The hard facts: ancient DNA: Lacking in Africa, present in Eurasia

When they discuss the Out of Africa (OOA) theory, scholars use DNA samples taken from contemporary, modern, existing populations, and add some (very few) ancient DNA samples to the dataset. However, are we certain that the modern genetic landscape reflects events that happened 60,000 to 100,000 years ago (60-100 ky)? And, more importantly, how old are these "ancient" DNA samples, belonging to ancestral humans.

DNA decays as time passes, the chemical bonds in the molecule break down due to the action of water, oxygen, temperature, and the pH of the soil in which the remains were preserved. So, we have relatively few samples of ancient modern human DNA. These "oldest" ones are: the Ust'-Ishim DNA from a man who lived in what is now western Siberia, Russia, around 45 ky ago. This is the very oldest of all specimens. The oldest East Asian sample is from Tianyuan, China, close to modern Beijing, roughly 39 to 42 ky old. In Europe proper, the sample from Czechia known as Zlatý kůň which are said to be 45 ky old (more on its age below). But, what about Africa, the purported cradle of mankind? The oldest DNA sequenced in Africa is roughly 18,000 years old, and comes from the Mlambalasi site, in Tanzania (source), the dates are not direct radiocarbon ones, but "...well constrained to the Late Pleistocene based on multiple indirect dates" Not so old after all!

Why is this relevant? The importance of ancient samples is that these people harbor, at least in Eurasia, Neanderthal admixture, at higher levels than current populations (as they were closer in time to the admixture event, and also, because depuration of harmful introgressed alleles hadn't had much time to take place). They also carry signals that were lost in later populations. But, in the case of Africa, we are lacking really old DNA, so all arguments about "diversity", "divergence" and distinctness are based on modern, living Africans. These contemporary people could have undergone admixture events with archaics, suffered selective adaptation, accelerated mutation rates over the past 45 ky, that altered their genetic makeup, so current comparisons may be misleading.

A look at the really ancient DNA in Eurasia

Eurasia has provided several samples older than 35,000 years and the DNA extracted from these individuals has paint a complicated migration process out of Africa. I can only imagine what surprises really ancient DNA samples from Africa would reveal.

A five-year-old paper, published by Prüfer K, Posth C, Yu H, et al., titled A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia (Nat Ecol Evol. 2021 Jun;5(6):820-825. doi: 10.1038/s41559-021-01443-x. Epub 2021 Apr 7. PMID: 33828249; PMCID: PMC8175239)🔓, reports the genetic makeup of the oldest European modern humans. Of course, as with all genetic publications, the Out Of Africa event is taken for granted and buttressed by each additional paper (even when there is no direct link between OOA and the study in question).

In this sense, this paper explains that "Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2–3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000–5,000 years." In one streak they constrain the date of human expansion into Europe and Asia to 40 ky ago, and limit the admixture with Neanderthals to the Levant, ~50-60 ky before they expanded across Eurasia.

Interstingly this woman from Zlatý kůň "...belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians". A lineage that became extinct.

In this, she wasn't alone. The Ust'-Ishim person has no direct descent among contemporary Eurasians. This lineage also died out.

Another population, identifided by three individuals 42,580 to 45,930 years old, discovered in Bacho Kiru Cave, Bulgaria didn't contribute to the later European populations either, however they "are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations." (Hajdinjak, 2021). They shared alleles with Oase 1, ancient Siberians, Native Americans, and the Far Eastern, 40,000 year-old Tianyuan man from China (who also shared his alleles with other populations: Amerindians and modern Asians).

This suggests a pan-Eurasian population of modern humans, spanning the continent from the Balkans to Eastern China (Oase 1, Tianyuan and Bacho Kiru are samples from it) with high levels of Neanderthal ancestry as we will see below.

The authors discuss the levels of Neanderthal introgression in Zlatý kůň and note that even though it is found at ~3%, similar to other specimens, like Ust'-Ishim (Note, however, that an old specimen from Europe, Oase 1, 40,000 years old, has two to three times those levels: 6 to 9% Neanderthal admixture) these are longer chunks, so they take this to signify that these segments didn't have time to break down into smaller segments (they are longer than those found in similar-aged Ust'-Ishim). This fact leads them to conclude that "... this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa". As you can see, this assumes OOA is a fact. Let's get some details.

