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 © 

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 © 

On human and Neanderthal - Denisovan mtDNA

There is no evidence at all of extant Neanderthal mtDNA in modern humans. This seems quite surprising, and many explanations have been offered. But the most simple and clear cut one is, in my opinion, the lack of enough samples of Neanderthal mtDNA tested to date. And this is precisely what this paper says: No Evidence of Neandertal mtDNA Contribution to Early Modern Humans, by David Serre, Andre Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, Michael Hofreiter, Göran Possnert, Svante Pääbo (Published: March 16, 2004https://doi.org/10.1371/journal.pbio.0020057)

They clearly state the following:

"..Under the model of a constant human effective population size (Tavare 1984; Nordborg 1998) of 10,000 over time (Figure 4A), any contribution of Neandertal mtDNA to modern humans 30,000 years ago larger than 25% can be excluded at the 5% level (Figure S3). A more realistic scenario may be that the spread of modern humans was accompanied by an increase in population size before and during their migration out of Africa and subsequent colonization of western Eurasia (see Figure 4B). In that case, the Neandertal contribution that can be excluded is smaller (i.e., less gene flow could have taken place)...
It is noteworthy that under the model of constant population size, about 50 early modern human remains would need to be studied to exclude a Neandertal mtDNA contribution of 10%. To exclude a 5% contribution, one would need to study more early modern human remains than have been discovered to date. Thus, definitive knowledge of the extent of a putative contribution of Neandertals to the modern human gene pool will not be possible... ."

The authors indicate that the Neandertal fossil remains carry "closely related mtDNAs that are not found among current humans", in fact all reads are very similar to each other and, different to the standard modern human reference.

They mention the possible causes for this lack of Neanderthal mtDNA in H sapiens: "...such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils.".

Both causes seem very reasonable and the authors fin that this "... excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution."

So, after all, there may have been a small introgression of Neanderthal mtDNA into us.

An intersting point to ponder is that "Although mitochondria retain their own genome, the vast majority of the >1000 proteins that function in mitochondria are encoded in the nucleus" (from The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Joel Sharbrough Justin C. Havird Gregory R. Noe Jessica M. Warren Daniel B. Sloan. Genome Biology and Evolution, Volume 9, Issue 6, 1 June 2017, Pages 1567–1581, https://doi.org/10.1093/gbe/evx114).

This means that the mitochondrial genes and the nuclear genes that encode these proteins (known as N-mt genes), proteins used by the mitochondria, have to adapt to each other during episodes of introgression in order to function correctly and not cause the death of the hybrid individual.

Sharbrough et al then apply this concept to Neanderthal ⁄ Denisovan admixture with H. sapiens:

"The potential for mitonuclear interactions among hominins is of interest because, unlike in the nuclear genome, there has not been any detectable mtDNA introgression from Neanderthals or Denisovans into modern human populations (Krings et al. 1997; Serre et al. 2004). Regardless of what has caused this lack of mtDNA introgression, one consequence is that all introgressed Neanderthal and Denisovan nuclear alleles must function on a modern-human mitochondrial background..."

In other words if there is no Neanderthal or Denisovan mtDNA in humans, our modern mtDNA however must have had to adapt to the N-mt genes that did introgress from our older relatives (Neanderthals and Denisovans). And their paper looks into this.

They concluded that "... genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes."

In other words there wasn't much incompatibility between the mtDNA and the N-mt genes after all! And this was because our and their mtDNA and nuclear genes were, or are, very similar. Which is what you'd expect anyway, we all branched off from the same tree not that long ago (say 750 Ky).

I do look forward to mtDNA sequences more complete in nature, from more individuals (archaic H. sapiens and Neanderthal & Denisovans), who knows, we may actually find one with a shared mtDNA Haplogroup...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

An even older Out of Africa event (270kya)!!

A paper published in Nature, by Cosimo Posth et al, published in Nature looks into the odd discrepancy in the age of the split between Modern Human and Neanderthal genomes

The date of the split between humans and Neanderthals differs when you consider their nuclear or their mtDNA:

• Nuclear DNA says that humans and Nearnderthals split some 765,000 to 550,000 years ago
• Mitochondrial DNA or mtDNA says we split 365,000 to 400,000 years ago

I believe that discrepancies are what makes science leap forward (like the problems caused by the "ether" theory that led to relativity and quantum physics). And a gap like this of several hundreds of thousands of years is a big discrepancy. Either the dating is all wrong and has to be reviewed (ie. mutation rates and so forth), or the current ideas on the migration and origin of Homo sapiens are incorrect.

The paper looks into the mtDNA extracted a "complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago..."

This date of 270 kya is actualy the average, the real divergence date between HST and all other Neanderthals (95% HPD) is between 316 and 219 kya. The Altai Neanderthals split from the other Neanderthals some ∼160,000 years ago (95% HPD of 199 - 125 kya).


This paper tries to explain the genetic incongruence of Sima de los Huesos (see my post Sima de los Huesos remains, Neanderthals, Denisovans and their nuclear and mtDNA), the remains from Sima de los Huesos in Spain which are 430 ky old, have mtDNA that resembles that of Denisovans more closely than that of the Neanderthals. But, their nuclear DNA is more similar to that of Neanderthals than to Denisovan nuclear DNA.

The authors write (Bold is mine) that the nuclear DNA (nDNA) "... from the Sima de los Huesos site... confirmed their closer affinity to the Neanderthal lineage, suggesting that at least by ∼430 ka, Neanderthals and Denisovans had already diverged. However, in contrast to genome-wide data, the Sima de los Huesos mtDNA was found to branch off with the deeply divergent Denisovan mtDNA lineage. The phylogenetic discrepancies could be reconciled if the mtDNA of early Neanderthals was indeed Denisovan-like and was subsequently replaced by a more derived mtDNA lineage.".

This "derived mtDNA" got into the Neanderthals through " a genetic introgression event from African hominins into the early Neanderthal population that gave rise to the ‘Late Pleistocene’ Neanderthal mtDNA lineage".

This introgression took place long ago, and came from " an African source, which we constrain taking place more than ∼270 ka". In other words the paper suggests an Out of Africa event over 270,000 years ago which admixed human mtDNA into Neanderthals, mtDNA which replaced the older mtDNA -i.e. Denisovan and Sima de los Huesos hominin, with a new lineage, the "African mtDNA that evolved into the Late Pleistocene Neanderthal mtDNA type". And this "new" mtDNA spread from the HST Neanderthal in Germany to all others, including Sidron in Spain and eastwards all the way to Altai. Thousands of kilometers from the Atlantic to Siberia.

Furthermore, they estimate that "if Ne (effective population) was <5,000 units, a mean temporal interval of 300 ka is sufficient for an incoming mtDNA lineage below 0.1% in frequency to drift up to fixation." in other words, a very small initial input of "African genes".
But looking at this theory with a critical eye, we must point out that Neanderthals were spread out over a very wide area, which makes it very difficult for this replacement to take place in the whole population.

Furthermore a different explanation can be found: if modern humans were already outside of Africa i.e. in Asia, and they mixed with the Neanderthals outside of Africa -no Africans involved in the introgression. They would have had plenty of time to admix over a wide area, and this would also explain why there was an Ancient gene flow from early modern humans into Eastern Neanderthals 100,000 years ago as suggested by Martin Kuhlwilm et al, in Nature, Feb. 2016. DOI:10.1038/nature16544.

So instead of suggesting an earlier migration (it actually took place 1.8 Mya when Homo erectus left Africa for Asia) why not think about H. sapiens living in Eurasia and mixing with Neanderthals?

I wonder how this ties in with the Oldest Homo sapiens remains dating back to 315,000 years ago, found in Morocco?
 
Sources

(1) Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals, Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause. Nature Communications 8, Article number: 16046 (2017). doi:10.1038/ncomms16046.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall ©