Another post on dental enamel protein AMBN 273V or M in Denisovans, Neanderthals, and Humans

In three different posts I mentioned dental enamel protein as a tool to investigate ancient ancestry, admixtures, and archaic introgressions.

The first post looked into a paper by Quiamei Fu, et al., 2026, Enamel proteins from six Homo erectus specimens across China, published in Nature on May 13, 2026 (vol. 655, pp 141–147 https://doi.org/10.1038/s41586-026-10478-8), it suggests archaic introgression from Homo erectus into Denisovans, and from them, into modern humans, which shared a protein found in teeth enamel, named AMBN(M273V) from erectus via Denisovans to us, Homo sapiens.

The second post mentioned another protein found in teeth, called COL17A1 that is found in its ancestral form in Paranthropus robustus and Homo naledi, and in derived form in--Denisovans, Neanderthals, and modern humans. Suggesting that naledi may not be a homo (see Madupe P, Taurozzi A, Koenig C., et al., Proteomic analysis of dental enamel from 20 Homo naledi individuals shows no male markers. Cell, 2026; 189, 4415-4424.e11).

The third post mentioned another recent paper that questions the archaic introgression hypothesis proposed by Fu et al. and suggesting other alternatives for the presence of AMBN 237V in Denisovans and humans, that don't require an introgression with Homo erectus (see No signal of a super-archaic origin of the Denisovan AMBN gene, a comment on the protein affinity of Homo erectus and Denisovan enamel proteins, Ioannis Patramanis, Frido Welker, Laurits Skov. bioRxiv 2026.08.11.744165; doi: https://doi.org/10.64898/2026.08.11.744165).

Today I will discuss a fourth paper on the subject of dental enamel proteins, published last week, on August 26, 2026 by Paula Kotli; Enamel Palaeoproteomics Successfully Distinguishes between Denisovans and European Neandertals (bioRxiv 2026.08.22.746388; doi: https://doi.org/10.64898/2026.08.22.746388).

Kotli compared DNA from the Penghu jawbone, dredged up from the sea in Taiwan, and a Neanderthal from Portugal and found that the AMBN V273 variant (with a Valine aminoacid substitution there —hence the "V") was exclusively Denisovan while the Neanderthal carried a Methionone aminoacid there (M273 variant). These two proteins can serve as markers to identify the origin of ancient teeth when DNA is not correctly preserved; tooth peptides last longer than DNA.

Most modern humans carry the M273 variant, shared with Neanderthals, while not only Penghu, but other Denisvoans (like the Denisova 3 specimen) carry the V273 variant. Unsurprisingly, the region with the highest levels of Denisovan admixture, the Philippines, also has the highest level among all modern humans of the V273 variant: It reaches "a notably elevated frequency of ∼21% in modern Philippine populations (compared to <1% globally)."

Africans and archaic admixture

While researching about ancient teeth proteins and their prevalence among modern humans, Neanderthals, and Denisovans, I came across a good paper on the subject: Zanolli C, Hourset M, Esclassan R, Mollereau C. Neanderthal and Denisova tooth protein variants in present-day humans. PLoS One. 2017 Sep 13;12(9):e0183802. doi: 10.1371/journal.pone.0183802. PMID: 28902892; PMCID: PMC5597096. In it, they mention the presence of rare variants found in Denisovans and Neanderthals, inside Africa. This is quite unexpected because both of those ancestral lineages are not known to have existed within Africa and the current view is that they admixed with the humans that left Africa in the Out of Africa migration. So, how did these rare variants find their way into the genes of Africans?