Age of Zlatý kůň

When the remains of this woman were found, they were estimated to be 30,000 years old based on faunal remains and stratigraphy. However, radiocarbon dating gave much younger dates!: "direct radiocarbon dating resulted in a much younger date of ~15 ka (12,870 ± 70 years bp; GrA-13696)... In an attempt to clarify [its] ... age... , we radiocarbon dated a cranial bone fragment, resulting in a significantly older date of ~27 ka (23,080 ± 80 years bp; MAMS-36077)... A third date, ... produced a younger date of ~19 ka (15,537 ± 65 years bp; OxA-38602)." These young dates were attributed to contamination so they tried another method and tested an amino acid (hydroxyproline) from the bone collagen. It gave them a similar (young) date of ~34 ka (29,650 ± 650 years bp; OxA-38022). Finally (seeking something to provide a really older date) the authors used a phylogenetic tree by comparing the mt DNA from the Zlatý kůň woman, and assigned it to haplogroup N and comparing it to mtDNA from the Bacho Kiro site in Bulgaria (43 to 47 ky old) they reckoned that this fossil was roughly 43,000 years old (31.5–52.6 ky). It had to fit, by hook or by crook. So they got the old date they were looking for.

The Neanderthal "twist" to obtain an even older age

The oldest samples of DNA with Neanderthal admixture in Eurasia are, the Oase 1 (40 ky), Ust'-Ishim (45 ky), and this Zlatý kůň ("45 ky"). The level of Neanderthal introgression in other old remains from Eurasia are around 3%. All, except one, Oase 1 who lived 40,000 years ago, had a very high Neanderthal component. The authors try to explain this fact away: "Oase 1 carried more Neanderthal ancestry (6–9%) than other modern human genomes sequenced to date, owing to admixture with Neanderthals that occurred within the six generations before the individual lived."

The paper reporting Oase 1 gave (see Table 5) its average Neanderthal content as 7.11%, Ust'-Ishim as 3.08%, Kostenki 14 as 2.18% (Romania, 37 ky old), The Bacho Kiro ubduvudyaks carried 3.8%, 3.4%, and 3.0% respectively. Finally, Tianyuan, in China carried 4% to 5% (Yang, 2022) of Neanderthal alleles.

Compared with these, the 3.2% of the Zlatý kůň is normal and there is nothing unusual about it. So the authors tried another track.

They found that "Zlatý k&367;&328; shares more alleles with Asians than with Europeans." Which is not unusual all of these ancient Europeans are part of a pan-Eurasian population. But they explain it differently: modern Europeans originated in a "deeply divergent out-of-Africa lineage referred to as basal Eurasian" found mainly in the Caucasus, Levant and Anatolia. While all ancient European specimens don't carry any traces of this lineage.

Basal Eurasians

This population somehow did not admix with Neanderthals, and later replaced all of the ancient populations (those carrying high Neanderthal admixture).

The Basal Eurasian ancestry is strange; it carries "... little if any Neanderthal admixture and... separated from other non-African lineages prior to their separation from each other" (Lazaridis, 2016) because they split "from other Eurasians before the latter received Neanderthal gene flow" (Feldman, 2019)

So there is a population that left Africa and never mixed with Neanderthals (Basal Eurasians), one that moved into Europe and Asia, all the way to China (Zlatý kůň, Ust'-Ishim, Oase 1, etc.) mixing with Neanderthals, but they did so before the rest of the Out of African population moved east and north into Eurasia. Complicated scenario.

The authors argue, based on their data, that "Zlatý kůň falls basal to the split of the European and Asian populations... This suggests that Zlatý kůň was part of a population that split earlier from the population that later gave rise to Ust’-Ishim and other Eurasian populations."

The longer vs. shorter "chunks" of Neanderthal DNA found in Zlatý kůň is used as an argument to support its older age, and closeness to the Neanderthal introgression, but there are factors that could cut the admixed DNA into smaller pieces beyond recombination caused by the passage of successive generations. For instance, natural selection could have maintained long segments in Zlatý kůň because they provided an adaptative advantage, or these people were part of a larger population, which reduced the impact of genetic drift and segment shortening.

Veller, 2023 notes that demography also influences recombination (shortening of introgressed segments), populations don't admix in an instantaneous pulse, they mate over time, and mates are not randomly assigned, they may be chosen (non-randomly, or "assortative mating) and this reduces recombination's effects and the purging, or loss of introgressed segments. Choosing a mate with similar ancestry adds introgressed segments to the mix, reducing recombination and segment shortening. This effect could have acted among the people at Zlatý kůň preserving longer segments and causing the impression that they are older, when, in fact, they are not.

