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 © 

Western and Eastern Neanderthals Were Very Divergent

New research published last week revealed the genetic makeup of a Neanderthal man (Denisova 17) who lived in the Denisova cave in Altai, 110,000 years ago. The paper reached some surprising conclusions.

This is the paper: D. Massilani,S. Peyrégne, et al. A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals, Proc. Natl. Acad. Sci. U.S.A. 123 (13) e2534576123, https://doi.org/10.1073/pnas.2534576123 (2026).

Key findings:

• Population Replacement. The Denisova 17 Neanderthal man was closer to the older (~120 kya) Altai Neanderthal from Denisova (a woman known as Denisova 5) than to more recent European Neanderthals (the Vindija Cave woman, from Croatia and the Goyet female) and to the Neanderthal woman from Chagyrskaya Cave in the Altai region (80 kya, called Chagyrskaya 8 (Chag 8 for short). Suggesting that more recent Neanderthals replaced the older population in Altai.
• Denisovan admixture. The 120 and 110 kya Neanderthals from Denisova Cave (Denisova 17 and Denisova 5) had Denisovan admixture. This is not seen in the later Neanderthals of Western Europe or Chagyrskaya Cave.
• The estimated age of the common ancestor of the Y chromosome of Denisova 17 and modern human beings is ~395 ± 44 kya.
• The Eastern Neanderthals lived in groups of less than 50 individuals, these were smaller, and also more isolated than those of Western Eurasian Neanderthals.
• Replacement. The Western Neanderthals moved eastwards across Eurasia and replaced the older Eastern Neanderthals. But there was no admixture so the authors conjecture that both populations never met "perhaps because the older Neandertal population disappeared before the younger population from the west appeared in the Altai Mountains... Western-derived Neandertals are thought to have replaced the Eastern Neandertals in the Altai Mountains, and presumably elsewhere, sometime between ~110,000 and ~70,000 y ago."
• Interaction with modern humans: comparing non-African modern human genes with Neanderthal genes and counting the matches, the authors find that Western Neanderthals, especially the Vindija type were closest to the Neanderthals who admixed with humans. Those matching Eastern Neanderthals were four-times smaller. I wonder if modern humans leaving Africa mated with Western Neanderthals, who may have carried Eastern alleles? or perhaps they also intermingled with Eastern Neanderthals.

Mutation Rate and Divergence

The most interesting part is how divergent both Western and Eastern Neanderthal were, when compared to modern human beings. The paper states that:

"... it is striking that the allele frequency differentiation between Eastern Neandertals (D5 and D17) and Western Neandertals (Vi33.19 and others) (FST = 0.30, 95% CI: 0.29 to 0.31) exceeds that of even the most differentiated pairs of present-day populations, such as the Mbuti of Central Africa and the Papuan Highlanders of New Guinea (FST = 0.27, 95% CI: 0.26 to 0.27). The divergence between Mbuti and Papuan is estimated to have occurred 130 to 220 kya, resulting in separate genetic drift along the two lineages over 260 to 440 ky. The divergence between Eastern and Western Neandertals occurred about 35 ky before D5 and D17 and about 80 ky before Vi33.19 lived resulting in separate genetic drift along the two Neandertal lineages over about 115 ky. This suggests that Neandertal populations reached greater levels of differentiation over shorter timescales than modern humans did. This is also illustrated by the modest differentiation between a ~45,000-y-old modern human genome from Siberia (Ust’Ishim) and present-day populations (FST = 0.052, 95% CI: 0.049 to 0.056)."

The authors suggest that the small bands of Neanderthals underwent higher genetic drift, that led to high frequencies of different alleles in the two populations. So even though they were not far apart in Eurasia, they were, nevertheless isolated from each other. The point is that "Neandertal populations accumulated allele frequency differences more rapidly than the ancestors of present-day human groups." So much for the molecular clock and its regular ticking rate.

In my previous posts on the MUC19 allele that introgressed into humans from Denisovans via Neanderthals wo were not related to the Altai Neanderthal (Denisova 5), I wondered if the Neanderthals who were ancestral to the Chagyrskaya and Vindija individuals but not to Denisova 5, the Altai Neanderthal were the ones who had admixed with modern humans. This paper seems to suggest it was them.

If there was an Early peopling of America by Neanderthals, it was surely done by the Older Eastern Neanderthal Group.

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

Denisovan, Neanderthal, and modern humans: the Y-chromosomes

A few days ago, in my post about Y-chromosome haplogoup P (the root from which Eurasian R, and Amerindian Q haplogroups arose) I mentioned that the source of P (haplogroup K), which has been said to be located in Indonesia, Island South East Asia. This is interesting because this region is also a hotspot for people carrying a high frequency of Denisovan alleles. I wonder if Denisovans and haplogroup P are connected. This post will look into that possibility.