Zanolli et al. write (highlight is mine): "The finding in living Africans of rare derived polymorphisms that were present in Neanderthals (Fig 2: ENAM G389S, 5%) or Denisova (Fig 3: CEMP1 R80H, 0.5%) is difficult to reconcile with the fact that interbreeding of AMH with Neanderthals occurred out of Africa. However, as mentioned above, this could be explained by the inside Africa admixture between the ancestors of AMH and archaic hominins, or by the possible back migration of Neanderthal gene flux. Further genome analysis of the Neanderthal and Denisova polymorphisms in AMBN, ENAM, and CEMP1 certainly deserves attention as they could trace back an African ancestor common to Neanderthals, Denisova and early anatomically modern humans" The final comment is expected: these rare alleles could be the faint trace of the last common ancestor shared by Humans, Neanderthals, and Denisovans. I choose to believe that they are the result of admixing between archaics and recent Africans within Africa.

The ENAM G389S variant is, according to the supplementary material found at rates of zero in Europe, South Asia, and East Asia, at 5% in Africans, and at 0.3% in America. So how did it exist in Neanderthals but leave no trace elsewhere, but in Africa and America (Maybe slave trade brought it to America?). The other variant, the Denisovan CEMP1 R80H is found at zero levels everywhere except Africa where it reaches 0.5%. Denisovans in Africa?

K 55 E variant

Another ancient (ape variant) is found at surprisingly high levels in Africa, with 26%, but only at 2% in Americas, 0.2% in Europe, zero in East Asia, and 0.1% in South Asia. This variant is known as K55E (rs13331643) in CEMP1, and is commonly shared in this ancestral form with gorillas and chimpanzees.

So, basically, all modern humans in the rest of the world carry the derived allele of K55. Surprisingly, the ancestral variant, found in Africa at 26% frequency, is also found in Denisovans and Neanderthals. Again, a contradiction to the belief that Africans never mingled with those hominins.

The paper tries to explain this incongruity as follows (note that AMH means "anatomically modern humans"): "This suggests that the ancestral variant may have not been favorable to AMH outside Africa or, conversely, that the derived allele was specific to AMH and evolved out of Africa due to a founder effect. The ancestral archaic variant could also explain in part the tendency of people with African origins to have larger crowns and root volume and surface. Indeed, this variant is also found in Neanderthals teeth, characterized by high crown dimensions and frequent taurodontism. The presence of this variant in Denisova is also compatible with such traits."

Why would the non-Africans, who mated with Neanderthals and Denisovans not uptake their ancestral K55 variant in higher frequencies, and instead retain a mutation (the derived form), while Africans, who supposedly never met the Neanderthals & Denisovans, carry the ancestral variant?

I don't see how this fits in with the Out of Africa theory. The admixing of Denisovans in Asia can explain its presence there, and also in America, and Europe where Neanderthal admixture is higher, but why is it so prevalent in Africa? Maybe, the cause is an introgression of super-archics into the recent African populations.

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

San (Khoisan) and Europeans

Following my previous post on similarities between San people in southern South Africa, and Europeans, I read a paper about the San (Khoisan) and their "antiquity". It reports them as an ancient population that retained a large effective population while that of other groups fell (i.e. other Africans, Europeans, Asians, and the Out of Africa migrants).

The paper published in Nature in 2014 by Kim et al., (Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history). The image below shows how Ne (effective population) evolves over time (oldest to the right), for San, African Yoruba, Europeans, and Asians. As you can see all groups (actually, the ancestors leading to each of these populations) have similar population sizes till 100,000 years ago when a dramatic drop in population sizes occurs. I don't understand how they obtained Ne values for hominin populations 2 to 4 million years ago, this was the days of Australopiths and probably Homo habilis.

Effective population sizes for San, Africans, Asians and Europeans. Fig. 3 a in Kim et al., 2014

This drop in effective population size is attributed to climate changes within Africa. The paper includes a series of maps as Fig. 12 in its Supplementary Material to explain the process. They can be seen below:

Modern humans originated in Africa (a), blue circle in South Africa seems to imply an origin there, though the paper does not specify the location. Then these people spread north (b), the orange oval marks the new territories. Then came the climate change (c) around 150 or 100 kya. Drought in western and central Africa hit the humans there in central, western, and eastern Africa, but spared the San people in the southern part of Africa. This coincided with a fragmented population (structured) with isolated groups that did not interact with each other (see the different dots and colors on the map, marking these groups). Populations declined central and western Africa, and when the ancestors of Non-Africans (green arrows) (d) migrated Out of Africa (OOA), they carried this lower Ne, and it dwindled even more due to bottlenecks and founder effects as they advanced into Eurasia. The San, however, kept their population intact.

