Chris Stringer on reviewing the Out of Africa theory

This will be a very short post about a relevant subject: how the Out of Africa theory has been upset by the discoveries that have taken place over the past twenty years. I came across a podcast by Chris Stringer RETHINKING "OUT OF AFRICA", and I encourage you to read it.

Christopher B. Stringer (born 1947), is a British anthropologist who has always backed the Out of Africa (OOA) theory (as the source of modern humans). However, the genetic evidence of admixture between Neanderthals, Denisovans, archaics and even super archaics with humans has led him to reconsider his position. Stringer has come to admit that we are a complex mix of different hominins. He now supports a modified version of the OOA theory that contemplates interbreeding.

In the podcast, Stringer describes the original concept on which the OOA theory was built: a single, isolated group in Africa, evolved into modern humans, and spread across the globe replacing all other hominins without mixing with them. He recognizes that it was very simplistic. The presence of Neanderthal DNA in Eurasians, Oceanians and Amerindians hints at a first contact in Southwest Asia and not a gradual intermingling as modern humans trekked into Europe. Furthermore, the presence of Denisovan ancestry in Eastern and Southern Asia and Oceanians also shows that humans also met these mysterious hominins and intermingled with them.

Below are some quotes from this work with my comments.

On Neanderthal Introgression; how, when, and where

Stringer points out a remarkable fact: the uniformity of Neanderthal introgression in Eurasians. If we had met them in Europe, the Europeans would have more Neanderthal DNA than other groups, after all, Neanderthals lived in Europe, but the situation is different. Stringer says: "The extraordinary thing is the level of DNA is about the same in a modern European, a modern Chinese and a modern New Guinean. One possibility is that an interbreeding event happened early on in southwest Asia. As modern humans first emerged from Africa, they met some Neanderthals —maybe only 25 Neanderthals and 1,000 modern humans. That would be enough. And then that DNA gets carried with those modern humans as they spread out from that area and diversify."

This is the first time I have seen the admixture event quantified. It is rather small-scale, isn't it? But it sounds realistic. The location in SW Asia (the Levant) is also reasonable.

On Archaic admixture inside Africa

Just as in Eurasia, ancient hominins survived in Africa until recently and admixed with African humans. This is something that I have posted about several times : "...some African people have acquired [DNA], perhaps even from Homo heidelbergensis... In Africa itself, archaic humans could have lingered in parts of the continent as well. From some recent genetic analyses, there is evidence of an input of archaic DNA into some modern African populations as recently as 35,000 years ago. So even in Africa, the process was more complicated than we thought."

Regarding this point, I notice that it seems to be a taboo-like subject in academic circles. Do scholars consider it discriminatory to suggest archaics or super archaics had sex with modern humans in Africa? Why can we say this about Eurasians and Oceanians, exchanging body fluids with Denisovans and Neantherthals, but not about Africans? It is just pure wokeness.

On the Flores Island "Hobbit" the Homo floresiensis

This hominin is remarkable, it survived until very recently (17,000 years ago), it has a large brain in relation to its size, it crossed a deep sea barrier to reach Flores Island and thrived in its island ecosystem. Where did they come from? Are they Homo erectus that shrunk in size to survive on the island? Are they the outcome of an even earlier hominin? Stringer ponders:

"... The suggestion is now that this [hominin] might represent an even earlier stage of human evolution, one that's closer to Homo habilis or even to Australopithecus, creatures that lived two million years ago or more in Africa. Although we've got no evidence of it happening yet, the argument is that one of those more primitive forms got out of Africa more than two million years ago, somehow found its way over to southeast Asia, and survived in isolation on the island of Flores until 17,000 years ago, when it went extinct. That would be an even more extraordinary story than a Homo erectus getting there and dwarfing, that you've actually got a relic of an earlier stage of human evolution that got all the way over there."

Unsolved questions

Stringer also mentions that "We've got a whole unknown history" for the Flores Island hominins and also for the Denisovans. More on this subject in my next posts.

He suggests that the Homo erectus probably evolved in Europe, resulting in the Homo antecessor, in Spain. That the Homo heidelbergensis evolved into Neanderthals in Europe, and also into Denisovans and modern humans (Though he does not say where the H. heidelbergensis originated!).

He hints that H. heidelbergensis who also lived in Africa, survived there until recently, possibly admixing there with modern Africans: "Africa had an overlap of modern and archaic humans, with the possibility in a continent so large that there were other descendants of heidelbergensis living there alongside Homo sapiens. These populations could have exchanged DNA too, evidence of which might be found in the genomes of living Africans."

Stringer concludes (highlight is mine): "We end up with quite a complex story, with even some of this ancient DNA coming back into modern humans within Africa. So our evolutionary story is mostly, but not absolutely, a Recent African Origin."

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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 © 

Neanderthals, Denisovans, territory and admixture

Icame across an interesting map while browsing the Internet, it shows the habitats where Denisovans and Neanderthals could have lived in Eurasia. Mind you, habitats or ecological regions suitable for them, which does not necessarily mean that they lived in this whole territory. It also found overlapping areas where both populations could have met, and exchanged genes.

The paper was published in 2023: Jiaoyang Ruan et al., Climate shifts orchestrated hominin interbreeding events across Eurasia. Science 381, 699-704 (2023). DOI:10.1126/science.add4459.

Neanderthal-Denisovan habitat overlap (dotted area). Fig 2 A in Ruan et al.

Denisovans and Neanderthals coexisted in Eurasia from around 400 ky ago to 30 ky ago. They met and mixed several times. This paper looked into the climate and how it altered their habitat forcing them to move east, west, north and south as it worsened or improved during the Ice Ages.

The paper points out the different enviornments each group lived in: "Both Neanderthals and Denisovans are simulated to have lived primarily in environments characterized by annual temperature, precipitation, and NPP of ~−10° to 20°C, ~500 to 1300 mm/year, and ~200 to 800 g of carbon per square meter per year, respectively. Yet, compared to Neanderthals, Denisovans were present in hot and humid climates, which points to a comparatively wider niche space. Whereas Neanderthals were more abundant in temperate forests, Denisovans were present in both boreal forest and tundra." Denisovans lived in Southeast Asia, but fossil preservation in that area is poor, so no remains have been found, but there are genetic markers of Denisovans in the modern humans living in that region, the Phillipines and Papua New Guinea.

During the marine isotope stage (MIS) 5 around 135-105 kya, the Neanderthals spread into Northeastern and Central Europe, and further east into Southern Siberia. During the cold glacial maximum periods, they retreatedinto refugia in Southern Europe and around the north of the Black Sea. The authors suggest that these differnt habitats during the glaical and interglacial periods can explain the divergence of Neanderthal haplogroups, and their split (See my post on Western and Eastern Neanderthals Were Very Divergent).

Regarding Denisovans, the paper finds that due "to glacial cooling, Denisovan habitats vanish in Scandinavia, mildly increase in its core areas from eastern Europe to Siberia, and show massive fragmentation in Asia."

Where did they interbreed?

In a previous post, I wondered where did Denisovans and Neanderthals admix, Ruan et al. answer that question: Both species overlapped for around 400,000 years and there were hotspots like the Altai region where Denisova cave is found, occupied by Neanderthals and Denisovans (yellow star in map above). The authors find that there were six interbreeding episodes between the two groups: "the five younger events cluster during the warm MIS 5, whereas the oldest event, although with considerable dating uncertainty, occurs in the cooler MIS 6. Because some of these events occurred thousands of years earlier than the fossil dates, they could have happened in places far away from the places where the specimens were found. Our simulation of Neanderthal-Denisovan overlap suggests that these MIS 5 interbreeding events took place in central-southern Siberia... By contrast, the MIS 6 event likely happened in eastern Europe."

They note that there was "bidirectional gene flow" between both groups in Siberia. And that European Neanderthals don't have signs of admixture suggesting the Denisovans didn't mingle with them in Europe, however, they also point out that "large-sample genetic analyses have recently revealed Denisovan ancestry in modern European populations in France and in Iceland, which suggests the possibility for more widespread and prevalent interbreeding than previously thought. These results are consistent with our model simulations, which indicate the presence of suitable Denisovan habitats in Europe under optimal orbital conditions" It isn't clear if they suggest that Denisovans intereacted with modern humans in Europe, or with Neanderthals who later admixed with modern humans. Another option is that Eastern Siberian modern humans picked up their Denisovan genes there, and then moved into Europe later, carrying them with them.

I did find interesting the extended Neanderthal habitat, reaching into Central, Western, and Eastern Africa, India, Korea, Eastern China, Southern Mongolia, Myanmar, Saudi Arabia, Yemen, Morocco. Not so long ago, Neanderthals had been confined to Western Europe and the Middle East. Now we see them spread across Eurasia. This has many interesting implications.

The paper also included a map with sites where Denisovan and Neanderthal remains have been found the caption reads: "Neanderthal and Denisovan locations and their corresponding climate and biome conditions. (A) Hominin fossil, archaeological, and genetic data compiled for HSMs; candidate Denisovans (dashed circle)". I reproduced it below.

The lonely brown circle on the right side of the map, is the easternmost Neanderthal outpost in Eastern Asia (in the map above) is Jinsitai Cave, North China. We will look into it in my next post.

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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 © 

A New March 2026: Paper on Archaic introgressions in Humans

March 2026 has seen plenty of research papers published regarding hominins! This post will look into another introgression paper, that found not one, but two separate admixture events with archaics. One took place within Africa before Modern Humans set out on their Out of Africa migration, the second one affected people in Melanesia and Papua New Guinea, Oceanians.

This is the article: Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, Priya Moorja, (2026). Recovering signatures of archaic introgression using ancestral recombination graphs, nioRxiv 2026.03.03.709416; doi: https://doi.org/10.64898/2026.03.03.709416

Introgression Inside of Africa

They detected a first admixture with a ghost (unknown population) that added genes from a "super-archaic lineage" into the ancestors of all humans (Africans and Non-Africans), because it took place before the Out-Of-Africa event, in Africa.

"The ghost lineage, with a divergence time similar to Neanderthals, could plausibly correspond to Middle Pleistocene Homo groups or African Homo heidelbergensis populations that directly admixed with modern human ancestors before the OOA dispersal. For the super-archaic lineage, one potential candidate —compatible with the split time of approximately 1.8 Mya— is Homo erectus, as suggested by earlier studies."

The authors admit that it could have been one, single event, or there could have been more: "additional episodes of gene flow among structured African populations may have occurred but remain difficult to resolve with present data."

They noticed that the introgressed alleles could have been modified due to the action of natural selection perhaps because they provided adaptative benefits.

The paper says that their software (TRACE) found the following archaic ancestry in contemporary people from different regions, where N is Neanderthal, and D, Denisovan:

• Europeans. N: 0.99%; D: 0.03%.
• East Asians. N: 0.97%; D: 0.10%.
• South East Asians. N: 0.78%; D: 0.10%.
• Oceanians. N: 0.73%; D: 0.66%.

But, apart from Neanderthal and Denisovan alleles they also detected an introgression from a "ghost" source distantly related to Neanderthals and Denisovans: "Ghost segments exhibit deep divergence in marginal trees and show nearly identical genetic affinity to both sequenced Neanderthal and Denisovan genomes, indicating that they originated from an unsequenced lineage equally related to both archaic groups."

It was found in all modern humans at frequencies that ranged from 0.49 to 1.1%. This includes Sub-Saharan Africans.

Africans have more unique segments

The interesting part is that although non-Africans and Africans share alleles of the ghost introgression, "...both East and West Africans harbor a greater diversity of unique ghost segments." The authors don't attribute this enrichment and divergence to a recent or ancient admixture with archaics after the OOA event. Instead, they attribute it to the bottleneck caused by the OOA that led to the loss of these variants, now only found in East and West Africans.

Dates

The calculated "coalescence time" between human and ghost genes is, on average, 830,000 years (95% CI: 0.61–1.27 Mya).

This data leads the team to conclude that "an unknown archaic population, which diverged over 500,000 years ago, introgressed into the common ancestors of all modern humans prior to the OOA migration, resulting in similar patterns of ghost ancestry in non-Africans and Africans."

Denisovans injected super-archaic ancestry in Oceanians

Then they found a second introgression!

Previous studies have suggested that Denisovans may have mated with a super-archaic hominin (possibly Homo erectus), and as Papuans, Melanesians, and Southeast Asians have the highest level of Denisovan ancestry (they admixed when humans reached Sundaland, and the Philippines), the researchers wondered if the admixing led to a flow of super-archaic genes from Denisovans to humans.

They looked for super-archaic alleles contained within the Denisovan segments found in modern Oceanians. Their analysis revealed the 0.73% of Neanderthal and 0.66% of Denisovan ancestry mentioned further up, and also, a 0.33% introgression of super-archaic "ghost" ancestry.

"we infer that the super-archaic segments embedded within Denisovan ancestry tracts contributed almost 0.3% of the total detected Denisovan ancestry in Oceanians. This estimate constitutes a very conservative lower bound on the true fraction of super-archaic ancestry, as our analysis is restricted to Denisovan-introgressed regions in modern humans, requires segments longer than 20 kbp, and excludes loci where the sequenced Denisovan carries super-archaic ancestry. Using the marginal trees in SINGER, we estimate the coalescence time between these super-archaic segments and modern human lineages to be approximately 1.77 Mya (95% CI: 1.13–3.98 Mya), consistent with earlier reports."

The age given above points at Homo erectus, who was present in Eurasia 1.77 Mya.

The two introgressions. Copyright © 2025 by Austin Whittall

I prepared the map above to show what the paper says: An archaic ghost population in Africa (red circle) admixes with Modern Humans prior to the OOA (blue circle). These introgressed modern humans go into Eurasia (losing some of the archaic alleles due to founder effects and bottlenecks, and also spread across Africa (violet arrows) where the archaic signal remains stronger, one group heads towards SE Asia, Sunda and Melanesia, where Denisovans (green) live. These Denisovans had previously admixed with a Super-Archaic (yellow) somewhere in Asia (dashed yellow line). (2) is the Denisovan-Oceanian admixture, and (1) is the admixture within Africa. The red population is linked distantly to Denisovans and Neanderthals.

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

Neanderthals actually came from Human Beings! (March 2026 paper says)

A very interesting suggestion was prepublished on March 13 in Biorxiv by David Reich, 2026, it is work in progress, and a model, but its title tells it all: Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins.