Archaic Y-chromosomes

The Denisovan and Neanderthal Y-chromosomes were studied by Martin Petr et al. (2020) in their paper The evolutionary history of Neanderthal and Denisovan Y chromosomes (Science 369, 1653-1656 (2020). doi:10.1126/science.abb6460 🔒). The following image is adapted from the paper's Figure 2.

Figure 2 A in Petr et al., (2020). Source

The tree shows Denisovans, Neanderthals, and modern humans; the oldest haplogroup A00 is in Africa, and the others are non-African. The authors comment this figure as follows: "Unlike the rest of the nuclear genome, which puts Denisovans and Neanderthals as sister groups to modern humans, the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes."

A more recent paper by Peyrégne et al., (2025) added the specimen known as Denisovan 25 to the tree, in the upper green branch. (See Fig. 2 C in that paper).

Petr et al., (2020) also defined the dates of the splits between the branches after calculating a mutation rate and dating the oldest A00 human haplogroup [249 ka ago (bootstrap CI 213 to 293 ka ago)]: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago (Denisova 8: 707 ka ago, CI 607 to 835 ka ago; Denisova 4: 708 ka ago, CI 550 to 932 ka ago) (Fig. 2B and table S12). By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago: 353 ka ago for Spy 94a (CI 287 to 450 ka ago), 370 ka ago for Mezmaiskaya 2 (CI 326 to 420 ka ago), and 339 ka ago for El Sidrón 1253 (CI 275 to 408 ka ago)."

This study found that, unexpectedly, the Y-chromosomes of Neanderthals was closer to modern humans than to Denisovans (puzzling, because the autosomal DNA of Denisovans and Neanderthals is closer between those two groups than either group to modern humans). To explain this incongruent finding, the authors suggest "that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago." ↺

In other words, a first and oldest "Out of Africa" event of modern humans that took place some 100,000 to 370,000 years ago resulted in mating between human men and Neanderthal women. The male hybrid offspring of these trysts carried human Y-chromosomes (these pass from fathers to sons) and these human Y-chromosomes spread among the Neanderthal groups. These first-out-of-Africa modern humans then went extinct in Eurasia, and for that reason they are not related to the final Out of Africa wave of modern humans who mixed for a second time with Neanderthals in Eurasia 50-70 ka. Complicated? Far-fetched? Possibly.

Comment: The authors of this paper noticed different branch lengths in their phylogenetic trees, suggesting that mutations accumulate at different rates. This subject discussed in my previous post.

No surviving Neanderthal Y-chromosomes

The final mating episode (~100 to 50 kya) between modern humans and Neanderthals led to hybrids, and the male offspring of Human males and Neanderthal females carried modern human Y-chromosomes. However, the Neanderthal Y-chromosomes became extinct, meaning that the sons born from Neanderthal men and human women may have had some incompatibility due to the Neanderthal Y-chromosomes. Could this have triggered stillborn or miscarried sons in modern human mothers?

Neanderthal Y-chromosomes carry proteins that can provoke a immune response from mothers during pregnancy "Such effects could be important drivers of secondary recurrent miscarriages and might play a role in the fraternal birth order effect of male sexual orientation... It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations." (Source).

Another explanation is that the small size of Neanderthal populations compared to those of Modern Humans, and their isolation, led to an accumulation of damaging mutations in their Y-chromosome, and this affected male fertility while modern humans coupling with Neanderthal women had more offspring (boys carrying the human Y-chromosome). Over several thousands of years of intermingling, the Y-chromosomes of the Neanderthtals died out, extinct for good, replaced by those of Modern humans.

Another theory wass put forward by Juraj Bergman and Mikkel Heide Schierup (2022) who study an area of the human sex chromosomes X, and Y, known as the pseudoautosomal region 1 (PAR1). PAR1 is involved in the male meiosis process (where the 46 human chromosomes in testis cells are split in half to form sperm cells with 23 chromosomes — including a Y or an X, sexual one, so that when the sperm fertilizes an egg to form a complete cell, it will contain 46 chromosomes). PAR1 is subject to mutations and recombination (a shuffling of DNA). This paper found that even though the Neanderthals received human Y chromosomes, they retained their PAR1 sequences. The human PAR1 was not passed on to the Neanderthal offspring, only the part of Y that determines sex, and it is likely that this part was under the pressure of selective forces, which favored the modern human Y component.