The authors reconstruction of this period is summarized as follows: "After the earliest split, between the ancestral Khoisan and non-Khoisan populations ~100–150 kyr ago, the ancestral Khoisan population maintained their high genetic diversity, while the effective population size of the non-Khoisan continued to decline for 30~120 kyr ago and lost more than half of its diversity. The ‘Out of Africa’ migration ~40–60 kyr ago accounts for the observed population split between African and non-African populations, and the subsequent smaller effective population size of non-Africans compared with non-Khoisan Africans."

Comments

However, and interestingly, as pointed out in my previous post, the San and Europeans share several unique allele variants that are ancestral (found also in Neanderthals and Denisovans) which confer lighter pigmented skin than that found among the remaining Africans and also South Asians and Australo-Melanesians, who carry a later (derived) mutation for darker pigmentation.

How does this similarity between a specific OOA group and San people tie in with the evolution and migration sproposed by Kim et al.?

Not well. We would have to imagine a group that split from the San, moved north, lived in isolation in Central Africa, then survived the climate crisis there, moved north, left Africa, surviving the founder effect, bottlenecks and genetic drift, established themselves in Europe and somehow managed to keep their skin-color alleles intact. While all the other groups in Africa mutated and adopted a dark skin set of alleles. Too complex to be the explanation.

The San (Khoisan or bushmen) have always intrigued me since the 1980s movie "The Gods Must Be Crazy", I was taken aback by their pale skin and oriental factions. So different from the usual African features. People living in the deserts of Namibia with a hunter-gatherer culture in the 20th century! I have never found a paper explaining their similarity with East Asians. I will explore this strange trait in a coming post.

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

Into Africa, some proof on an Out Of America origin of modern Homo sapiens

Regarding my previous post where I mentioned a paper on the non-African origin of modern humans, I have come across another very interesting paper: "Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa" by Michael DeGiorgio, Mattias Jakobsson and Noah A. Rosenberg (Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38): 16057–16062. Published online 2009 Aug 17. doi: 10.1073/pnas.0903341106) which offers an interesting model which can explain the greater diversity of Africans and at the same time make them the "most recent" humans instead of the oldest ones.

The usual argument for an Out of Africa origin of Homo Sapiens is the higher diversity in Africa versus that of non-African populations. A typical example used as proof is the graph showing how Heterozygosity decreases with the distance to Africa (there are countless of these on the internet, with the Y axis showing Heterozygosity and the X axis showing the distance from Addis Abbaba), below is one of them:

A typical heterozygosity vs. distance to Ethiopia. From Fig. 2 in [1]

Notice the negative gradient of the graph (shown by the dashed line in the figure -Fig. B, on the right). Heterozygosity falls from left to right.

The paper by DeGiorgio, Jakobsson and Rosenberg which caught my attention explores a models to explain this fact. In doing so they analyze different alternatives. And the one they discard because it does not fit the current idea of an Out of Africa model, is precisely the one that explains the data, if you accept a non-African origin of mankind. Allow me to explain:

Archaic Persistence Model

The team developed this "archaic persistence model" in which an archaic population evolved-mutated and originates modern humans (Homo sapiens). And as this first original and most ancient Homo sapiens population expands outwards from its homeland, it spreads gradually forming colonies which move into a "collection of preexisting archaic populations". For instance Denisovans, Neanderthals or even surviving yet unknown Chinese hominds -or Homo erectus descendants...

