In my previous post about John Hawks take on the ancestral groups that merged (80:20 ratio theory) to form modern humans, I mentioned that he cited several research papers in his analysis. Today I will look into one of them, by Loya, H., Gupta Hinch, A., Palamara, P. F., Speidel, L., & Myers, S. R. (2026). Genome-wide genealogies reveal deep admixtures forming modern humans. bioRxiv. https://doi.org/10.64898/2026.04.17.719197
Loya et al., use a new algorithm called Ghostbuster to study ancient admixtures, and after validating it with recent admixture events, use it to evaluate PRDM9 alleles found in modern and ancient humans.
The PRDM9 gene is linked to genetic recombination. It codes for a protein called PR domain zinc finger protein 9, that plays an important role during meiosis (cell division that produces sex-cells, like sperm and egg cells, which carry half the normal number of chromosomes), it latches on to certain spots of the DNA strand and defines how the DNA recombines (how it is shuffled, and where snippets are added or removed).
Like all alleles, PRDM9 comes in different variants, that arise from mutations. And, these alleles are what Loya and team studied.
PRDM9 Alleles
Before continuing with Loya et al.'s paper, I would like to mention the frequencies at which different PRDM9 alleles are found in modern human populations. For an enlightening paper on the role of PRDM9, see Paigen and Petkov, 2019; it informs in an over-simplified manner that the alleles found globally "generally agree... with their “out of Africa” origins." It says so because Africans have a greater variety of alleles: 50% of allele A, 13% allele C and the other 37% a mix of different variants. The non-Africans, after the bottleneck caused by the OOA migration are almost exclusively A: "with ~90% alleles A and B (mostly A), which only differ in a serine/threonine substitution that does not affect binding specificity" Regarding the Denisovans and Neanderthals, this paper states that their "PRDM9 alleles closely related to rare contemporary alleles that are limited to Africans." I found this rather vague, so I looked for more information on alleles and their frequencies in different populations.
Alleva et al., 2021 investigated this matter and found that the A allele is the most frequent one, ranging from 90% in Finns (highest value) to 48% among Yoruba people in Ibadan, Nigeria (YRI) and 49% in Luhya in Webuye, Kenya (LWK), in between are the Chinese Han with 75% (CHB). The B allele, on the other hand, is higher among the Chinese CHB, with 13% and YRI = 7%, and much lower in other populations (0 to 3%). Another variat named L14 allele is found in Africa, ranging between 11% in LWK, to 3% in YRI, and not present in other non-Africans. The most relevant one is the C allele, it is found in all populations: YRI = 10%, LWK = 8%, CHB = 6%, and also in South American Peruivians from Lima (PEL) = 8%, lower in Italians from Toscana (TSI) and Pakistanis from Lahore (PJL), both with 4%, lowest among Finns with 2%. So, it isn't an exclusive African variant, it is rare in Europe, but present there.
Then come many other variants at lower frequencies in all populations. They add up to a 16% of the global PRDM9 alleles, but they vary between different populations. Most of them at levels of 30% and 31% are found in Africans (LWK and YRI respectively), followed by Tuscans (TSI) with 14% —probably due to recent African admixture in historic times. The rest of the world has levels of 7% to 9% (PEL, CHB, FIN, PJL).
Some rare alleles are exclusive to certain populations, like M1, found at "enriched" levels in Chinese HAN yet absent in all other populations. The D allele was only found in Finns.
Below is an image depicting a Table from the Supplementary Material of Berg et al., 2011, which also provides some frequencies for Europeans, Indians from India, and Africans. Notice the different variants and how the rare ones are exclusive to some regions. I highlighted those higher than 4%. It does not include variant M1 (from the Chinese).
Having said this, let's get back to Loya et al. who report that the most common one, PRDM9-A is found in all modern human beings at frequencies of 85% to 90%, and the PRDM9-C allele is less frequent globally, but high in Africa at 10% to 15% together with other rare variants (at 35% in Africa).
Their Ghostbuster algorithm provides evidence that the best model to explain this distribution is the following: there was an original basal lineage carrying the A allele as ancestral variant. Then it split into two stems, one carried the allele A (population HA), the other the allele C (population HC). These populations split and remained separated around one million years ago, then they met 300,000 years ago, merging, this was the time when modern humans, Homo sapiens appeared. Below is Figure 5c, from their paper, showing this scenario:
The Neanderthals and Denisovans form part of population HC. Through introgression, the C allele entered modern humans, and the Neanderthals, through admixture with us, got the A allele and a 10% contribution from humans to their genome. Regarding the Denisovans, "Denisovan PRDM9 alleles are distinct from present-day human genotypes, and at least one allele is more similar to PRDM9-C than to PRDM9-A."
The authors suggest that HA population contributed with 20% of the human ancestry. It was a larger population.
Who were these HA people?
The HA population lived for a long time, starting over one million years ago, and surviving until at least 300,000 years ago. It was widespread as it had to mix with the other HC population (in Africa, in accordance with the African origin of modern humans and demanded by the Out of Africa theory), and also in Eurasia, where it met the Neanderthals and admixed with them too. However it seems not to have been present in Eastern Asia because it didn't mix with Denisovans (though, later, modern humans and Denisovans mated there).
Considering the higher prevalence of the A allele outside of Africa, and the lower frequencies inside of Africa, the HA population was surely an established Eurasian lineage that partly migrated into Africa blending with HC there.
Due to the controversy around Mid Pleistocene fossils (the "muddle in the middle" conundrum), it is not an easy task to assign fossils to the HA population. Loya et al. timidly propose that "fossils attributed to H. heidelbergensis are a candidate for HA, as they possess the geographic and temporal properties suggested above." Perhaps they were a group living in the Europe, and the Levant, originating and descending from Eurasian Homo erectus, like the Homo antecessor whose remains have been found in Spain
Pending questions
If so, we can imagine that the superarchaic group from which HA and HC split is also Eurasian. This split took place long ago. Could the basal lineage be an ancestor of Homo erectus, a group that was present in Eurasia, like the Dmanisi hominins from the Caucasus?
The figure above shows that the subpopulation within HC that mixed with HA to form modern humans within Africa split from the remaining HC branch before this stem, in turn, split into Denisovans and Neanderthals. So, according to this figure, there is an "out of Africa" around 600,000 years ago, of the branch leading to Denisovans and Neanderthals, that totally removes this HC group from Africa (note that Africans do not carry Denisovan or Neanderthal alleles).
As mentioned further up, C allele is present at similar levels in Africa 10-8% as in Asian and American populations: Chinese and Peruvians 8-6%, but is much lower in Europe. Why? wouldn't admixing with Neanderthals (carrying C allele) enhance the frequency in Europe and Western Eurasia? Perhaps the predominance of a large HA population in Europe contributed to a higher frequency of A allele there, diluting the C allele frequencies.
Perhaps the most interesting part is the 35% of rare variants found in Africa, these probably derive from mutations in other archaic branches like H. naledi or Homo rhodesiensis they did not come from the HC or HA populations. They were archaics that blended into the modern Africans, and added their ancient, rare PRDM9 alleles. Another piece of evidence suggesting that diversity within Africa is due to the introgression of archaic hominins.
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