The Neanderthal Romeo and Human Juliet hypothesis

By Paul Mason

Diagram by Paul Mason

Scientists have had trouble reconciling data from analyses of human mitochondrial DNA and the male Y chromosome. Analyses of human mitochondrial DNA indicate that we all share a common female ancestor 170,000 years ago. Analyses of the Y chromosome indicate that we share a common male ancestor 59,000 years ago (Thomson et al. 2000). How can we account for the idea that our common grandmother is 111,000 years older than our common grandfather? Have we found evidence for the world’s oldest cougar, or is there a hypothesis (other than blaming it on statistical anomalies) that could potentially reconcile these two dates? Perhaps we are given a clue in recent findings that a small percentage of human DNA is Neanderthal. Against popular belief (NOVA), Neanderthals did not go extinct without contributing somehow to the gene pool of modern humans.

Sexual reproduction is successful because the process of chromosomal exchange and gamete fusion provides genetic variability between individuals. Asexual reproduction is the kiss of death in the long run due to deleterious mutations. Strangely enough though, inside each cell of our bodies there is a tiny energy regulating organelle that reproduces asexually. This symbiotic bacterium is vital to cellular function and is called a mitochondrion. Both boys and girls inherit their mitochondrial DNA exclusively from their mother.

In female Homo sapiens, the oocyte remains dormant in dictyate from the moment of formation in late foetal life until just prior to ovulation, thereby protecting itself from mutations in both the mitochondrial and nuclear DNA. The male germ cells on the other hand are in a ferment of mitotic and meiotic activity from puberty onwards with most spontaneous DNA mutations occurring in the testis (Short, 1997). Sperm are dependent on maternal mitochondrial DNA in the midpiece sheath for their motility, but these mitochondria are destroyed by the oocyte immediately after fertilization, so the fertilized egg contains only maternal mitochondrial DNA.

From studies of mitochondrial DNA published in Nature (Cann, Stoneking, & Wilson, 1987), population geneticists discovered that people alive today share a common female ancestor anywhere up to 200,000 years ago (most estimates are somewhere between 150,000 to 170,000 years ago). Studies of mitochondrial DNA from Neanderthals and humans have shown no indication that humans have a female Neanderthal ancestor (Ovchinnikov & Goodwin 2001; National Geographic, 2008).

Just this year, researchers have estimated that gene flow from Neanderthals to humans occurred between 80,000 and 50,000 years ago (ScienceDaily May, 2010). Researchers have long wondered if Neanderthals were an entirely separate species, and recent evidence suggests that they probably weren’t. (Actually, one of the problems teaching human evolution is that we use a Linnaean system of classification with a Buffonian definition of species—two incompatible systems). However, even if Neanderthals were a separate species, speciation without any loss of hybrid fertility is possible.

Take the example given to me by Professor Roger Valentine Short: the Camelidae that originated in Florida (The Atlantic, 1999).

The little ones migrated into South America and up into the Andes to become the Llama, Alpaca, Vicuna and Guanaco—phenotypically quite different species, but all of which will produce fertile hybrids when crossbred. The big ones migrated up the Rockies, across the Behring straits, through Mongolia and Northern China—where we find the two-humped Bactrian camel—and into India and from there into Persia and Saudi Arabia—where we find the one-humped Dromedary camel. The spread of the Camelidae from the Americas to the Middle East is an example of speciation in a sexually reproducing species as a result of reproductive isolation. However, there has been no loss of hybrid fertility. Researchers have been able to produce Camas by inseminating Alpacas with Dromedary semen. Interestingly, the reciprocal cross gave fetuses, but no liveborn young.