Comments

Out of Africa is painted as a simple migration that caused loss of genetic diversity due to founder effect and bottlenecks followed by admixing with Denisovans in the East, and Neanderthals in the West. As we have seen, this picture is oversimplified. The intermingling of ancient Eurasian lineages and modern humans were complex, with extinctions of local populations (this paper adds that the replacement of the original Eurasians by the Basal Eurasians was probably due to a massive volcanic event c.39 kya that altered the environment in Europe, the Campanian eruption, in Naples, Italy).

Africa, on the other hand has few, and very recent DNA samples. The discovery and analysis of older samples will surely make us rethink the Out of Africa theory and the origin of moden humans.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025by Austin Whittall © 

Denisovan admixture within America?

Last may I published a brief post about a paper by Castro e Silva et al., (2026). The evolutionary history and unique genetic diversity of Indigenous Americans. Nature. https://doi.org/10.1038/s41586-026-10406-w. The paper is an in-depth study of South American natives' genetics, the three waves that peopled the subcontinent, and the "remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years." It attributes this permanence across ten millennia because this admixture was positively selected for due to benefits these alleles provided to those carrying them.

Archaic Introgression

I re-read the article and took note of the part that says that the Australasian signal is not the result of an archaic introgression, which means that Denisovans didn't share these same genes with Oceanian and American natives, there were different groups admixing with each population. The paper states: "Furthermore, we identified candidate regions of adaptive archaic introgression from Neanderthals and Denisovans that contribute to functions related to immunity, metabolism and epidermal integrity, thereby reinforcing the role of archaic alleles in shaping the evolutionary trajectory of non-African populations. Importantly, our data indicate minimal overlap between genomic regions with Australasian affinity and those introgressed from archaic hominins, supporting the interpretation that these signals represent distinct evolutionary phenomena."

Australasian signal

The Australasian signal in Amerindians is very very peculiar, it has a high prevalence in some groups that live in the Southwestern Amazon region and Chaco (these groups are the Awajún, Ayoreo, Guarani, Karitiana, Sirionó, Suruí, and Tsimané). This is known as the introgression from a "Y" population, or Ypykuéra (a Tupi word meaning "ancestor") which is a "ghost lineage" of ancient Amerindians with a high Australasian genetic content.

The paper confirms that the distribution of Australasian "alleles" is not uniform, it shows a "partially discontinuous spatiotemporal pattern" which suggests, according to the authors that "this ancestry was present during the initial peopling of America." It is also very ancient because the paper finds that Amerindians "diverged from other continental groups between about 70,000 and 15,000 years ago."

The paper states that isolation of these Amazonian groups that carry the highest frequencies of these introgressed alleles and their inbreeding and small population sizes are all factors that led them to have such a high prevalence of them. However, I wonder if another factor was at play: Denisovans lived in that region and encountered humans there, admixing in that area with them. After all it is a kind of cul-de-sac in the Amazonian rainforest nowadays, why wouldn't it have been one for the Denisovans? They also seem to have thrived in the jungles of Indonesia, and the Philippines in Southeast Asia.

The comparison between different groups within America, outside of America, and archaics, didn't detect any "correlation... between Australasian and Neanderthal... or Denisovan affinity... By contrast, Neanderthal and Denisovan affinities were strongly correlated... consistent with homogeneous archaic ancestry in the founding populations."

This is interesting because the Australasian signal is independent from the two archaic introgressions. This suggests that the Denisovans and Neanderthals that admixed with the first Amerindians were different from those who admixed with Australasians (including the Onge people and the Hòabìnhian people from Laos).

The authors wondered if the Australasian-Amerindian similarity was due to "shared archaic ancestry" but when the checked the introgression from Denisovans and Neanderthals in both groups, they found a "minimal overlap of 0.4%, corresponding to 11 genes/genomic regions... This minimal overlap indicates that the Ypykuéra ancestry is unlikely to have been derived from a known archaic hominin." (This is not clear, what do they mean by "a known archaic hominin"?)

The paper did find a "shared ancestry component between Indigenous Americans and Australasians that extends deep into the past." So this shared ancestry probably came from a similar modern human group, yet, as mentioned further up, the ancestors of the Amerindians split from other H. sapiens 15 to 70,000 years ago. I favor the older date. But, intriguingly, these people did not admix with the same Denisovans or Neanderthals that the Australasians bred with!

This could be explained by a split in this basal Homo sapiens: one group went into Australasia and admixed there with a group of Denisovans, the other headed north into East Asia mixing with other Denisovans, and eventually reached America. However, why is there no presence of other East Asian signals in Amerindians? This leads to a second alternative: the admixture event between Denisovans and the modern human ancestors of Amerindians took place inside America?

The map below outlines this possibility, with the Denisovans splitting from the Neanderthals somewhere in the South Caucasus, and moving into East Asia along different routes, a northern one to Altai, and then Tibet and East Asia, another along South Asia, and South East Asia into the Philippines and Papua New Guinea. Another hypothetical route could have led them across Siberia into America. Their last stand was in the Tropical Amazon region. They seemed to thrive in all types of climate, from icy siberia and Altai, to the highlands of Tibet, and the jungles of Sundaland and Sahul. America offers all of them: Cold Alaska, Canada and Northern USA, Patagonia, high mountains and plateaus in Bolivia and Peru, as well as along the Andes in Chile and Argentina, and of course the Jungles east of the Andes from Colombia, Venezuela and Bolivia to Brazil, Paraguay and Argentina.

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

Oceanians & Denisovans, a new paper

A paper published in Science last week reported that Near Oceanians, that is, people living in the islands close to Papua New Guinea in Melanesia (New Britain, New Ireland, Bouganville, etc.) and the Solomon Islands, mixed with three different types of Denisovans and still carry their genes nowadays because they play a role in the adaptability and survival of these people.

This is the paper: Patrick F. Reilly, Stephen Rong, Daniela Tejada-Martinez, Samantha L. Miller, Audrey Tjahjadi, Chang Liu, Jared Akers, Alysa Pomer, Margaret E. Prentice, D. Andrew Merriwether, Françoise R. Friedlaender, George Koki, Jonathan S. Friedlaender, Steven K. Reilly, Serena Tucci. Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania. Science, 2026; 392 (6803) DOI: 10.1126/science.adr6749

The authors state that they found "previously unidentified archaic sequence and three times more Denisovan sequence than previous studies... We uncovered evidence for introgression from three Denisovan-like groups into the ancestors of Near Oceanians, revealing a new twist on our interactions with archaic hominins." The Denisovan introgressions impact on genes that affect "TRPS1, a skeletal development gene previously found under selection in central African rainforest hunter-gatherers and highland Ecuadorians", and also genes invovled in immune system pathways.

The paper points out that bottlenecks and subsequent genetic drift, and isolation of the populations in the region have shaped their genetics, causing wide differences between different groups.

Regarding the Denisovan introgression, this study "found that Oceanic genomes carry ∼2.5-fold more archaic introgressed sequence from all origins per individual than European genomes... and 14-fold more Denisovan sequence per individual than East Asian genomes."

But, the distribution of Denisovan genes was not uniform, to the contrary, it varied "by almost twofold from the New Guinean Sepik and Goroka groups to New Britain’s Nakanai and the Polynesian outlier groups of Bellona and Rennell... Sepik individuals harbored the most Denisovan introgression, 25 times more than East Asians... In line with prior work, we found that the genomic proportion of Denisovan introgression in Island Southeast Asian and Near Oceanic groups increased with greater shared ancestry with New Guineans, with the Philippine Agta as the sole exception" (the Agta people carry a very high proportion of Denisovan genes with a very low New Guinean shared ancestry, perhaps an indication of admixture within the Philippines).

Neanderthal genes

Interestingly, the authors say there is a high level of Neanderthal admixture in this Oceanian population, and refer to table S6 in the Supplementary material. Checking the table I found that the highest Neanderthal content is found in the Surui people of the Amazonian region in South America! the second highest is found in the Santa Cruz islanders of Oceania. See the adapted image below, from Table S6 in this paper:

However, the authors downplay the highest levels of average Neanderthal genetic content found in these Oceanians by using the excuse of bottlenecks. See how the try to minimize or understate this fact: "We found that despite harboring 41% more Neanderthal introgression per individual and having ~45% larger sample size in our dataset, Oceanic genomes had 28% less Neanderthal coverage than Central and South Asian genomes (tables S6 and S7). One possible explanation for reduced archaic coverage is a population bottleneck after admixture, which would also lead to increased homozygosity of archaic tracts. In support of this, we found both elevated homozygosity of archaic tracts and 2.3 to 3.4% less archaic coverage than expected given per-individual levels of introgression in five Oceanic groups with bottleneck signals..."