Trying to explain why the split date between the human lineage and Neanderthals differs when you consider nuclear DNA (765-550 kya) or mtDNA (365-400 kya), or why the original Y chromosome of Neanderthals appears to have vanished, and what we have found is so similar to ours, and that their mtDNA is remarkably similar to ours, Reich suggests that they are a population that arose from modern humans introgression with archaics in Europe. This also explains some incongruent dates and other oddities found in the Atapuerca Sima de los Huesos remains. Simple hypothesis that is very similar to the proposal maed by Cosimo Posth published in Nature, which I commented in a post back in 2017 (An even older Out of Africa event (270kya)!!). Posth suggested that African inflow was "responsible for providing the mtDNA to the Late Pleistocene Neanderthals might have been an even earlier Middle Pleistocene gene flow from Africa, occurring in a time interval that we date between 413 and 268 ka... The temporal corridor for this introgression event between 460 ka and 219 ka is compatible with the evidence of archaeological similarities between Africa and western Eurasia during the Lower to Middle Paleolithic transition39 and potentially may explain the dissimilarities in Middle Paleolithic industries between eastern and western Eurasia. Environmental changes across this time span might have facilitated a hominin expansion out of Africa and potentially spread cultural innovations such as the Levallois technology into Eurasia." Reich developed the concept. Below is the Abstract of Reich's paper

"Abstract.
This paper demonstrates the feasibility of the hypothesis that Neandertals formed when a population using recently developed Levallois stone tool technology expanded between 400-250 thousand years ago (ka). In Europe, their range expansion into an area with Sima de los Huesos-like people led to massive introgression of local archaic genes producing a population with around 95% archaic ancestry (Neandertals); if this range expansion was sex-biased it would provide a simple explanation for why Neandertals retain modern human lineage Y chromosomes or mitochondrial DNA. In Africa, interbreeding with local archaic humans led to more modest archaic admixture and the deep substructure detected in all modern humans today. This proposal explains four previously perplexing similarities of modern humans and Neandertals—sharing of mitochondrial DNA, Y chromosomes, Levallois tools, and 300-200 ka date of formation by mixture—even while Neandertals and Denisovans cluster genome-wide."

This is the paper: Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins David Reich. bioRxiv 2026.03.11.711219; doi: https://doi.org/10.64898/2026.03.11.711219.

This paper is interesting because it also mentions humans mixing with archaics inside of Africa, a source of diversity:

"... ancestors of all modern humans including sub-Saharan Africans were deeply substructured, due to the coming together a few hundred thousand years ago of lineages that began diverging a million or more years ago. For example, ref. 16 models modern human ancestry as largely derived from a mixture of about 80% from a lineage that was most closely related to Neandertals and Denisovans, and 20% from a lineage that diverged from it around 1.5 million years ago, with the two coming together around 300 ka. The remixture is estimated to date to around the same time as the genetically inferred interbreeding of modern humans and archaic humans in the ancestors of Neandertals 300-200 ka. This raises the possibility that these mixtures in Europe and Africa had related causes: a range expansion of a successful population interbreeding with local archaic groups. In Europe, there was massive introgression of local genes because barriers to producing viable offspring were few. In Africa, the mixture was with a more divergent archaic lineage, result in a lower γ (cross-group interbreeding rate), and less introgression..."

This is the reference "ref. 16" cited above: Cousins T, Scally A, Durbin R, (2025) A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet 57, 856–864.

Comments

I am surprised at the different conclusions that the same datasets of human genes and fossils produce (some are mutually exclusive): humans and Neanderthals are the same, humans and Neanderths split after the Denisovans split, Denisovans and humans split after the Neanderthal split, dates that range from 500 to over 1 million years, introgressions all over (Denisovan to Neanderthal to Human, Human to Neanderthal, Denisovan to Human, one or more lineages of superarchaics introgressing into different hominins). Surely they can't all be right.

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

Blood Groups, Denisovans, Neanderthals, and modern humans

A research paper by Villanea FA, Huerta-Sanchez E, Fox K., (2021) investigated the ABO Genetic Variation in Neanderthals and Denisovans (Mol Biol Evol. 2021 Jul 29;38(8):3373-3382. doi: 10.1093/molbev/msab109. Erratum in: Mol Biol Evol. 2021 Dec 9;38(12):5835. doi: 10.1093/molbev/msab261. PMID: 33892510; PMCID: PMC8321519). This is very interesting, because contrary to what one would expect, these ancient relatives belong to the same ABO blood groups that modern humans have.

Blood Groups: A, O, B

This study looked into the ABO allele (gene) that is located on chromosome 9 and that codes certain enzymes known as glycosyltransferase that in turn modify H antigens on red cells, this defines an individual's blood group: group O individuals have the H antigen, a precursor for A and B antigens, group A has only A antigen, group B carries B antigen, and group AB has both A and B antigens, and as mentioned, group O have neither A or B antigens.

Original and Later A blood group

The original and ancestral A allele appeared ~3.5 million years ago. However, according to Kitano et al., 2012 it vanished around 2 million years (My) ago and remained absent for 1.75 My. The modern A blood group found in humans originates from an ABO*A allele that was created recently in the first H. sapiens some 260,000 years ago, from the fusion of ABO*B with ABO*O (B and O blood group alleles).

O Blood Group

O blood group allele appeared after the Δ261 deletion in the A gene, around 2 million years ago as the O02 variant.

It is therefore older than Neanderthals, Denisovans, and Modern humans. It was first carried by the common ancestor of those hominins. Lalueza-Fox C., Gigli E., et al., (2008) detected genes for blood group O (finding a variant known as O01) in the remains two Neanderthal men from El Sidrón, Spain, dated to ~50.000 years ago (50 kya). But O01 is a "newer" variant, O02 is the basal one.

B Blood Group

The B blood group, according to Gueuning et al., 2023 emrged "from the recombination between ancestral alleles of ABO∗A2 and ABO∗O.O2."

O haplotypes

There are two main branches within the O haplogroup: O01 and O02, and they include sub-branches.

Haplotype O02 is also the most ancestral of the O blood group variants. Kitano et al., 2012 place it as the oldest branch of this group ~2 million yers old, followed by the second variant, O01, 1.5 million years ago.

Recent research conducted by Gueuning et al., 2023 studied ABO blood groups using samples gathered in Zurich, Switzerland (so we can imagine a farily uniform Central European population). I will focus on their findings regarding the O blood group.

They found the following frequencies: ABO∗O.01.01: 40.95%, and ABO∗O.01.02: 22.65%, followed by a very low frequency of the ancestral variant, ABO∗O.02: 2.11%.

Regarding the phylogenetic tree it is shown below adapted from Fig. 3 in Guening et al., 2023:

The tree shows O02 separated from the O01 variant, and within the O01 variant, two separate branches, one O.01.02 more divergent and basal, followed by O.01.01 (which contains to sub-branches).

The authors noted these splits: "we observed in the phylogenetic tree deep splits separating the ABO∗O clades. The split between ABO∗O.02 and ABO∗O.01 alleles was even more pronounced in the phylogeny... The 2 major O-phenotype groups (ie, ABO∗O.01 and ABO∗O.02) were paraphyletic to each other with deep (ie, ancient) splits, showing that these groups are not closely related in evolutionary terms." Furthermore, the younger O01.01 "ABO∗O.01.01 appeared evolutionary closer to the cluster of ABO∗A1, A2, and B than ABO∗O.01.02."

O01.02 and Native Americans

This is relevant and interesting, because the O.01.02 variant represents half of the Amerindian O blood group variants. And O itself is found at very high frequencies in Native Americans (up to 100% in some groups). More on this below.

Native American Anomaly: extremely high O frequency, and their haplotypes

Blood group O is the most frequent blood group in the world. Its approximate global the frequencies are the following (Source): African: 50.2%, East Asian: 40.4%, South Asian: 39.4%, Middle East: 38.3%, European: 42.3%, and the highest prevalence is found among people of Latin American descent, with 57.4%. But Latinos are an blend of Native Americans (the ones that survived the Great Dying caused by the Discovery of America), African slaves and Europeans, so what is the prevalence among genuine or pure Native Americans?