(For more information, please see Short 1997; Skidmore, Billah, Binns, Short, and Allen 1999; Skidmore, Billah, Short and Allen 2001;

Modern humans may in fact be hybrids. Since Old World and New World Camelids are some 10 – 12 million years apart, we can be pretty certain that Homo neanderthalensis and Homo sapiens were able to hybridize. However, we must remember that studies have not shown any evidence of mitochondrial DNA from Neanderthals in humans (Potts & Short, 1999:59). Studies have shown though that modern humans share a common male ancestor who lived 59,000 years ago. Could this male ancestor have been Neanderthal? Indeed, the date of our closest common male ancestor correlates well with estimations of gene flow between Neanderthals and humans around 50,000 to 80,000 years ago. If H.neanderthalensis and H.sapiens were able to mate, then it is plausible that only the male H.neanderthalensis and the female H.sapiens were able to produce fertile offspring. The reciprocal cross may not have been successful.

According to Haldane’s law, the heterogametic offspring of interspecific hybrids are likely to be absent, rare, or sterile (Short, 1997). If Haldane’s Law applied to the offspring of H.neanderthalensis and H.sapiens, we would expect to find female hybrids quite commonly, but male hybrids much more rarely. The male hybrids would have carried a Y chromosome very similar to that of the original hybridizing male. The lack of Neanderthal mtDNA suggests that the initial hybridization involved a Neanderthal male, but there would probably have been few if any male hybrid offspring, so the Neanderthal Y chromosome and the mtDNA would have been quickly lost. Nonetheless, the Neanderthal autosomes would have happily mingled and interchanged with human autosomes, eventually losing their identity in the process.

Could it be that Homo neanderthalensis males were able to mate with Homo sapiens females but that the reciprocal cross was unsuccessful? Alternatively, were male H.sapiens disastrously incapable of wooing the physically more powerful H.neanderthalensis females? Or were H.neanderthalensis females simply unable to give birth to hybrid offspring? Perhaps male H.neanderthalensis outcompeted early male H.sapiens and eventually the male Neanderthal genes gained dominance (and maybe H.sapiens females somehow out-competed H.neanderthalensis females for partners). All of these possibilities potentially explain how we share a common male ancestor 59,000 years ago, but a common female ancestor 170,000 years ago. Simultaneously, these hypotheses explain why comparisons of DNA sequences in mitochondrial DNA from Neanderthals and modern humans have indicated that there was no interbreeding between these two exceedingly similar species (Potts & Short, 1999:59). Mitochondrial DNA from Neanderthals simply may not have made it into the modern human lineage. The nuclear DNA of Neanderthal males, however, possibly did.

Paul Mason is a doctoral candidate in anthropology at Macquarie University. He is currently finishing his dissertation on the relation between music and movement, and the implications for cultural evolution, in fight dances in Indonesia and Brazil.  When he is musing about evolution, he is not working on his dissertation. [Greg: PAUL!  Get back to your grindstone!]

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38 Responses to The Neanderthal Romeo and Human Juliet hypothesis

  1. Pingback: Your Great x 2360 Grandpa was a Neanderthal! « Neuroanthropology

  2. miko says:

    Studies of mitochondrial DNA from Neanderthals and humans have shown no indication that humans have a female Neanderthal ancestor

    If you have any Neanderthal admixture, you have both male and female Neanderthal ancestors, since regardless of the sex of the most recent Neanderthal ancestor, that individual had a Neanderthal mother and father, who are also your ancestors. We may have no direct female lines to Neanderthals.

    Also, I don’t think there is any reason to expect Y-chromosome and mitochondrial ancestry to trace back to the same time or place. It’s not a statistical anomaly–it would be a mind boggling coincidence if they did date from the same era. Every segment of our genome has its own history and coalesces into some unique (but sometimes changing) individual in the past who is our most recent common ancestor for that particular stretch of DNA. We would expect that these common ancestors lived 100s of thousands of years apart from each other.

    Finally, I think the Y-chromosome common ancestor dating estimates include genetic data from Africans, who do not have Neanderthal admixture.

    • Paul Mason says:

      Thanks Miko. You first point is entirely correct, and I should have been more explicit that the limited data indicates that we share no direct female Neanderthal ancestor through a hybridisation with a male human. However, the Neanderthal parents of the male Neanderthal (who mated with a female human) would obviously have contributed to our gene pool if this hybridisation did occur.

