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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