Native Americans

The Native people of South American "are unique in that they have completely lost both the A and B alleles" the O blood group is found at frequencies close to 100% (Source), especiall among South American Native Americans.

The Nomenclature! an equivalence table

As with most things related to genetic names, the nomenclature changed over the years, papers published 10 or 20 years ago employ one notation, and more recent ones use another. This is frustrating for a layman like myself. However, to simplify things see the following equivalence table:

in italics the dbRBC or old name and in brackets, the (alt.) name (Source).

• ABO*O.01.01 = O01 (O1)
• ABO*O.01.02 = O02 (O1v)
• ABO* O.01.75 = O75 (O1v(G542A))

Below is the table, modified to show the new naming, it shows the mutations in the bases that distinguish the basal O(1) from A1, all are the same except for the deletion at 261. Then there are the mutations from O(1) to O(1v) where "v" stands for Variant. This table comes from Llop et al, 2008

I will be using the "old" notation from now on.

Almost all Amerindians belong to one of the three following haplotypes: O(1), O(1v) —O1 variant, and a specific mutation of O(1v) known as O(1v(G542A)), also written as O1v542.

O(1v), including its mutation G542A is the most common among Native Americans, accounting for 70-80% of all Amerindian O blood type individuals (Source) except for the peculiar Ecuadorian natives, the Cayapas, where O1 is more prevalent. They also have a rare mtDNA which may hint at a different source for their original, founding population.

Haplotype O(1) is the next most frequent, followed by some other very rare alleles as you can see in the following frequency table (1 = 100%), which includes some Amerindian groups.

Amerindian O haplogroups adapted from Table 6 and Table 10 in Estrada-Mena, 2010

The second table shwon above compares different Amerindian Populations with Asian ones. Translation of the Spanish words: Población is population, Aymara from Bolivia (Aymara b) and Chile (Aymara Chi), Japanese (Japoneses), Chinese (Chinos), and Koreans (Coreanos) and Mixed Latin-Native - Mestizo (Mest Chi).

The Mutation G542A

The G542A mutation is consistently found across Native American populations in frequencies of 12% to 45% of the total O blood group haplotypes.

It is rare in the rest of the world and found at very low frequencies (Estrada-Mena et al., 2010 and Llop et al, 2008 and Gueuning et al., 2023.)

Below is another table showing the mutations that distinguish O variants from the basal A1 blood group. The table is adapted from Yip, 2000. I added the O(1v) G542A line, and highlighted the two mutations, the deletion at position 261, and the marker for the 6542A mutation, where a guanine base flips to adenine G→A at position 542.

Mutations A and O groups adapted from Table 1 in S. Yip, 2000

As you can see, O1 differs from the A1 allele by the deletion Δ261 (marked with "—) at position 261. The O1v allele has another 9 substitutions besides de Δ261. O1v is found in Eurasians and Table 1 from Villanea et al., 2021 show it at a 28% frequency.

Rare outside of America

Estrada-Mena, 2010 indicates that the O1v(G542A) haplotype has been found in some non-American populations: 6 Danes, 2 Kuwaitis, and 1 person from England. (He cites Olsson et al. 1998; Yip 2000; and Yip et al. 2006).

The study conducted in Zurich, Switzerland identified Gueuning et al., 2023 two, 2, (out of 154 samples) carrying the O1v(G542A) mutation (in the modern nomenclature it is called ABO∗O.01.75, and described the mutation as the regular O1v (modern name ABO*O.01.02) as follows: "ABO∗O.01.02 background with additional c.542G>A." The ABO∗O.01.02 is what they call O1(v), present in 31 out of 154 samples, or 22.65% frequency.

According to Estrada-Mena, this extreme rarity in the Old World of the O(1v(G542A)) or ABO* O.01.75 allele could be due to three options:(1) Gene flow of Native Americans or Latinamericans into the Old World, after European discovery. (2) Recurring mutation, it turns up by chance, infrequently, the G542A mutation crops up in different populations, but this is unlikely, as it needs to appear within the O(1v) haplotype to cause this mutation which is almost exclusively Amerindian. (3) It is an ancestral polymorphism, that appeared before human beings, in one of our ancestors. But since it is found at such a low frequency, and absent in all other Eurasian and African populations, this is also unlikely. Option (1) seems the most logical. I agree.

The Society of Blood Transfusion (ISBT) nomenclature shows that ABO*O.06 (former O53 or O6) and ABO*O.01.11 (former O11) both carry the c.542G>A mutation, but neither are within O1v, and they also carry other mutations.

Why is it so prevalent in America?

While the North American native people have a high prevalence of O, the Aleut, Eskimo/Inuit and Athabaskans of northern North America have high frequencies of A and B haplogroups. This difference is due to a later migration into America and a different genetic origin compared to the first wave to reach America ~20 kya (orthodox dating).

The high frequency of blood type O among current Native Americans could be due to a founder effect (it was already present at a very high rate among the people who first reached America), genetic drift (random mutations led other blood groups to fade away and vanish while O increased its frequency), natural selection due to the new environment and pathogens found in America that favored O over the other blood groups. The diseases introduced by Europeans, like smallpox could have also played a role in enhancing O group among native populations.

A study by Halverson and Bolnick, 2008 analyzed the blood types of ancient remains from eastern North America and found that "The precontact ABO frequencies were not significantly different from those observed in extant Native Americans from the same region, but they did differ significantly from the ABO frequencies in extant Siberian populations... [these] findings are most consistent with the hypothesis of a founder effect during the initial settlement of this continent.

The similar frequencies in ancient and contemporary populations seems to show that selection hasn't played a role. The difference with Siberians, on the other hand is interesting, orthodox intrepretation is of course, the founder effect, but it could also imply that current Siberians are not related to the people that were the source of the migrants that moved into America./p>

Interestingly, one of the co-authors of the Neanderthal, Denisovan, and human O-type blood paper that is the subject of this post, Fernando Villanea, in his 2010 thesis, Evolution of the ABO Blood Group Locus in Pre-Columbian Native Americans, evaluated and analyzed "four hypotheses... to explain the low overall Native American diversity and the high within Native American variance of ABO allele frequencies: a) Founder’s effect in the original population, b) Post-European contact reduction of diversity, c) PostEuropean contact natural selection and d) High population structuring following subsequent migrations into the continent."

In his conclusions, Villanea did not attribute the blood-type distribution among Amerindians to an initial founder effect, but to one due to the dispersal of small populations across the vast continent. He found that the "results are consistent with ABO diversity being lost as a result of isolation as populations migrated deeper into the continent and not as a result of a bottleneck in the original founder population." (Hypothesis d). Small groups or bands of natives moving across an empty territory, and expanding quickly in them plus genetic drift associated with these small populations shaped the blood groups of the New World.

Regarding smallpox, it is true that ABO bood types play a role in immunity, and it is possible that the O allele provided better fitness against that disease, but Villanea also found (like Halverson and Bolnick, 2008) that ancient pre-contact blood types that he sampled, this time, from West Coast remains from the U.S. show a similar diversity to the current one.

These comments about the relevance of O-type blood among Native Americans are significant, yet the paper by Villanea FA, Huerta-Sanchez E, Fox K., (2021) did not include any Amerindian or American data!! Below I will discuss this paper.