Denisovans

As you can see, the Denisovan levels are highest in Oceanians, and those living in Island South East Asia, followed far away by Amerindians and East Asians.

The paper states that "Denisovan introgression likely occurred in multiple pulses from multiple distinct Denisovan-like groups... We recapitulated previous findings of introgression from two Denisovan-like groups in East Asians... and found evidence for introgression from three distinct Denisovan-like groups with differing genetic affinity to the Altai Denisovan into almost all sampled Oceanic populations... we show that these signals are more widespread than previously thought, highlighting the complex dynamics of Denisovan admixture with modern humans."

Implications

It is time to look at who the Denisovans were, and also, the route followed by the Neanderthal admixture into both, Oceanians, Amerindians and East Asians. We also need to understand more about the differences between the Densivoan populations. Their evolution in Altai, East Asia, and especially Sahul and Sunda. Their presence in American Native genes is also relevant.

The simple model of humans meet Neanderthals in the Levant on their Out of Africa migration and mingle with Denisovans on their trek along South Asia into East Asia and Oceania is missing something.

Denisovans must have been a thriving group, all along the eastern, central and southern regions of Asia, perhaps also, Oceania when they were met by Homo sapiens, smoke screens arguing bottlenecks, genetic drift, and isolation can't explain away the fact that a group in the Amazon jungle has the highest levels of Denisovan ancestry in the whole world.

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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 © 

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

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

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

It Adds diversity

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

Denisovan and Neanderthal admixture in PNG

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

MUC19

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

The timing of the introgression

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

Centromeres

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

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

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

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

African divergence and superarchaic introgressions

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

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

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

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

All the Introgression posts in one place

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

Our lewd ancestors and their dallies

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

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

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

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

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

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

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

Last Updated on April 18, 2026

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

Neanderthal males mated with Human females (says study published in Science)

An article published in the latest issue of Science (Alexander Platt et al., Interbreeding between Neanderthals and modern humans was strongly sex biased. Science 391, 922-925 (2026). DOI:10.1126/science.aea6774) suggests that male Neanderthals had a soft spot for female Anatomically Modern Humans (AMH), or that AMH women chose male Neanderthals as mates, or both.

Thos of us who trace our ancestry to a non-Sub-Saharan African ancestor, carry snips of Neanderthal DNA in our chromosomes. These come from an admixture (mating) episode that took place some 45,000 to 49,000 years ago. A few thousand years later, the Neanderthals vanished and our human ancestors replaced them. But these Neanderthal genes are not uniformly distributed across our chromosomes. Why?

The Neander men mated with Human women!

The authors came to this conclusion (human women mating with Neanderhtal men) after looking at the distribution of Neanderthal alleles in our human genome. Although our ancestors mated with Neanderthals, and all humans living outside of Sub-Saharan Africa carry Neanderthal genes, there are vast swaths of autosomal genes in our 22 chromosomes that are devoid of Neanderthal alleles. An interesting anomaly is that the X chromosome us even more depleted of Neanderthal alleles (we carry another four chromosomes, either two "X" or an "X" and a "Y" if we are women or men, respectively). Why would the "X" chromosomes carry less alleles than the others? Well, this paper says that it reflects how Neanderthals contributed to our ancestry, the X chromosomes don't show Neanderthal ancestry because they are mainly human ones, mostly from human women and much less from Neanderthal women. Women contribute their X to all offspring, men do so only to their daughters, as their sons carry their Y chromosome. There could also be another factor that added to this distortion, natural selection that selected against the Neanderthal alleles.

The paper begins by stating in its Abstract that "By observing a 62% relative excess of AMH ancestry in Neanderthal X chromosomes, we characterized the interbreeding between the two groups as predominantly male Neanderthals with female AMHs" They suggest two explanations for this skew, to explain the "Neanderthal deserts across the modern human X chromosomes: (i) The lack of Neanderthal loci amongst the X chromosomes in the mode, or (ii) the contribution of Neanderthal X chromosomes was reduced from the very beginning and represents an original interbreeding that was biased toward male Neanderthals and female anatomically modern humans (AMHs)."

To validate which hypothesis is correct, they looked back, at the first admixture between AMH and Neanderthals, that took place 250 ky ago, and observed the fate of Neanderthal alleles in their offspring and applied these conclusions to the more recent admixture that ocurred 50 kya.

So they analyzed the genes of Neanderthals who lived after the AMH-Neanderthal admixture, including the Altai Neanderthal (122 kya), the two females from Chagyrskaya (80 kya) and and Vindija (52 kya). The authors concluded "that the lack of Neanderthal alleles in the modern human gene pool is not simply the result of excess incompatibility loci on the X chromosome". They also discarded genetic drift due to a small population size for the Neanderthals. Regarding the effects of Natural Selection, they found that "the Neanderthal X chromosomes did not suffer from sufficient mutational load to cause them to be generally deleterious compared with AMH X chromosomes." So evene if natural selection acted, it "was not likely sufficient to drive the broad lack of Neanderthal ancestry in the modern human X chromosome gene pool"

Caveman Courtship

Buster Keaton, Margaret Leahy and Wallace Beery in a scene from The Three Ages, 1923 . Source

Then they looked at dispersals and relocations between human and Neanderthal populations due to pair-coupling and mating (where female AMHs relocate into their Neanderthal partner's community) and modeled different scenarios. For instance, if all the AMH women of an exclusive all-female migration, mated with Neanderthal men, the excess ratio of AMH ancestry in the X chromosome of the hybrid offspring would be 1.33 (or +33%), but they observe a 1.62 excess ratio (+62%). One also has to consider the opposite effect of AMH males mating with Neanderthal women, which would lower the AMH presence in the X chromosomes of their hybrid offspring.

Since this can't raise the proportion of AMH presence in X chromosomes, they reasoned that the alternative was "mating preference" and describe it as follows: "the patterns that we observed in AMH-Neanderthal divergence and hybridization follow traditional processes of speciation and were likely colored by a persistent preference for pairings between males of predominantly Neanderthal ancestry and females of predominantly AMH ancestry over the reverse. The bias that we inferred seems to have remained consistent across admixture events separated by 200,000 years. Although we do not know what drove the biases in either event, the potential for preferences in mate choice to persist across time and space have been documented in both human and animal studies." So Neanderthal men liked AMH women more (or viceversa, or both!)

Simple one step mating Neanderthal man, and AMH woman. © 2026, Austin Whittall

The same issue of Science has a commentary on this paper (online here) and its title is suggestive: "Surprising partner preference found in matings between Neanderthals and modern humans. Male Neanderthals tended to pair up with female modern humans, but whether intercourse was consensual is unclear." It describes the article and interviews some scholars about it, concluding that "The mating bias Tishkoff and her co-authors have uncovered reflects something about the cultures and social behaviors of both species, she says. The team did not venture to guess whether the intercourse was consensual or coerced. But to Steven Churchill, a Duke University paleoanthropologist who was not involved with the research, the finding implies aggression. If males from one species monopolized females from the other, he says, “it’s hard to reconcile that with anything but a competitive, unfriendly interaction.”"

Closing Comments

I don't see why these interactions had to be violent, but given apes and humans tendency to be sexual, and aggressive it is an option, or perhaps wokism trying to explain ancient mating behavior.

Back in September 2011, I posted on the admixture of Neanderthal males and Human females and tried to answer the question of why there is no Neanderthal (NH) mtDNA in Homo sapiens (HS) (there should be if a matrilineal lineage had survived until now, with an original Neanderthal female passing her mtDNA across the generations until the present). I reasoned that: "Since nowadays there is no Neanderthal mtDNA in HS, we can conclude that mating between HS men and NH women (was as limited) or, if more frequent, it did not lead to a continuous lineage of hybrid N/HS women... if Neanderthal men got human women pregnant, they would not pass on any NH mtDNA (the children would have their human mom’s mtDNA). But, the Neander-Dad would pass on his nuclear DNA . So, Man (NH) and Woman (HS) would be a viable route to get Neanderthal DNA into our Homo sapiens cells. This explains why we have Neander DNA (autosome chromosomes)."