      With regards to your second point, I wouldn’t expect Y chromosome and mitochondrial ancestry to trace back to the same time or place either. And, I don’t believe that the findings are the product of a statistical anomaly. I do find it quite intriguing that our family trees overlap at a male some 59,000 years ago and at a female anywhere from 150,000 to 200,000 years ago. A difference of 91 to 141 thousand years is quite large. But, if the difference was in the other direction, I think it would be harder to explain.

      Thirdly, yes, I am pushing it to suggest that the male living 59,000 years ago was a Neanderthal. In fact, if Haldane’s law applies to the Neanderthal-human cross, then we would expect to see less male offspring than female offspring. But entertaining an idea before discounting it is more important than never thinking about it at all. The idea that the male where our family trees overlap 59,000 years ago was a Neanderthal pushes buttons. You are right though, that from our limited sample of Neanderthal DNA, we have not yet found evidence of Neanderthal DNA in African populations and the work of Thomson et al. (2000) did use a worldwide sample (but they didn’t describe the composition of this sample).

  3. Francisco says:

    Very interesting and very well written idea. I am trying to reconciliate the fact that the recent study about Sapiens and Neanderthals hybridization indicates that this only happened only in non-African populations with the contrasting fact that our common male ancestor (around 59,000 years ago) includes African populations.

    • Paul Mason says:

      Thanks Francisco.

      The Neanderthal sample we used is very small–Off memory, I think it was taken from a Croatian fossil. Where it shows connections, then we have an interesting result. Where this sample doesn’t show connections, then we await more samples.

      The major contribution I make in this post is that the initial hybridisation would have most likely been a male Neanderthal and a female human (with the reciprocal cross not providing fertile offspring). If Haldane’s law applies to the male-Neanderthal/female-human cross, then we would expect to see less male offspring than female offspring.

      The idea that a Neanderthal male is our most recent common male ancestor is one of the more far out hypotheses I put forward in the above post. If more nuclear DNA samples from Neanderthals become available, will they show that somehow Neanderthal DNA migrated back into African populations? Wacky thought, and maybe unlikely, but somewhat entertaining…

      • Adriana says:

        The Croatian fossils were all females, so we have no Y chromosome information from them. I remember only one study with some snippets of Y chromosome DNA from only one bone, one specimen, and those segments looked very divergent from modern human’s Y chromosome DNA (I think this was in the FOXP2 paper, PMID: 17949978). This helps your wild (but interesting!) hypothesis about the male hybrids not being fertile or very viable.

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  5. lionel says:

    Another possiblity is that neanderthal mitochondrial dna has successfully been transmitted to “modern human” women but that the female descent of those women became extinct somewhen between then and now.
    As hybrids would only be a small percentage of population this is statistically possible.
    The MtDna genome is fully transmitted at each generation, but gets a 50% odd not to be transmitted at all as well, meaning end of the journey for ALL the genes it includes.
    For the biggest part of the genome, it’s different : every single coding gene get 50% odd as well, but they are in the 10 000 for the first generation hybrids (half the gene pool), so the probability for all of them to disappear because of “bad luck” in something like 5000 generations seems quite low.
    This is regardless of any competitive (dis)advantage for one Neanderthal gene compared to its modern human equivalent.

    • Paul Mason says:

      Thank you for the complementary set of hypotheses, Lionel.

      Mitochondrial DNA has been linked to some forms of Alzheimers, rare forms of blindness, late-onset diabetes, and muscular wasting in adults.

      If mitochondrial DNA somehow accumulated deleterious mutations that wiped out the carriers, then both male and female carriers would be wiped out. Males may have lived just long enough though to pass on their DNA before dying. Successive generations of Females carrying an inefficient strain of mitochondria would also have been wiped out.

      • Paul Mason says:

        p.s. But in agreement with you, just because people carry deficient mitochondria doesn’t mean they can’t pass on their nuclear DNA to offspring who don’t have the deficient mitochondria, or to their grandchildren…

  6. M says:

    Ehh, some girls like ’em burly.