Neanderthal and Denisovan Blood Group O in modern humans

Going back to the paper by Villanea, Huerta-Sanchez, and Fox, 2021, which is the subject of today's post, the relevant part is that they detected the allele that is responsible for O blood group in two Siberian Neanderthals, the Altai Cave specimen, and the Chagyrskaya person, as well as in Denisovans.

These two Neanderthals lived in different periods, with the Altai Cave person living around 120,000 years ago (120 kya) and the other individual from nearby Chagyrskaya, living 80 kya.

We all carry two copies of an allele for blood group, one inherited from our mothers, the other from our fathers. The Altai Cave Neanderthal carried two O2 variants (he was homozygous, as both were identical, meaning they were both Os), while the Chagyrskaya Neanderthal had one O2 and one O1 (also homozygous). They also analyzed the genes of the Croatian Vindija Neanderthal from 50 kya, who carried one O1 allele and a rare variang called-cis-AB that does not code for O blood group (he was heterozygous); the Chagyrskaya Neanderthal individual was homozygous carying O1 and O2 alleles. Finally they analyzed a Denisovan from ~50 kya and found that it carried two different O1 alleles which have not yet been found in humans.

The authors note that "perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians." They then suggest that both alleles O1 and O2 were passed on to humans due to admixing with Neanderthals and that they have been positively selected for as they are more divergent than other chuks of Neanderthal genome in humans, meaning that they are still with us because they serve an adaptive purpose.

The image below summarizes Villanea et al.'s paper's findings:

Fig. 1.Archaic ABO haplotype sharing through time, and geographic location for three Neanderthal and one Denisovan individuals. The O2 allele found in the earlier Altai Neanderthal is found in modern humans in Europe and Southeast Asia. The Chagyrskaya Neanderthal presents the same O2 allele (but different haplotype background) and a O1 allele shared with the later Vindija Neanderthal, and found in modern humans East Asia. The Denisovan O variants are not directly shared with either Neanderthals or modern humans.. Adapted from Villanea FA, Huerta-Sanchez E, Fox K., (2021)

Below is Table 1 from this paper, captioned "Genotypes for Eight ABO Variants and their Frequencies in the 1,000 Genomes Panel, Including Chromosome 9 Position in the Human Genome (Hg19, build37), as well as Genotypes for Each Chromosome in the Four Archaic Individuals."

The Nomenclature Changes!!

As you can see in the table above, Villanea et al. don't use the terminology "exon 7, 542 G→A", instead they employ numbers (top row) like 136131056 but this terminology which replaced the exon and SNP one, has also been superseded! The NIH gene viewer, for the ABO locus now uses a different number system (see here) so the numbers that ranged from 136125788 to 13615061709 for the ABO gene now are 133250401 to 133275201. See the gene online here.

The Amerindians Were Ignored in This Study

Surprisingly, this paper only included data from Old World modern humans, the authors discarded American populations, which is surprising, considering that Native Americans have the highest frequencies of O blood group in the world, almost 99% of Amerindians in South America carry O blood group. Why ignore it?

Villanea with Bolnick and others, 2013 studied the uniqueness of Amerindians finding that "Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus." So the preceding, basal root for this 542 mutation, the O1v had to be either Beringian or Siberian. Not an introgression from Europe after 1492. But see what the current paper says:

The authors justify this exclusion of Amerindians arguing that the O group samples that they found were of European origin (even among the African Americans they sampled). I quote them, and have introduced my comments in bold font:

"Identifying the origin of archaic introgression in admixed populations is complex. For example, American populations can trace portions of their genomes to European and African ancestry, as a consequence of European colonization of Native Americans, and the African slave trade. Because of these historical events, archaic introgression present in modern American individuals can be inherited from any of these sources in brackets.
[But what about isolated and almost pure natives like those of the Amazon? Why not include ancient samples of pre-contact people, like the ones used by Villanea, co-author of this paper, in his thesis?]
For the American populations in the 1,000 Genomes Project panel, including two African populations sampled in the Southwest United States and Barbados, we used ancestry calls from Martin et al. (2017) to distinguish if purported archaic ABO alleles sit in European-ancestry genome tracks. This allowed us to properly track archaic introgression to Europe, rather than being retained ancestrally in African populations, or introgression with the Asian ancestral populations from which Native Americans descend. For our genetic distance results, we thus excluded six populations sampled in America (MXL, PUR, PEL, CLM), including two African populations (ASW, ACB), after determining that all introgresssed ABO haplotypes are exclusively located in European ancestry tracks, thus providing a confusing look at archaic introgression."
[Why use Latinos? They are admixed by definition, MXL (Mexicans from Loa Angeles), PUR (Puerto Ricans), PEL (Peruvians from Lima), and CLM (Colombians from Medellín) all carry European and also African genes from the past 500 years! "Pure" contemporary and Amerindian samples are available, and would have come in handy to expand the scope of this study.]

Furthermore, study after study has shown that Amerindians and Latinamericans carry particular variants of blood group O, that are prevalent in America, how can these belong to "European ancestry tracks"? It seems odd to me.

Diego and Neanderthals

Estrada-Mena, 2010 suggests that the uniquely Amerindian mutation O1v(G542A) emerged in Beringia during the "standstill" there as a founder effect. This would explain its absence in Siberia and its exclusive presence in the Americas. A sound explanation.

But I am not bound by orthodoxy so, as I posted back in 2014 "the ample distribution of O1v(G542A) could also be explained by admixture with a Neanderthal population carrying the allele, which arose promoted by the selective advantage of conferring resistance against the infectious diseases of the New World. On the other hand, the alleged "cradle" of Amerindians, Eastern Asia, has the highest global frequency for type B blood allele. America... has the lowest, mostly among in Western Alaska due to recent East Asian admixture" Yes, we could also attribute the lack of B blood group to a founder effect or genetic drift, but there is additional proof.

There is a very rare blood group, called Diego (see my 2015 post about it), found in America and Central Asia. It is an Amerindian trait and dates back to the peopling of the New World. According to a paper published last year in Nature by Stéphane Mazières, Silvana Condemi, Wassim El Nemer & Jacques Chiaroni, 2025, it is ancient, the AR33K woman, from Amur in China, dated to 33 kya, carried the Diego D1*01 allele, however, her blood group was B. The paper states: "... before 30ky the Diego blood group might have already taken shape, before settling the Americas and comigrating with the nomads of the Mongolian steppes. Unfortunately, we could not corroborate any other DI*01 in Siberian individuals dating from the initial colonization of the Americas. " The next earliest ancient individual comes from a later population from Yana River, NEO239, Who lived 7,500 years ago. The paper also reports that "two Band3 Memphis alleles (Diego blood group system) have been observed in ... Denisova11 and Yana1." Denisova 11 or "Denny" is 90 ky old, and a hybrid of Denisovan and Neanderthal, while Yana1 id 30 ky old. The authors add that the D1*01 "may have appeared in South Siberia before migrating to the Americas and Central Asia."

O Blood Group and Amerindians

There is a clear link between Neanderthals, Denisovans, and blood group O. Apart from those mentioned futher up, the O2 type which is currently rare (1.1% frequency) was reported ( Mazières et al., 2025) in other ancient human beings from Russia 34 ky old, Sunghir2 and Sunghir3, as well as two Neandertals, Chagyrskaya D (50-60 kya) and GoyetQ56-1 (43 kya), so it was probably more prevalent in the distant past. Then there is Denisova 3 ("Pinky") from 52-72 kya, who carries the O blood group allele (Condemi et al., 2021).