However, my reasoning did not lead to a higher prevalence of Human X chromosomes in the case of Neander-Human matings! I believe thtat this is so because I took into account Haldane's Law of sterile male offspring. As you can see in the image further up, if you eliminate the boys, who each carry an X in their XY sexual chromosomes, the two girls, would make it a 50-50 proportion as each carry a Neanderthal X and a Human X. In the same ratio! Maybe Haldane's Law does not apply?

Haldane's Law or Rule "JBS Haldane noted that when hybrid crosses affect one sex more significantly than the other, it is almost always the heterogametic sex that is so affected1. Thus, the risk is greatest for XY male hybrids in mammals... A century of observations has confirmed this rule." (Source).

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

Neanderthals in Africa?

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

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

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

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

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

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

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

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

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

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

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

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

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

Early Out Of Africa

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

West Africa

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

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

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

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

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

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

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

Sub Saharian Africa (SSA)

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

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

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

An introgression within Africa

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

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

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

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

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

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

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

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

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

No Neanderthals or Denisovans, but an archaic introgression

Last but not least, Lorente Galdos et al., (2019)" found no signals of Neanderthal or Denisovan introgression in the sub-Saharan individuals... We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.... Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans. "

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

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

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

Comments

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

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

Did Humans admix with Neanderthals? Paper in Nature says NO

Research published in Nature on Dec. 13, 2024 suggests, as its title says, that some models used by scientsts may lead to assume the existence of false introgressions. The word spurious used in the title means "based on false reasoning or information that is not true, and therefore not to be trusted". The paper can be found online: Tournebize, R., Chikhi, L. Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events. Nat Ecol Evol 9, 225–236 (2025). https://doi.org/10.1038/s41559-024-02591-6🔒

A preprint free version is available on line in Biorxiv 🔓

The paper's Abstract is quoted below:

"Abstract
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation."

Notice how the authors criticise the models used ("mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure [but, ignoring] population structure can lead to the inference of spurious demographic events ").

The authors assumed that there were two population groups. One named metapopulation M_A tht generated a second one, M_B between 9 Million years ago and 500 ky. This created two populations (Bipartite structure) within Africa. Then, some individuals from the M_B group left to colonize Europe and Asia splitting some 650 ky ago from the remaining populations that stayed in Africa. Those who went to Eurasia became the metapopulation M_N, originating the Neanderthals or Hn population. The African metapopulations M_A and M_B evolved into Homo sapiens (Hs). Later Hs left Africa and colonized Eurasia forming an M_C metapopulation there. The paper states that "the new Hs Eurasian metapopulation M_C with the African Hs metapopulation M_B (itself connected to the Hs metapopulation M_A). Note however that none of the Hs metapopulations (M_A, M_B and M_C) ever exchanged gene flow with the Hn metapopulation (M_N). In brief, our model does not allow admixture between Hs and Hn."

Therefore this study suggests that instead of actual mating between Homo sapiens and Neanderthals, as a means by which genetic material was shared by both groups, the common fragments of genetic material may have originated in ancestral populations that split and carried them with them through time with no need for admixtwure.

Below is Fig. 1 from the paper, and the original caption is the following: "Simplifed representation of the 1D structured model considered in this study. Time flows from top (past) to bottom (present), with an initial metapopulation M_A consisting of nA (=10) demes exchanging migrants with their neighbours. At some point in the past, the rightmost deme of M_A founds a new metapopulation M_B of nB (=10) demes, with which it will continue exchanging migrants till the present. Later, the rightmost deme of M_B founds the metapopulation M_N of nN (=10) demes which will become Neanderthals. The MN metapopulation will never exchange migrants with any other deme from the other metapopulations. Closer towards the present, the rightmost deme of M_B founds M_C which corresponds to the expansion of H. sapiens towards Eurasia. White feet represent the sampled populations (not the specific demes) for respective sampling times. The location of the sampled demes (within the corresponding metapopulations) is a random variable... Fifty individuals are sampled in M_A and in M_C to represent modern-day YRI and CEU samples respectively. For the Neanderthals (M_N), one individual is sampled at 50 kya."

Fig. 1 in the Biorxiv preprint. Source

Comments

Interesting indeed! Could these admixture events be mere artifacts of these black-box statistical models used by scholars? I have posted some critical comments on these models in the past (See: Some thoughts about the tools used in genetic admixture analysis, Biases in Genetic Models that are generally overlooked). I favor admixture, yet, I also consider that the software used by scientists may not accurately reflect the real population dynamics of our ancestors.

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