Extinction

Regarding selection Aaron Ragsdale (2025) wrote that "if human-related haplotypes carried fewer deleterious alleles due to their larger long-term effective population size, human-introgressed DNA would have been favored in Neanderthal genomes. The replacement of Neanderthal mitochondrial and Y chromosomes by early human haplotypes appears to support this model of post-admixture positive selection in the Neanderthal lineage... haplotypes that have accumulated more deleterious mutations, e.g., from a population with small long-term effective population size, will be selected against under either direction of gene flow. Introgressed ancestry at a given selected locus will decrease in frequency in one introgression scenario and increase in the other. This may explain the replacement of MT and Y chromosome DNA in Neanderthals by human haplotypes after early human-to-Neanderthal introgression and the absence of such Neanderthal haplotypes in modern humans."

But not only lack of fitness can lead to loss of the archaic Neandrthal Y chromosomes, David Reich (2026) argues that "Males have more variation in reproductive success than females, and if females prefer mates whose fathers were from the modern population, this would rapidly remove introgressing archaic Y chromosomes without there having to be reduced biological fitness associated with archaic Y chromosomes. In fact, a model of a matrilineal human range expansion has some empirical support based on estimates of more Neandertal introgressed segments on the X chromosome than the autosomal average." My recent post commenting a paper about Neanderthal men preferring human women is in line with this assumption regarding X chromosomes. It seems then, that Neanderthal women preferred human males and that the male offspring of Modern human-Neanderthal matings were less successful than the opposite progeny.

Back in 2016, Mendez FL, Poznik GD, Castellano S, and Bustamante CD. (The Divergence of Neandertal and Modern Human Y Chromosomes. Am J Hum Genet. 2016 Apr 7;98(4):728-34. doi: 10.1016/j.ajhg.2016.02.023. PMID: 27058445; PMCID: PMC4833433) noted that Neanderthal Y chromosome was very different from that of modern humans: "The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups." This also explains why hybrids would miscarry or be stillborn. The Neanderthal Y chromosome are an outgroup to modern human Y chromosomes. This team analyzed the ∼49,000-year-old Neandertal man from El Sidrón site in Spain. But, these conclusions contradict the findings of Petr: who suggested an introgression of Anatomically Modern Humans into Neanderthals long before the El Sidrón man existed! Petr wrote (see further up): "the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals.".

These incongruences are a signal that further research is needed to clarify the picture.

Regarding Denisovans, as mentioned at the beginning of this post, they lie on an even more distant branch, and are quite distinct from Modern Human Y chromosomes.

There is the remote chance that someone out there, a man, carries a Neanderthal or a Denisovan Y chromosome. The number of people who have had their full genome sequence is around 2 million, globally, out of 8 billion people, roughly 0.025%, a very small sample. Those who have had these tests are mainly urban people in develped countries. So there is the possibility that a man in the wilderness in Turkmenistan carries a yet undetected Y chromosome of a Neanderthal or a Denisovan.

Denisovans and haplogroup P?

Getting back to the question that led me here, could the Haplogroup P be linked to Denisovan Y chromosomes? I believe the answer is no. The only possible way a Denisovan could belong to this haplogroup is that his father was a modern human carrying the haplogroup, and his mother Denisovan, he'd be a hybrid. Haplogroup P is the outcome of a long line of mutations from an original, ancestral basal lineage, i.e. the root linking A00 and other A haplogroups, in Africa. Another alternative is that the timelines of Y chromosome haplogroups is completely wrong. This option will be the subject of a future post.

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

The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

• Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes"). This is what one would expect.
• Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
• They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
• And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Haplogroups of Humans and Neanderthals and Denisovans: mtDNA and Y chromosomes)

I have just read a paper that refutes my closing comments of this 2014 post: A shared Y chromosome lineage Neanderthals and Modern Humans but it does support the image I posted in it, pictured below:

Hypothetical Y chromosome phylogenetic tree for humans and Neanderthal. Copyright © 2014 by Austin Whittall

I explained the image as follows: "the ancestral population of both humans and Neanderthals, split into two groups: one that would later evolve into modern humans, and another that would evolve into Neanderthals. Each would carry, in the beginning, the "original" archaic Y chromosome of the ancestral population, which, as each lineage accumulated mutations due to chance and positive selection would begin to grow in different directions, forming two distinct branches, which then in turn would continue branching as more mutations appeared."

And that is what the paper states (Reconstructing the genetic history of late Neanderthals by Mateja Hajdinjak et al., 652 NATURE VOL 555 29 march 2018, doi:10.1038/nature26151.) Figure 2 in the article is shown below, and it agrees with the Y chromosome tree that I proposed back in 2014:

Phylogenetic trees for mtDNA, autosomal DNA and Y-chromosome of humans, Neanderthals, Denisovans and Sima de los Huesos hominin. From Hajdinjak et al.

The Human haplogroups are on distinct branches, well away from those of the older hominins.

See this Sept. 2020 update.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall ©