Neandertal introgression and admixture

By Razib Khan | September 12, 2011 3:11 pm

Ed Yong has a good good review of a new Neandertal introgression/admixture paper in PNAS. It’s not live on the web yet, so let me quote Ed:

Even if the odds of successful interbreeding were just 5 percent, Neanderthal genes would make up the majority of the human genome today. As it is, a lack of viable sex explains why none of the Neanderthals’ mitochondrial DNA made its way into modern humans, and why so little of their main genome did.

Currat and Excoffier suggest that either modern humans and Neanderthals didn’t have sex very often, or their hybrids weren’t very fit. They favour the first idea. According to their model, it would only have taken between 197 and 430 liaisons between ancient humans and Neanderthals to fill 1-3 percent of modern Eurasian genomes with Neanderthal DNA. Considering that they two groups probably interacted for 10,000 years or so, it would have been enough for one human to sleep with one Neanderthal every 23 to 50 years.

From what I gather in the comments this is due to the fact that if there was a wave of advance very small levels of admixture per unit of advance can build up rather rapidly. I think this is easy to express in temporal rather than spatial terms.

For example, let’s imagine a population of modern humans expanding into a population of Neandertals. The original source population doesn’t receive any more contributions after the initial push, so you have a series of admixture events over time. Assuming 5% admixture per generation, this is the dilution of the “original ancestry” which would occur over 30 generations, or 750 years:

The model outlined in Ed Yong’s post needs to be examined with care though. No doubt there are all sorts of assumptions which can be disputed. Though I think I accept the final result as entirely plausible.


Comments (12)

  1. Ron Strong

    This analysis assumes that there is a ready supply of “pure” Neanderthals to mate with ancient humans, generation after generation, as ancient humans and Neanderthals mate.

    Assuming 5% interbreeding, Neanderthal genetic makeup would include more and more genes from ancient humans. If there is no net advantage for the genes of either population, wouldn’t the ultimate makeup of ancient humans (and remaining “Neanderthals”, for that matter) be proportional to the size of the original pure Neanderthal and pure ancient human populations?

  2. 1. The lack of Neanderthal mtDNA is easy to explain. Neanderthal mom’s had kids who ended up in Neanderthal tribes and their descendants died out with the Neanderthals. Only hybrid kids with modern human mothers and hence modern human mtDNA ended up in modern human tribes that survived in the long run.

    It could be that modern humans got Neanderthal women pregnant as often as Neanderthals got modern human women pregnant. Indeed a few hybrid Neanderthals could help explain the advance in Neanderthal tool culture near the very end of the Neanderthal era after hundreds of thousands of years of relative stagnation, despite the apparent absence in the archeological record of mixed Neanderthal-human communities.

    But, unless Neanderthal-modern human liasons were long term stable relationships as opposed to brief sexual episodes between neighboring groups that had little to do with each other and didn’t actually marry, the children are always going to end up in the mother’s tribe nine months later (give or take, who knows if Neanderthal gestation was precisely the same in length). Even affairs of a few months in length while a Neanderthal and modern human tribe were near each other for a season, for example, wouldn’t prevent the child from ending up in the mother’s tribe.

    2. Haldane’s law is the best way to explain the lack of Neanderthal Y-DNA (hybrids tend strongly to have the same sex determination chromosome). Another possibility is that the Neanderthals were more sex dimorphic than modern humans, so hybrid boys may have been more different from the modern human norm than hybrid girls, and hence may have integrated less well and had more trouble finding mates.

    3. Random drift to explain the lack of Neanderthal mtDNA and Y-DNA doesn’t fit well with an estimated 197-430 liasons. The law of averages iterated that many times in an expanding modern human population would catch up with you to keep mtDNA and Y-DNA in the population at similar rates to other autosomal traces otherwise.

    You need a scenario that acts very soon (within a couple of generations) to purge both mtDNA and Y-DNA, and very consistently, when you have hundreds of liasons to keep all Neanderthal mtDNA and Y-DNA out of the Eurasian gene pool. Declining and stable populations jettison low frequency genes. But expanding populations that have the same genes repeatedly reinjected into their gene pools generally don’t nearly as easily. And, it is hard to explain introgression that occurs time and time again leaving no Y-DNA or mtDNA in circumstances that still somehow leave some siginificant traces (on the order of 2%) in the autosomal genome that can reach fixation, without some causal reason that Y-DNA and mtDNA behave differently.