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  8. Si says:

    Regardless of deleterious mutations, if you consider that only small bands of people existed in cohabited zones (this is the end of the last ice age) and that hybridisation may have been rare, there would have been a high chance of mt lineage loss just through chance events such as a hybrid female having no daughters or through death.

  9. Si – coalescence would explain part of the story but how does it explain the maintenance of nuclear DNA in the absence of mtDNA? This post may be pushing it to suggest that our common grandfather is a Neanderthal, but I think the dude is onto something when he talks about how to interpret the likely hybridizations that occurred.

  10. Thompst says:

    I’m having a hard time reconciling the estimated Y-Chromosone date of 59k (as per Thomsen) with the other evidence that suggest, for instance, that Australia was populated before this, without significant later gene influx. Or that the San group is said to have split off over 150k ago. I don’t know if Thomsen, et al included San or Australian genetic data in his estimation, but he should have. Care to explicate?
    Also, you state that “modern humans are hybrid” but there is, as of yet, no indication of Neanderthal genetic data in most African lineages, and these are surely “modern humans”–unless I’m missing something, this was inartfully said…..

  11. Dirk says:

    …seems like Jean Auel will need to rewrite Clan of the Cave Bear! lol

  12. Bernie Brightman says:

    Maybe the idea of a molecular clock is off in the first place. It’s hard to prove that mutations happen at regular intervals. Perhaps Y chromosomes are more exposed to the earth’s radiation and thus change more quickly than do X.

  13. Paul Mason says:

    Thank you for your responses.

    From your responses, Most people seem unhappy with the estimates of our closest common female and male ancestors. My colleagues and friends in genomics and bioinformatics inform me that these dates could
    be out as much as 50,000years, so those of you who take issue with the estimates can feel reassured for your doubtful suspicions.

    The element that excites me about all of your responses is that no one has taken issue with the idea that perhaps only male Neanderthals were able to mate with female humans. I’m happy to put the common ancestor debate aside. The more engaging discussion is
    probably about the types of interbreeding that could have occurred between Neanderthals and humans. Was it influenced by speciation without loss of hybrid fertility, sexual selection, cultural factors between the groups???

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  15. ohwilleke says:

    There are more parsimonious ways to explain autosomal descent without obvious mtDNA or Y-DNA traces.

    First, one infers that Neanderthal/human hybrids were children of infrequent and brief liasons (perhaps during periodic meet ups of human and Neanderthal tribes for trade, and at any rate for periods of less than nine months) or less romantically rapes, rather than sustained relationships, and that the children ended up in the mother’s tribe and not the father’s as a result. Children of Neanderthal mothers ended up in Neanderthal tribes and their descendants died out with the rest of the Neanderthals. Children of modern human mothers ended up in modern human tribes and their descendants survived to become about 2% of the future Eurasians (they were probably small in number but introduced when the founder population of Eurasians was quite small). Thus, no surviving Neanderthal descendants in modern human populations would be expected to have any Neanderthal mtDNA.

    According to Haldane’s law the offspring of H.neanderthalensis and H.sapiens, we would expect to find female hybrids quite commonly, but male hybrids much more rarely. So, a disproportionate share of the children of Neanderthal fathers and modern human mothers are girls. Thus, most of the Neanderthal hybrids in the first generation who end up in modern human populations that survive, as opposed to Neanderthal populations that eventually go extinct, are girls who have neither Neanderthal mtDNA or Neanderthal Y-DNA, and a disproportionate share of boys who were born would be expected to have been infertile.

    Given the low percentage of Neanderthal autosomal DNA believed to found in modern Eurasians (1%-4%), and the likely quite small effective population size of the Eurasian founder population at the time of Neanderthal admixture ca. 100,000 to 50,000 years ago, and the greatly disporportionate number of fertile hybrid Neanderthal descendants who would have been women with no mtDNA or Y-DNA lineages from Neanderthals, it doesn’t take much in the way of either selective disadvantage of Neanderthal hybrid males, or propensity to have female children (as a result of Haldane’s law diluted a little in a second generation), or just plain bad luck, for this very small number of Neanderthal Y-DNA lineages to be removed from the gene pool entirely.