In the words of the authors, this is what they observed as the populations moved away from the original nucleous, the first modern human population:

"Heterozygosity increases, LD decreases, and the ancestral allele frequency spectrum slope increases with increasing colony number. These results can be understood from the fact that in the long time since the initial divergence, the K archaic populations have enough time to develop distinctive localized variants. As the migration wave travels through them, it accumulates diversity, gathering new variants from each population through which it passes. Thus, heterozygosity increases with increasing colony number in the same way that it increases in the archaic admixture model at the population in which admixture occurs. The difference between models lies in the fact that in the archaic persistence model, archaic admixture occurs in every population, so that heterozygosity increases at each step rather than at a single location. This occurrence of archaic admixture at each step also explains the decrease in LD and increase in the slope of the ancestral allele frequency spectrum that occur at each step...

In other words they observed that if the original, the "first real" human group, was in Africa, as we moved further away from there we should find more heterozygosity, which we don't. Hence the model is wrong and despite having originated in Africa we did not go through this type of admixture.

But lets just look at this with a more open mind:

Turn it around!

However if the original home of modern humans (Homo sapiens) was in America and not Africa, then, as they migrated outwards from America, into Asia, Oceania, Europe and went through each of the archaic populations in the old world, adding diversity and finally reached Africa mixing with the archaics there, the heterozygosity would be lowest in America and grow towards Africa, which is exactly what their model finds and which coincides with the observed heterozygosity cline in modern humans.

So It all makes sense if you invert the origin of the first humans: form Africa, to America.

Below is the image showing how heterozygosity grows as you move away from the original H. sapiens population if you assume the Archaic Persistence Model, the authors discard it because the actual observed heterozygosity falls as you move away from Africa:

From Fig 6 in DeGiorgio, Jakobsson and Rosenberg, adapted by A. Whittall

Now let's turn this same figure around and the result is a graph with a negative gradient which is exactly the same as the first graph we used in this paper (the distance to A. Abbaba & heterozygosity):

Same figure as above but we change the location of the first modern humans
Adapted by Austin Whittall

As an engineer, I sometimes get the feeling that Anthropology and those who study the origins of humanity are like the late 1800s Physicists who despite all the evidence kept on pushing the notion of ether or fiddle with the data to uphold classic mechanics. It took Einstein and Plank to change the paradigm with their Relativity and Quantum theories. Something similar took place in the 1500s, with Copernicus explaining with graceful simplicity the movement of the planets, doing away with the complex Ptolomean system. A shift in mindset is needed to look at the same data to find the necessary changes and to avoid adhering to theories that contradict that data.

Sources

[1] Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, et al. (2014) Patterns of Admixture and Population Structure in Native Populations of Northwest North America. PLoS Genet 10(8): e1004530. doi:10.1371/journal.pgen.1004530

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Into Africa gaining strength

A paper pubished in Science (Gallego Llorente et al., 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science DOI: 10.1126/science.aad2879 two days ago, reveals what has been suspected for some time: All Africans have a Eurasian component in their genes.

The abstract says so clearly:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

As it is behind a pay wall, I checked the web and found the following additional data:

• "the scientists believe up to 25% of the DNA of modern Africans can be traced back to this event."
• "... if you go to the corners of Africa, all the way to West Africa or South Africa, even populations that we really thought were purely African have 5-6% of their genome that dates back to these western Eurasian farmers."
• "...it is also interesting to discover now that even sub-Saharan Africans have a bit (0.3-0.7%) of Neanderthal ancestry."

Who knows, perhaps this is the first step into a serious analysis of the real roots of mankind, and may lead to a revision of the conclusions of another recent paper (L. Pagani, 2015, Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians Cell):

"... the Ethiopian and Egyptian genomes showed different patterns. In particular, the Egyptian0 genomes displayed a more recent split from both the West African (21,000 years ago) and the non-African (55,000 years ago) genomes than did the Ethiopian genomes (37,000 and 65,000 years ago, respectively). This suggests a higher similarity between non-African and Egyptian components than between non-African and Ethiopian components, which is consistent with the fact that Egypt is the last stop on the way out of Africa. Such split dates also hint at a recent interaction between Egyptians and West Africans..."

They too noticed a similarity between Egyptian and Eurasian genes, but their conclusions are different.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall ©