the question of Neanderthal admixture in Africans. I discussed this in a 2019 post and in a 2020 post but more papers have appeared on the subject as we will see below.

The generalized notion is that human beings admixed with Neanderthals, who lived in Eurasia, during the Out Of Africa migration. Since there were no Neanderthals in Africa, those humans who remained behind in Africa never mingled with the Neanderthals, and therefore have no genetic input from them. But, back in 2018 a paper reported a Neanderthal genes in East Africa, they were carried there by Eurasian humans who had admixed with the Neanderthals in Eurasia

In and Out of Africa. Copyright © 2026 by Austin Whittall

The map above shows the homeland of the OOA migrants, in the Horn of Africa (Ethiopia) and the red arrows mark the OOA migration across Eurasia and Oceania. In Europe and Western Asia they met the Neanderthals who lived there, mated, admixed, and some modern humans returned to Africa (blue arrows) carrying Neanderthal alleles with them.

The 2020 paper mentioned above suggests that "Back-Migration with Non-Africans and Pre-out-of-Africa Human-to-Neanderthal Gene Flow Contribute to Apparent Neanderthal Ancestry in Africans", two mechanisms, one, the backflow and second, an early gene flow from an early, failed OOA migration that introgressed human alleles in Neanderthals (100-250 ky ago), and which appear as shared between Neanderthals and humans when they are compared.

Below is an image from A. Ragsdale (2023), that shows these gene sharing events (early-OOA with Neanderthals, and Neanderthal-Later OOA admixture and backmigration of Eurasians to Africa).

Figure 1. A history of reciprocal introgression between humans and Neanderthals. (A) Population structure among the ancestors of modern humans extended deep in the past, though common ancestry of all present-day humans is more recent than the expansion of early Homo sapiens out of Africa that resulted in human-to-Neanderthal admixture. Arrows indicate major migration and admixture events.. Fig. 1A in Ragsdale (2023)

The Neanderthal admixture was present in samples obtained from LWK = Luhya in Webuye, Kenya, East Africa. GWD = Gambian in Western Division, Mandinka, in West Africa. MSL = A Mende population from Sierra Leone in West Africa. YRI = Yoruba in Ibadan, Nigeria, in West Africa. ESN = Esan in Nigeria, West Africa. This is a pan-African presence.

This paper found that "of the Neanderthal sequence identified in African samples, more than 94% was shared with non-Africans..." only a small part was uniquely African, as you can see in the following image, Fig. 2 B in that paper captioned: "Venn diagram showing the amount of overlap in identified Neanderthal sequence in non-African and African populations." Europeans have ~80% more unique Neanderthal alleles than Africans, yet they have their own unique alleles not shared with Eurasians, they seem to have been lost in Eurasia, or, did they come from introgressions with other archaics in Africa, carrying these alleles?

Then they "also performed extensive simulations and found that the signal of Neanderthal ancestry in Africans was unlikely to be explained by false positives due to shared ancestry." They therefore attribute the signal to admixture. But where? In Africa or due to a backflow?

The paper states that they considered both options: "studied models where non-African individuals, who carry Neanderthal sequences inherited from hybridization, migrated back to Africa and models of human-to-Neanderthal gene flow due to an early pre-out-of-Africa (pre-OOA) dispersal of modern humans." Note that they don't consider the inside-of-Africa mixing but, instead, admixing in an Early out of Africa mixing (more on this below).

Regarding backflow they found that "These data are consistent with the hypothesis that back-migration contributes to the signal of Neanderthal ancestry in Africans. Furthermore, the data indicate that this back-migration came after the split of Europeans and East Asians, from a population related to the European lineage."

Early Out Of Africa

The paper then finds that there is "strong evidence that human sequence in the Neanderthal genome also contributes to the signal of the Neanderthal ancestry we detect in Africans." The first out of Africa event which supposidly took place betewwn 100 and 150, or even 250 ky ago introgressed human genes into Neanderthals, a gene flow from H. sapiens of this first wave into Neanderthals. Previous studies have noted the genetic contribution of a pre-out-of-Africa gene-flow event from humans into Neanderthals. So, when comparing Neanderthals with current modern humans, we find that we share some alleles (of course, they were originally human genes).

West Africa

Both the 2020 paper mentioned above, and anothe paper by Anders Bergström (2020) found ancient admixture of Neanderthal genes in West Africa. West Africa! which is on the opposite side of Africa from which the OOA event ocurred. How could there be Neanderthal genes so far from East Africa?

Bergström assumes it is a backflow from Eurasia, but also adds that they may be relict alleles from the period that predates the OOA event, and that preserved these genes in Africa, which were lost elsewhere:

"We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa....
Alleles private to Africa, however, include a higher proportion of ancestral alleles, and this proportion increases with allele frequency, reflecting old variants that have been lost outside of Africa. For the same reason, many high frequency private African variants are also found in available Neanderthal or Denisovan genomes."

If Africans carry variants of Neanderthal and Denisovan genes not found elsewhere it means that these introgressed into Africans, within Africa, maybe from isolated populations of these ancient humans found inside of Africa.

When it comes to splits within African populations, Bergström's paper assumed "a mutation rate of 1.25 × 10−8 per base pair per generation and a generation time of 29 years" and calculated the splits between populations but found that "all of these curves are clearly inconsistent with clean splits, suggesting a picture where genetic separations within Africa were gradual and shaped by ongoing gene flow over tens of thousands of years. For example, there is evidence of gene flow between the San and the Biaka until at least 50 kya, and between the Mbuti, the Biaka, and the Yoruba until the present day." This is in line with an "enrichment" of modern Africandiversity by agglutination of the past diversity preserved in isolated African populations, as mentioned in my recent posts.

Ancient structure influenced modern diversity: "For the deepest splits, there is some evidence of genetic separation dating back to before 300 or even 500 kya... The implication of this is that there lived populations already at this time that contributed more to some present-day human ancestries than to others... but also a small fraction of present-day ancestries retaining traces of structure that is older than this, potentially by hundreds of thousands of years." Here, I ask, are these ancient alleles result of recent post OOA introgression of ultra-archaic hominins in Africans? or the common ancestors of humans and Neanderthal-Denisovans?

The presence of Neanderthal alleles in Africans was quantified by Bergström as follows: "The West African Yoruba also display a Neanderthal admixture signal that is similar in shape but much less pronounced than that in non-Africans (Fig. 6D and fig. S9). Other African populations do not clearly display the same behavior. These results provide evidence for low amounts of Neanderthal ancestry in West Africa, consistent with previous results that were based on other approaches, and we estimate this at 0.18 ± 0.06% in the Yoruba using an f4-ratio (assuming that the Mbuti have none). The most likely source for this is West Eurasian admixture and, assuming a simple linear relationship to Neanderthal ancestry, our estimate implies 8.6 ± 3% Eurasian ancestry in the Yoruba."

Sub Saharian Africa (SSA)

The people living in Africa south of the Sahara also carry Neanderthal alleles, a study by Harris et al., 2024: " As a percentage of the genome, therefore, Neanderthal ancestry in the 180 SSA dataset ranges from 0% to ~1.5%, with the highest levels observed in the Amhara and Fulani."

They favor the sequence: early migration of anatomically Moderh Humans (AMH) out of Africa ~250 ky ago, admixing with Neanderthals in Eurasia, leaving a ~6% AMH genetic trace in Neanderthals. Then, the final OOA event with modern humans, who mated with Neanderthals (~40 to 55 kya), receiving these AMH haplotypes from the Neanderthal (NIRs). Then, " Third, at least two subsequent recent migrations of non-sub-Saharan African AMHs into sub-Saharan Africa brought introgressed Neanderthal haplotypes (NIRs) to sub-Saharan African AMH populations with whom they admixed."

Perhaps the best theory is the one that suggests that the Neanderthal signal was acquired inside Africa, as we will see below.

An introgression within Africa

Arun Durvasula and Sriram Sankararaman (2020) on the other hand suggest that the Neanderthal genes came from a direct "within Africa" admixing event:

"We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans... Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."

They compared three different models in which part of the West African ancestry comes from, (A) people who split from their ancestors after modern humans and Neanderthals split; (B) people who derive from the ancestors of Neanderthals after they split from modern Humans, and (C) people who split from the ancestors of modern humans and Neanderthals before modern humans and Neanderthals split. They found that (C) was the best model:
"support for a contribution to the genetic ancestry of present-day West African populations from an archaic ghost population whose divergence from the ancestors of modern humans predates the split of Neanderthals and modern humans.
... We determined the posterior mean for the split time to be 625,000 years before the present (B.P.) [95% highest posterior density interval (HPD): 360,000 to 975,000], the admixture time to be 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction to be 0.11 (95% HPD: 0.045 to 0.19). Analyses of three other West African populations (ESN, GWD, and MSL) yielded concordant estimates for these parameters. Combining our results across the West African populations, we estimate that the archaic population split from the ancestor of Neanderthals and modern humans 360 thousand years (ka) to 1.02 million years (Ma) B.P. and subsequently introgressed into the ancestors of present-day Africans 0 to 124 ka B.P. contributing 2 to 19% of their ancestry."

This means that an ancient, relict population that split from the branch leading to Modern Humans and Neanderthals between 360 and 975 ky ago, on avg. 625,000 years ago, mated with Homo sapiens people in Western Africa, and this event ocurred after the OOA event that peopled the rest of the world, this admixture inside of Africa took place roughly 43,000 years ago (0 to 124 ky).

Maybe later there was backflow from Eurasia, but this introgression in Western Africa with an ultra archaic human is the one tha injected Neanderthal-like genes into this population. It must have surely contributed to the diversity of these populations, adding more heterozygosity to them.

This idea is supported by Nina Hollfelder, Gwenna Breton, Per Sjödin, and Mattias Jakobsson, (2021):

"Another possibility is that the large Ne is shaped by multiple introgression events from divergent lineages, which are hard to distinguish without archaic reference sequences. Unfortunately, many studies of archaic or ghost introgression in Africa focus on a few populations and/or use only one method for inference, so that the effect of the identified archaic or ghost introgression is not yet comparable across all major branches of modern humans in a systematic way.
Interestingly, many studies identified a fairly recent time for the introgression from extinct lineages in Africa, with introgression events even after the split from non-African populations, hinting at survival of archaic human populations until relatively recently in time."

Where Ne is the effective population, the large Ne of the African population is considered as one of the factors that created its diversity vs. the rest of the World, with lower Ne's due to bottlenecks and lower diversity. Here, we see that multiple introgression from diverse populations that merge can also lead to the effect of a high Ne!

I personally support the idea of super-archaics mixing with Africans after the OOA event, adding diversity and heterozygosity to their genetic makeup, and I don't exclude a backflow from Eurasia with Neanderthal genes.

No Neanderthals or Denisovans, but an archaic introgression

Last but not least, Lorente Galdos et al., (2019)" found no signals of Neanderthal or Denisovan introgression in the sub-Saharan individuals... 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.... Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans. "

The timeline given in this paper is the following: "the AMH lineage and the one from the archaic Eurasian populations diverged 603 kya (95% credible interval (CI) ranging from 495.85 to 796.86 kya). The ghost XAf archaic population and the AMH lineage split 528 kya (95% CI of 230.16 to 700.06 kya), whereas the Denisovan and Neanderthal lineages split 426 kya (95% CI from 332.77 to 538.37 kya). Archaic introgression estimates from XAf to African populations range from 3.8% (95% CI 1.7 to 4.8%) in Khoisan and 3.9% (95% CI 1.3 to 4.9%) in Mbuti to 5.8% (95% CI 0.7 to 0.97%) in West Africa. Our analyses also identified the archaic introgression from early AMHs into Neanderthal."

I wonder if the AMH introgression into Neanderthals (also mentioned further up) which is said to have taken place during the early OOA event 250-100 ky ago, isn't just the reflection of the common origin and relatedness between Neanderthals and these early AMHs. They split in Africa and had common genes. Seems a simple, straightforward explanation.

Regarding the ghost archaics XAf population, I have posted about them in the past (see this post, this post, this one, and this post among others), they are indeed a source of diversity, rare alleles, and heterosygosity for contemporary Africans.

Comments

As you can see, many research papers, authors, models, interpolations, algorithms, and softwares used and different interpretations from the same basic genetic samples!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©