    The big problem with a Neanderthal ancestor to all modern humans hypothesis, is that that 59,000 year old Y-DNA Adam is the ancestor of all modern humans, both African and non-African, yet non-Africans show significant admixture that is not present (at least incrementally) in Africans. There is no evidence to support a total genocide of African men by Neanderthal descendant men ca. 59,000 years ago.

    • ohwilleke says:

      ” children of infrequent and brief liasons (perhaps during periodic meet ups of human and Neanderthal tribes for trade, and at any rate for periods of less than nine months) or less romantically rapes, rather than sustained relationships, ”

      Or, to expand just a little, to be even less demanding in my assumptions, one could merely assume that liasons that were not brief consentual relations or rapes took place in societies that were matrilocal. Notably, matrilocality is characteristic of the !Kung San of Southern Africa who are frequently considered archetypical to the greatest extent of any modern population of the kind of society that was present in the hunter-gatherer era of early modern humans.

      One also can infer from data in existing human populations that a strong endogamous tendency now even between populations far more genetically and phenotypically similar populations than those of the Neanderthal and early modern humans in the period when they shared territory or adjacent territories, so an expectation of low levels of admixture in the small founding population, even if you have long term couple relationships in matrilocal societies, is not at all a stretch.

  16. Paul Mason says:

    Thank you for your insightful scenarios Ohwilleke! I was amazed to learn online that you are actually a lawyer. I am pleased to see a lawyer who does not accept biological explanations at face value. I don’t know much about the courtroom, but my anthropologist colleagues would be happy to learn lawyers recognise the importance of cultural explanations.

    With Neanderthals, we are dealing with cultures that are extinct and our ability to refer to cultural explanations is limited. The evidence from mtDNA and nuclear DNA from Neanderthal fossils is a convincing biological artefact that indicates the types of reproductive success between Neanderthals and our ancestors.

    I believe that your scenarios are complementary to the biological explanation i offered about male Neanderthals and female humans being the parents of predominantly female hybrid offspring (the reciprocal cross being unsuccessful). The biological data must come first due to the paucity of assumptions we can make about social behaviour 50,000-80,000ya.

    Ian Tattersall in PNAS suggests that if humans and Neanderthals were separate species, then we would have to understand Neanderthals on their own terms. The recent data, that Neanderthals and humans were able to mate, demonstrates that the story is indeed much more complicated.

  17. Alan says:

    Any idea when Neanderthal Y- chromosomes will be sequenced sufficiently to indicate haplogroup?
    That would be quite telling….

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  19. Cate says:

    Not really – Ohwilleke’s ‘scenarios’ don’t have to have any biological underpinning evidence, it is enough that they show credible explanations (ie, not at odds with the biological evidence) for the idea of ‘reciprical crosses’ being unviable to not be invoked.

    IE, if it can be shown there are perfectly sound cultural alternative explanations for why modern human mtDNA survived, and Neanderthal mtDNA didn’t, then the the biological data (that shows this is the case) does not constitute a compelling need to invoke ‘biological’ fertility/viability causes for this. That remains just one more possible scenario to account for the biological data, which in no way favours biological over cultural explanation. (Because all the biological data does is tell us ‘one type survived, one didn’t’.)

    • Cate says:

      Sorry, that was in response to this:

      “SoI believe that your scenarios are complementary to the biological explanation i offered about male Neanderthals and female humans being the parents of predominantly female hybrid offspring (the reciprocal cross being unsuccessful). The biological data must come first due to the paucity of assumptions we can make about social behaviour 50,000-80,000ya.”

  20. Charlotte Elizabeth Ostrowski says:

    Haldane’s Law, The loss of both mtDNA and Y chromosomes from one of the two species contributing to a hybrid population, can be demonstrated today in the hybridization of cats. In the last several decades, Several small cat species have been bred with the domestic cat, including oncifelis geoffroyi, and caracal serval. Male wild cats and female domestics are… almost exclusively used since the female wild cats aren’t usually able to carry hybrid fetuses to term. (Interesting that the domestic cat has a less discriminating immune system than it’s wild domestic cousins.) This means that the mtDNA in the resulting f1 and f2 ancestors is completely felis catus/domestic cat. The Y chromosome also becomes extinct in the resulting hybrid population since almost all male f1 off-spring are sterile.

  21. Nightvid Cole says:

    Maybe the Neanderthal females just weren’t sexy…

    • nick says:

      Well looking at Chelsea Clinton’s brow ridge ,you get a feel of how attractive a female neanderthal could look. I find it cute,as I have a slight brow ridge and tilted forehead(see Paul McCartney’s),but I’m sure most low % hybrid humans and zero %hybrid humans(bullet heads) don’t,find her so much to look at.

  22. Joe says:

    From what I’ve heard the small amount (4%) of Neanderthal DNA is found in non-african populations, so surely the same would be true of Y-chromosome DNA? i.e. if the Y-chromosome is the same for all including african populations then the Y-chromosome ancestor can’t be Neanderthal?

  23. Bill Haught says:

    The author of the Neanderthal Theory of Autism at has been saying pretty much the same thing as Paul Mason above for 12 years. As far as anthropology goes the hybridization date of 50,0000 to 80,000 years is probably close enough to the dates of Aspie Quiz to be considered to be in agreement. He figured the matings were between Neandertal males and H.s.s. females.

  24. Bill Haught says:

    I should have read the article before posting. It appears that what Paul is saying is more extreme than even what the Neanderthal Theory suggests.

  25. Hagit says:

    I realized this is an old posting, so the author and others may not be returning to comments any more. At any rate, the problem with the assumption that hybrids existed in both communities is the fact that the Neanderthal DNA shows no human effects, mitochondrial or Y related. So there really were no hybrids born to Neanderthal females, and my first hunch about why would be differences in the birth canal or other physiological factors that prevented babies from coming to term, or resulting in birth defects.

    Now if we assume a constant rate of pairing, both human F with Neanderthal M and Neanderthal F with Human M, even if it is a very small percent, and we further assume that babies stay with Human mother, and that Neanderthal F has no live births or surviving offsprings, and give it 50,000 years or so, what you get is a significant dwindling of size of population, with the correlating diminishing ability to protect resources, and eventually extinction. And there lies, quite possibly, the key to the disappearance of the Neanderthals.

  26. Janis says:

    ” … were male H.sapiens disastrously incapable of wooing the physically more powerful H.neanderthalensis females?”

    Any particular reason for the delicate language here? I’d trust anthropology a lot more if it didn’t read like a modern gothic novel sometimes.

  27. Thanks for taking the work and time to jot down some matter which is really good

  28. Autism: The Eusocial Hominid Hypothesis

    ASDs (autism spectrum disorders) are hypothesized as one of many adaptive human cognitive variations that have been maintained in modern populations via multiple genetic and epigenetic mechanisms. Introgression from “archaic” hominids (adapted for less demanding social environments) is conjectured as the source of initial intraspecific heterogeneity because strict inclusive fitness does not adequately model the evolution of distinct, copy-number sensitive phenotypes within a freely reproducing population.

    Evidence is given of divergent encephalization and brain organization in the Neanderthal (including a ~1520 cc cranial capacity, larger than that of modern humans) to explain the origin of the autism subgroup characterized by abnormal brain growth.

    Autism and immune dysfunction are frequently comorbid. This supports an admixture model in light of the recent discovery that MHC alleles (genes linked to immune function, mate selection, neuronal “pruning,” etc.) found in most modern human populations come from “archaic” hominids.

    Mitochondrial dysfunction, differential fetal androgen exposure, lung abnormalities, and hypomethylation/CNV due to hybridization are also presented as evidence.

    A short video introduction

    The full 2-hour video presentation

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