Kitano et al., 2012 speculated that "Homo erectus had only B and O alleles until its later stage... [and] that the frequency of O allele was quite high among Neandertals."

So, blood group B, virtually absent among the first wave of people to reach America is also ancient, found in the heterozygous Neanderthal from Vindija. and in the AR33K woman. It was also present among ancients, but at lower frequencies.

There is an association between O blood group, Diego group, and Neanderthals, Denisovans, and modern Amerindians. The admixing could have taken place in Asia, with a swift migration, as mentioned in my previous three part posts on MUC 19 from South Siberia, into America. It could also have ocurred with Neanderthals in America.

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

MUC19 - Part 3 (The early peopling of America)

This is the third, and final post on MUC 19 (links to part 1 and part 2). Following the MUC19 gene inherited by Humans from Neanderthals, who in turn got it from Denisovans, led me to a paper by Peyrégne et al., 2020 which adds a very interesting piece of evidence about the introgression dates of Denisovans and Neanderthals into Americans, one that the authors find inconsistent with accepted theories (it is far too old!). In this post we will look into these very early dates.

When did Denisovans and Neanderthals Admix with Humans?

In Peyrégne et al., 2020 paper in the section Dating Denisovan gene flows into modern humans the authors "estimated Denisovan admixture times using the exponential decay of the linkage disequilibrium between alleles inherited from Denisovans in present-day individuals" What this means is that groups of genes that are close to others along a DNA strand tend to be inherited together, as a group, in a non-random manner (this is the definition of Linkage Desequilibrium) these chunks of genes imply a shared origin or inheritance, introgression. The "exponential decay" means that these connected genetic packets tend to decay, or break down over time (due to processes like recombination), across generations, following a mathematical rule, which follows an curve known as an exponential curve.

This enabled the researchers to "estimate Denisovan admixture times of 50-39ka in South Asians and 44-35ka in East Asians, approximately 20% and 29% more recent than Neandertal admixture time estimates in these populations (62-49ka – the range of estimates obtained for Eurasians), respectively." They displayed these results in the paper's Extended Figure 3 Estimation of Denisovan and Neandertal admixture dates and in Supplementary Note 11. Below you can see Figure 3. The introgression dates are given in generations. But since the paper states that generation time is 29 years, I converted the values to years in the table further down.

Extended Figure 3: Estimation of Denisovan and Neandertal admixture dates. (A) Admixture dates in present-day Oceanians . (B) Admixture dates in other present-day populations . Source

As you can see, for each Eurasian group and the Oceanians (Papuans), the Denisovan admixture generation number ranges from 937 to 1511 generations ago, but form the Mexican (Los Angeles) or MXL group the figure is 50% higher: 2097 generations. A similar effect can be seen in the Neanderthal introgression date for non-Americans it varies between 1070 and 1862 genertions, the MXL have a value of 2097 generations.

The caption acknowledges this incongruency and gives a vague explanation (excuse): "The estimate of the Neandertal admixture in Native Americans is inconsistent with estimates for all other groups. This seems to be driven by over-estimates of the recombination rates in the population-specific recombination maps perhaps due to the complex admixture history of Native Americans." Many words, but no beef!

Heading to Supplementary Note 11 on page 170, the authors write (highlighting is mine): "we re-analyzed the admixture linkage disequilibrium decay in the 1,000 Genomes populations... using the same ascertainment strategy described above while measuring genetic distance based on the respective recombination map available for each population. This yielded Neandertal admixture time estimates that are consistent with previous estimates, except for American populations where the estimates are older (Figure S100). This discrepancy likely represents uncertainties in inferring recombination rates in these admixed populations, as similar biases were observed when using the recombination map inferred in American populations to measure genetic distance in other populations. A similar trend was observed for the Denisovan admixture time, with estimates ranging between 1,146 and 1,705 generations ago (33ka-49ka) in most populations, and between 2,069 and 2,469 generations ago in American populations (Figure S100)."

Below is the Figure S100 mentioned above, I only show the data for Americans:

Figure S100 in Peyrégne et al., 2020

I prepared the following table with the data given by the authors and calcualted the date in years using the generation time of 29 years:

Table showing introgression dates in years and generation dates for different modern human groups. A. Whittall

The Large Gap in Introgression Dates

Comparing the MXL individual with the Han Chinese, the Denisovan and Neanderthal introgression in the former took place 24 ky before the latter one!

The authors, in the supplementary material note some anomalies regarding the Native American groups: "We see that Native Americans exhibit lower match rates to Denisova 3 and Vindija 33.19 for both Denisovan-like and Neandertal-like segments, respectively, than other populations (except Oceanians, where some Denisovan segments may be misidentified as Neandertal segments; Figure S102 andFigure S103), suggesting a higher false positive rate in Native Americans (i.e. modern human ancestry misidentified as archaic ancestry)." Interestingly, Denisova 3 is a recent Denisovan, from Altai, and the Vindija individual is from Croatia, in Europe, so one would not expect them to be present in the American Natives who had already received the introgression of a different, and more diverse group of Denisovans and Neanderthals as their admixture was earlier than that of the other groups (Figures and table above).

The authors explain it away: "It is likely that the results for Native Americans are confounded by greater genetic drift between the allele frequencies of Native Americans and those of Africans used as reference for distinguishing archaic and modern human ancestry."

The other thing noted by the authors (highlight is mine) is that "Native Americans and West Eurasians include considerably lower match rates than observed in Oceanians and South Asians, these likely represent a larger proportion of false positives (i.e. Neandertal or modern human ancestry) among the few Denisovan-like segments identified in Native Americans and West Eurasians. Restricting the analysis to segments of 0.1cM or longer removes most segments with a low match rate to Denisova 3 in both populations, which is consistent with an increased false positive rate in these populations, while the results remain consistent for other populations (Figure S106). As the difference in match rates for Native Americans and West Eurasians compared to Denisova 25 and Denisova 3 are then only marginally significant (p>0.01), it remains unclear whether these two populations also carry a more divergent Denisovan ancestry."

The MUC19 gene in Americans came from a Denisovan closer to the older clade of Denisovans living in SE Asia, and is distant from the Denisova 3 individual. This could account for the "low match rate to Denisova 3", regarding Europeans, they have a very low Denisovan admixture, so it isn't surprising it comes from another source and not the distant Altai Denisova 3.

According to Villanea et al., the MUC19 gene supposedly "... was inherited by modern humans through introgression with a population closely related to the Chagyrskaya and Vindija Neanderthal" Considering these individuals lived, in Altai, Siberia, Asia, and Croatia, Europe, respectively, this statement can only refer to a population of West Asian Neanderthals.

Admixture and an early date for the peopling of America

Çonsidering this data, the best explanation for the dates and populations is the one I outlined in part 2 of this series: The Humans that eventually reached America, were part of the first population to enter Eurasia, and admixture with older Neanderthals ~100kya in the Caucasus, Mesopotamia or Zagros Mountain region of Turkey, Georgia, Iran, Armenia, Irak (see Guran, Yousefi, Kafash & Ghasidian, 2024 with a great analysis with maps on the exact spot where introgression took place), on the fringe area between non-Altaian Denisovans (the ones that introgressed with SE Asians and Papuans, and probably are the source of the Austronesian signal in Amerindians), and West Asian Neanderthals. They then headed into Central Siberia.

This is in line with Yuan K, et al., 2020, and the admixture they found in the remains from Ust'Ishim, Siberia, which are 45,000 years old (he predates the admixture times given by Peyrégne et al., 2020 for the Eurasian populations, suggesting his lineage received an earlier introgression (Yuan et al., point out that they "also detected two waves of Neanderthal-like introgression in the Ust’-Ishim genome: a recent one (1.41–1.57%) that occurred 61.4–57.8 kya and a weaker and more ancient one (0.04–0.20%) that occurred 204.1–95.6 kya."

It is likely that Ust'Ishim is just a sample, of a sub-population that remained behind, part of the people who moved across Siberia, far from the Altai Denisovans, heading North (possibly the 38 kya Yana people in Northern Siberia are another sub-population along the migration route towards America. A group of people who entered the New World around 35-40 kya.

Index to this series of posts on MUC19

• Part 1 of the MUC19 posts
• Part 2 of the MUC19 posts
• Part 3 of the MUC19 posts(This one)

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

MUC19 - Part 2 (Neanderthal and Denisovan admixing)

My previous, first post on MUC19 gene ended with a question: Where (and when) did the Denisovans admix with the Neanderthals (Denisovans closer to the Sunda group than to the Altai group) passing the MUC19 variant to them, and when did Neanderthals mix with the Humans that eventually carried MUC19 to America?

Denisovans, Neanderthals and Humans how we split and mated along the way

The current consensus is that the lineage of the common ancestors leading to Neanderthals and Denisovans split from the branch leading to the ancestors of Modern Humans around 630,000-744,000 years ago depending on the study and the criteria adopted by the authors. As usual, genetics and bones don't quite match so there is an uncertainty in the actual date.

The split took place in Africa, with the Neanderthal-Denisovan ancestors leaving Africa, and our ancestors, who became Homo sapiens, remained in Africa.

Prüfer et al., 2017 find the following dates: "The estimated population split time between the Vindija Neandertal and the Denisovan is 390 to 440 ka and that between the Vindija Neandertal and modern humans 520 to 630 ka, in agreement with previous estimates using the Altai Neandertal. The split time between the Vindija and the Altai Neandertals is estimated to be 130 to 145 ka." Vindija is in Croatia, Europe, Altai is 5,131 km (3,188 miles) further east, in Asia, where China, Russia, Monglia, and Kazakhstan meet. Both Neanderthals are at the opposite ends of the Neanderthal territory.

Rogers, Bohlender, & Huff, 2017 disagree with Prüfer et al., and propose an earlier date: "our own date estimates inherit the uncertainty of the molecular clock. Using the YRI.CEU data, our point estimate of the Neanderthal–Denisovan separation time is 744 kya. Many authors prefer a higher mutation rate... Under this clock, our estimate becomes 616 kya..."

In 2020, the same Rogers of the 2017 paper, teamed with Harris and Achenbach, reviewed this work and updated its conclusions: "Our point estimate, 737 ka ago, is remarkably old... We suggest that around 700 ka ago, neandersovans expanded from Africa into Eurasia, endured a bottleneck of population size, interbred with indigenous Eurasians, largely replaced them, and separated into eastern and western subpopulations—Denisovans and Neanderthals."

I have posted about a paper published last September, Xiabo Feng et al., 2025 suggests a much older date for these splits: it includes Denisovans in a newly named clade, called Longi (name proposed in 2021): "The origin of the longi clade can be inferred to be about 1.2 Ma, slightly older than the Yunxian fossils. The origin of the sapiens clade is estimated to be about 1.02 Ma, also close to the age of Yunxian. The divergence between the longi clade and the sapiens clade is at about 1.32 Ma. The monophyletic Neanderthal clade, widely thought to be sister to H. sapiens, diverged from the longi and sapiens clades at about 1.38 Ma in our analysis." So it is exciting to see that the age of our branch of hominins is growing older, between 2 to 3 times older than previously suggested, I will expand on this in a future post.

Split in Western Asia

The introgression with "indigenous" Eurasians mentioned by Rogers, Harris, and Achenbach is an interesting point, and it could involve Homo erectus or the Homo antecessor (probably descended from the erectus group). There is of course the Homo heidelbergensis question. Vincenzo and Manzi, 2023 place the H. heidelbergensis as the last common ancestor of Neanderthals, Denisovans, and Modern Humans. So it probably lived in Africa and Western Eurasia at that time. Due to the lack of consensus (see Buck and Stringer, 2014 for a good review of this hominin), I will not mention it in this post.

Roger et al. 2020 have the Neanderthals moving west, into Europe, and the Denisovans heading east into Asia. There were no humans in Eurasia at this time ~600 kya, and it would remain this way until the first Out of Africa event some 120 kya.

Was it was during this period that the Denisovans and Neanderthals admixed and the MUC19 of the Denisovans introgressed into the Neanderthals?

Before trying to find out where and when this admixing took place, let's look at how the Denisovans spread across Eastern, Central, and Southern Asia after parting ways with the Neanderhtals in the Middle East around 440 kya

The Denisovan Groups

The Denisovan dispersal according to Rikai Sawafuji et al., 2024 took place as follows (it begins where Rogers left them):

"The common ancestor of Denisovans and Neanderthals which occupied around the Middle East interbred with a super-archaic hominin, and afterwards the Denisovan ancestors diverged from the Neanderthal ancestral group and moved into Asia. Some of them spread towards Papua and settled in Island Southeast Asia (D1). Another group remained in South or Southeast Asia (D2), and from there, another group moved further north into East Asia (D0, D3). During the early phase of this migration, they encountered a super-archaic hominin population and interbred. The D0 group settled somewhere in East Asia. The D3 group reached the Altai in Siberia (D3), where they met and interbred with Neanderthals. It is important to note that this only reflects the history of the Denisovan population that interbred with modern humans. If there were other populations that went extinct without any admixture, analysis of modern human genomes would not provide any information about these."

This distribution can be seen in the map below, which includes an undated phylogenetic tree, and shows what we currently know about Denisovans. It comes from Ongaro and Huerta-Sánchez, 2024 (free access here).

By the way, there are very few bones that have been assigned to Denisovans, and most of our knowledge comes from genetics.

Potential distribution of Denisovan lineages and their phylogenetic relationship
Ongaro and Huerta-Sánchez, 2024, Fig. 3

There is an additional clade not shown in this map, reported by Larena et al, 2021, the Denisovans of the Philippines: "Philippine Ayta... possess the highest level of Denisovan ancestry in the world —∼30%–40% greater than that of Australopapuans— consistent with an independent admixture event into Negritos from Denisovans. The Philippine archipelago is thus likely inhabited by multiple archaic groups prior to the arrival of modern humans."

Timeline

Using the information provided by Rikai Sawafuji et al., 2024, the D1 and D2 data from C. Jacobs et al., 2019m and D3 from Ongaro and Huerta-Sánchez, 2024, we can define a chronology.

I also included the cates proposed by Choin et al., 2021, which differ from the others and highlighted them in bold font.

• D0 : split from Altai Denisovans more recently. Territory: East Asia, China, Mongolia (100-150 kya) Here I have included the fossil from Harbin (with close affinities to Denisova 3), Baishiya Karst Cave (BKC), and Tibet, Penghu, Taiwan.
• D1 : split from the line leading to Altai Denisovans 283 kya (261–297 kya) - 222 kya. Territory: New Guinea and nearby islands (Island South East Asia).
• D2 : split from the line leading to Altai Denisovans 363 kya (334-377 kya) - 409 kya. Territory: Oceania and Southern, and Southeast Asia, India, Myanmar, Vietnam, Laos, Cambodia, Thailand, Malaysia.
• D3 : Altai Denisovans, Siberia (200-30 kya. More details below).
• D4? : ~300 kya?. Territory: Philippines.