    4. There are some skeletons from the Upper Paleolithic in Europe that seem to show possibly hybrid individuals or Neanderthal weighted traits in modern humans, suggesting that there may really have been some more admixed modern humans.

    5. If modern admixture is based on nearly 10,000 years of liasons spaced evenly during periods when the two species are in contact with each other at the frontier, it is virtually impossible not to end up with some cline of greater admixture in Europe than the rest of the world, since any admixture that took place in Europe itself after 50kya surely would have made its way into European gene pools but would not have made its way in any measurable way to coastal route Asia. More opportunities for liasons means more admixture even if only incrementally.

    A better way to explain this is that on the frontiers modern humans were more admixed with Neanderthals through successive liasons, but that a very small percentage of modern humans in Europe trace ancestry to European Cro-Mags with high levels of admixture on that frontier from 30kya. Instead, most Europeans trace their ancestors mostly to post-Neanderthal extinction people from less admixed areas to the Southeast – partially in the post-LGM repopulation of Europe and partially in the Neolithic and in possible later waves of migration (e.g. Indo-European) to the extent that they had demographic impact.

    It is realistic to expect that modern Europeans have less (perhaps much less) than 5% pre-LGM European Cro-Mag ancestry on average, which is diluted enough to make even 10%-20% Neanderthal admixture rates in final frontier European Cro-Mags disappear to undetectable levels.

    6. This said, an estimate of one admixture event in the proto-Eurasian modern human community per generation during the period of admixture in the Southwest and West Asian area for the period of interspecies contact prior to a meaningful modern human presence in Europe sounds about right as a ballpark estimate from back of napkin estimates without having to resort to very low fertility rates.

    Even within modern humans, differences between, for example, Chadic pastoralists and Fulani pastoralists are great enough to keep the Y-DNA pools of the two neighboring groups in the African Sahel extremely distinct from each other over periods of thousands of years. Neanderthals and modern humans can be expected to have had lower admixture rates than any two neighboring modern human populations known to history and not separated by significant geographic barriers. Surely, admixture rates would have been at least as low as between high caste South Asians and Dalits over the last 4,500 years or so, simply out of social factors and with no fertility effects.

    7. Even if you are going to posit that liasons were much more common, infanticide seems a more likely source of limited Neanderthal contribution than extremely low fertility, if we assume that Upper Paleolithic humans were no more “civilized” than e.g. the Romans were. In general, however, no low fertility rate estimate can address the fact that admixture is just as high in Asians as it is in Europeans despite a presumably shorter period of contact with Neanderthals for their ancestors.

  3. I may be missing something, but our lack of Neandertal mtDNA and Y-DNA seems rather unremarkable to me. After all, the motherline and the fatherline are but two lineages out of thousands and thousands.

  4. Bob Dole

    @Ron – The admixtures didn’t leave us with *any* neanderthal mtDNA. This means they were probably only male neanderthal + human female. This could be because hybrids born to neanderthals would have been less likely to survive and reproduce in their comparably tiny social groups. It might also have something to do with different reproductive machinery (or strategies). [Edit: looks like ohwilleke beat me to it]

    @Razib – If there is strong selection for specific neanderthal genes that came from a very small “hybrid founder population” (which, if I’m not mistaken, provided whole X chromosomes along with segments of DNA on the rest), then is it possible that autosomal recessive diseases (or CNVs) might be more common in those regions due to a long term coalescent founder effect?

  5. What’s with assumption that Neandertal DNA would diffuse amongst our early population? Those neanderthal lovers might have been an insular group later forming insular tribes like the Franks and Prussians etc.

  6. Ron Strong

    Bob – I understand that the admixture that did take place resulted in no surviving mtDNA. But I would think that result would be highly unliikely had there occurred anything close to 5% interbreeding over multiple generations, the assumption used to show that Neanderthal genes would have ended up dominating the modern human genome with such rate of admixture.

    Being essentially clueless as to mating practices of Neanderthals or early humans, we don’t really know where hybrid children would end up. It is quite possible that when those tiny social groups of Neanderthals lost some or all of their females, the mailes would try to capture females from any nearby group, Neanderthal or early human. In that case the offspring born in the Neanderthal group would have early human mtDNA.

    A question. Let’s assume that what interbreeding did take place resulted from Neanderthal capture of early human females and that the surviving Neanderthal DNA in modern humans resulted from early humans breeding with members of a few Neanderthal groups that had become “nearly” early human as a result of multiple human female captures over a few generations. Would there be any way the genetic record could be used to distinguish such practice from an occassional Neanderthal male breeding with a human female who remained in the human group?

  7. Justin Giancola

    Oh ohwilleke! Your first paragraph made me love you and your exhaustive mini-blog posts.

  8. Cathy

    Once again, Jean Auel might just have nailed it.

  9. John Roth

    It’s an interesting conundrum; I like both Dienekes’ and Ohwillike’s take on it. On a purely conceptual basis I like the notion that the sapiens ancestors simply had greater population density than Neanderthals were able to sustain, and that continuing migration from the south-east pushed the boundary north and west, with the frontier populations migrating with the boundary and eventually vanishing.

    This means that surviving Neanderthal genes would have to backflow against the population movement, which in turn suggests that the ones that survived had high selective advantage.

  10. glen

    I am not comfortable with the phrase: “…if the odds of successful interbreeding were just 5 percent…” Five percent would seem quite high when describing nomadic people who spent most if not all their time living in isolation separated by mountains, glaciers, deep snow, etc. Most likely they perceived each other as very very different.

    We have evidence in the form of artifacts that humans at least combed their hair and wore jewelery so it is likely that grooming was important. To the best of my knowledge no Neanderthal combs have ever been found or any other evidence of grooming. If you were living in near complete isolation in the middle of winter, it was ‘last call’ – and all you can find is the Neanderthal chick next door you might be able to drink her pretty if couldn’t find an ibex or something.

    Since they occupied the same general geography for a long period, they obviously tolerated each other but that doesn’t necessarily assume breeding. Let me liken it to Teaneck NJ where I lived in the 70’s. Large populations of Blacks and Jews living side by side but if they interbred five times it was a lot, let alone 5 percent. It is easy to imagine humans thinking of Neanderthals the way Indians think of the Untouchables.

    When humans and Neandethals did interbreed what are the odds they were accepted by either group? The breeding opportunities for mixed species offspring were probably very rare. It is hard to imagine early humans being any less tribal than we are today and if anything more so. In a time of high mortality rates it is easy to imagine interbreeding ending after only one generation.

  11. Lol wut

    Those Homo sapiens sapiens must have been pretty desperate. Just look up “Neanderthal woman” on Google Images.

  12. It is usual for the males of an invading force to rape the females of the resident group (even ugly ones). So the fact that Neanderthal mitachondrial DNA does not seem to turn up in today’s humans is a little puzzling. It could mean that there was little or no invading, and that the trace of Neanderthal in modern humans came from infrequent captures of anatomically modern women by groups of declining Neanderthals, the genes of the hybrid offspring being disseminated by ordinary demic diffusion. Even that idea is somewhat suspect, as I have seen several speculations that an AMH woman might have trouble birthing a hybrid baby that is more robust and has a larger cranium than the woman’s birth canal could readily accommodate. In my novel, CRO-MAGNON (by me, Robert Stimson), an AMH woman, having been rescued from drowning by a Neanderthal hunting party from a declining clan and subsequently impregnated, has a terrible time birthing a hybrid baby, has to be cut by a midwife, and barely survives the ordeal. I have also seen speculation that rapes of Neanderthal women by AMH men may have been infrequent, since Neanderthal women may have been stronger than AMH males. Add Haldane’s rule of hybrid sterility and inviability, and it seems no wonder that the proportion of Neanderthal genes in modern humans is 4 percent or less.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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