The Altai cave in Denisova, Russia, the site of the original Denisovan find includes the the D3 group, has produced several fossils, and they are grouped into two separate periods: the remains of Denisova 2, 8, 19, 20, and 21, and the Harbin, China, specimen, are Early Pleistocene, with ages ranging from 123 to 217 kya. The Late Pleistocene Denisova 3 and 4 are much more recent: 52 to 84 kya (Fu et al., 2025 and Z. Jacobs, 2025). I suspect the more recent Denisovans are associated to the D0 group.

The MUC19 introgression from Denisovans to Neanderthals

Neanderthals and Denisovans mixed many times, we know that they overlapped and shared the Denisova cave in Altai, over tens of thousands of years (Z. Jacobs, 2025), the remains of Denny a Denisovan-Neanderthal hybrid, was reported by Slon et al., 2018 (Denisova 11), who lived 90 kya. Her Neanderthal genes were a combination of alleles that were also found in a pure Altai Neanderthal genome and in the Vindija 33.19 Neanderthal genome (from Croatia). The genetic analysis suggests two possible hypothesis that are not mutually exclusive: " eastern Neanderthals spread into Western Europe sometime after 90 ka or that western Neanderthals spread to Siberia before that time and partially replaced the local population." Her Denisovan father also "had some Neanderthal ancestry... it is likely that there was more than one Neanderthal ancestor in his genealogy, possibly as far back as 300–600 generations before his lifetime [9000 - 18,000 years]... the Neanderthals that contributed to the ancestry of Denisova 11’s father were from a different population than her mother."

Furthermore, the first Denisovan to be identified, Denisova 3. (52-76 kya) also carries a small percentage of Neanderthal ancestry (between 1.8-2.5%, related to an old 120 ky Neanderthal group to which the Altai Neanderthal —Denisova 5— belonged).

So here we have evidence of Denisovans with Neanderthal genes (indicting admixture) from 52 to 108 kya. That Eastern and/ Western Neanderthals moved across Eurasia to and from Siberia.

Peyrégne et al., 2020 studied a specimen known as Denisova 25, 219,000 years old, who carried alleles of Neanderthal origin (3.6-5.2%). They found that the Altai Neanderthal specimen known as Denisova 5, had received gene flow from Denisovans and that Denisova 25 received his "Neandertal ancestry comes from a yet undescribed Neandertal population that split over 200,000 years ago from the Neandertal populations for which we have genomes" The team stresses that "both Denisovans inherited their Neandertal ancestry from multiple gene flow events... This indicates repeated contacts between Neandertals and Denisovans throughout their history."

But, we also have to consider which group interacted, because the MUC19 paper by Villanea et al. used Denisova 3 as the "Altai Denisova" in their analysis but specified that it was not the source of this allele.

The Supplementary Data Section S5 in Villanea's work says the following (my comments in bracketes, in regular font): "we believe that the sequenced Altai Denisovan [Denisova 3, with Neanderthal alleles belonging to Clade D0 or D3] belongs to a population that is divergent from the donor Denisovan population that interbred with modern humans [so the Denisovan was D1, or D2, the D4 were in the Philippines]...by analyzing the sequence divergence distribution of Denisovan introgressed tracts in Papuans, we confirm that the sequence divergence observed between the introgressed haplotypes and the Altai Denisovan at the focal 72kb region is consistent with a scenario of Denisovan introgression. However, the source of this introgressed segment likely did not originate directly from the population represented by the Altai Denisovan [ratifying D1 or D3 clades as the source]... This result suggests that the Denisovan-like segment observed at the focal 72kb region, while of Denisovan origin, was inherited by modern humans through introgression with a population closely related to the Chagyrskaya and Vindija Neanderthal"

The Neanderthal from Chagyrskaya Cave (Siberia) lived 100 km (62 mi.) from the Denisova Cave, while the Neanderthal from Vindija Cave lived in Europe, in Croatia. They both belong to recent Neanderthals who lived 50 to 60 kya. They are more similar to each other than to the Altai Neanderthal discovered at the Denisova cave (Denisova 5 specimen), who lived around 120,000 years ago.

The image below clarifies the situation, as it shows the convoluted interactions between all groups, it also includes some of the named specimens.

Relationships of Denisova 25 to archaic and modern humans.
Nuclear, mtDNA and Y-chromosome information, Fig. 2 in Peyrégne et al., 2020

Where and When did these introgressions take place

The D1 or D2 clades of Denisovans, in Southern, Southeastern, and Island South Asia, New Guinea and Australia are the ones that introgressed the MUC19 variant into Neanderthals. Though we have no evidence of Neanderthals in this vast region. Then the Neanderthals, close to the late Croatian and Altai individuals carrying that allele passed it on to modern humans who carried it into America, and some in East Asia and South Asia have an extremely low frequency of these MUC19 alleles, stray members of the group heading to America perhaps?

The most simple explanation is that the branch of Denisovans that led to D1 and D2 clades which must have moved along the south coastal route of Asia, carried the MUC19 variant. This was before these clades originated the D3 and D0 clades (200-100 kya). During this period they passed it on to a group of Neanderthals: "the introgressed haplotype at the 742-kb MUC19 region has a high affinity for the... two late Neanderthals, but not the Altai Neanderthal." So these Neanderthals were ancestral to the Chagyrskaya and Vindija individuals but not to Denisova 5, the Altai Neanderthal. As mentioned further up (Prüfer et al.) these two groups split around 130-145 kya

This would imply an admixture between D1 or D2 Denisovans and pre-split Neanderthals around 130 kya, and Neanderthal- Human mixing after the Out of Africa event (First? or Second?) which could have taken place around 120 kya or later (1st OOA), some 60 kya (Final OOA).

I came across an interesting analysis of archaic introgressions with modern humans and how the first Out of Africa event 120-60 kya and the second one >60 kya interacted with Neanderthals and Denisovans. The paper is this one: Yuan K, Ni X, Liu C, Pan Y, Deng L, Zhang R, Gao Y, Ge X, Liu J, Ma X, Lou H, Wu T, Xu S. Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nat Commun. 2021 Oct 29;12(1):6232. doi: 10.1038/s41467-021-26503-5. PMID: 34716342; PMCID: PMC8556419. It mentions the Ust'Ishim Siberian man who died 45,000 years ago. He was a human being and carried Denisovan introgression, and Neanderthal alleles, from two events: "we also detected two waves of Neanderthal-like introgression in the Ust’-Ishim genome: a recent one (1.41–1.57%) that occurred 61.4–57.8 kya and a weaker and more ancient one (0.04–0.20%) that occurred 204.1–95.6 kya."" This seems, in my opinion to point at an admixture during the first out of Africa event around 100 kya. In the Southern border between both groups, and one that allowed a route across Central Siberia. Possibly in the Caucasus region.

The telling inconsistency...

I am always on the look out for conflicting, incompatible, contradictory, or discrepant data involving Native American genetics and ancestry, ant this paper by Peyrégne et al., 2020 contains incongruous information. It adds one juicy piece of evidence about the introgression dates, of Neanderthals and Denisovans into Amerindians, one that the authors find inconsistent and try to explain away with vague, unfounded interpretations. The incongruity is that the admixture date for American data: it is far too old! Older than any Eurasian admixture events!. But this will be the subject of my third and final post on MUC19.

Index to this series of posts on MUC19

• Part 1 of the MUC19 posts
• Part 2 of the MUC19 posts (This one)
• Part 3 of the MUC19 posts

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