Denisovan-Neanderthal hybrid

They’ve found a Neanderthal-Denisovan hybrid.  But they should have been rare, very rare, less than one per generation: if not, the two groups could not have accumulated  lots of neutral-genome differences, which they did.

Possible explanation:  hybridization was happening in a population sink.

Neanderthals and Denisovans checked in, but they didn’t check out.


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60 Responses to Denisovan-Neanderthal hybrid

  1. Jacob says:

    I thought it simply shouldn’t have been F1. You could get mixes. Maybe there was something like a ring species situation, or maybe one was sweeping over the other when we wiped them both out.

    But from the tens of thousands of years between Neanderthals and Denisovans meeting, and our wiping them both out, how many first generation crosses could there have possibly been, as a proportion of the total? That would be like waiting 30,000 years, and then trying to find a Mexican who is exactly 50% Spanish on one side and 50% Native on the other.

    I like your idea; a population sink lying at the border would actually generate far more F1s than we might expect otherwise. Such a population sink could have been a geographic barrier which pushed them towards speciation in the first place.

    • DRA says:

      ….or maybe one was sweeping over the other when we wiped them both out.

      Didn’t Toba explode about the same time as anatomically modern humans moved out of Africa? Perhaps that, and the following advance of the ice age had something to do with it. Maybe with the anatomically modern population bottleneck as well.

      • Jacob says:

        Neanderthals lived long after Toba, but there are people saying that a glacial period may have helped do the Neanderthals in. Personally, I think that AMH had to have something to do with it.

        As for Denisovans: who knows? I would bet on AMH again because of the admixture. But we don’t know much about them.

  2. Trelane says:

    There’s plenty of room at the Hotel California

  3. Ursiform says:

    Must have been something happening for one out of a small number of Denisovans found to turn out to be a hybrid.

    • Lampukistan says:

      Fertile, as opposed to normally, infertile mules are extremely rare. But horse and donkey lineages have been seperated much longer. Grevy and common Zebras produce hybrids in the wild, though.

      • Ursiform says:

        She appears to have been a 1st gen hybrid. To happen one out of hundreds of fossils, not shocking. To happen one out of single digit fossils, you ask “why?”.

        • dearieme says:

          Because God willed it. It’s His way of encouraging geneticists to work out what he was up to. He’s lost patience with all the Abrahamic types and wishes to encourage The People of Darwin.

  4. Unladen Swallow says:

    Was it the same cave as the original Denisovan? That would be interesting, how much farther east is this than the closest previous Neanderthal fossil?

  5. Phille says:

    These hybrids being almost always infertile seems to be a better explanation. Of course an area where these populations meet and mate but don’t produce fertile offspring would be a population sink.

    • Cloveoil says:

      why would they be infertile if there are sapiens x Denisovan hybrids? Denisovans were closer to neanderthals than to us and were heidelbergensis: were the Denisova tooth found in Europe it would’ve been assigned as such.

      • epoch2013 says:

        That is interesting, as there were classical Heidelberg samples from Italy [1] that for all practical purposes were contemporary to the Sima de los Huesos samples. From the latter we know their mtDNA was closer to Denisovans than to later Neanderthals, yet we also know their autosomal DNA was proto-Neanderthal.


        • Cloveoil says:

          Antecessor was already on the heidelbergensis-neanderthalensis-‘Denisova’ line; you can throw in the ‘Atlantanthropus’ fossils from North Africa too. Heidelbergensis is a chronospecies with neanderthals as the descendant: Homo antecessor is probably a superfluous label, and if you want to trea it as a chronospecies, its probably a junior synonym of H. mauretanicus.

          • Cloveoil says:

            It gets more complicated further east: Narmada man was – on balance – closest to neanderthals. It is also similar to Maba which has long been noted for its similarity to European neanderthals re: orbital form, nasals. Neanderthal-like traits, and other Chinese fossils (Xuchang, Xujiayao) have been noted to have neanderthal-like features. China was a location of mixture between neanderthals (or similar) and the Asian erectus line, but in effect the great heidelbergensis-neanderthal line replaced them. It is doubtful that H. sapiens ever met the Asian H. erectus, but somehow actual neanderthals spread their genes into South China and not just the Altai.

            • freethinker says:

              “It is doubtful that H. sapiens ever met the Asian H. erectus.” I doubt that. I think the Denisovans were Asian H. Erectus, and their descendants can be found in modern Australian Aborigines. Also Solo Man seems to be about a 50/50 of mixture Erectus and modern humans.

              • Cloveoil says:

                Denisovans are closer to neanderthals than they are to sapiens: almost all palanths agree erectus had diverged beforehand. Though, Solo man did persist late on Java (Ngandong), to an uncertain date. Solo man seems clearly erectus except the cranial capacity and the endocasts… these seem to show admixture from crownwards, but its still closest to Sambungmacan and other Javan erectus.

                Ofc the North Chinese Middle Paleolithic hominins show both erectus and neanderthalensis (or Denisovan?) traits: there was continuity in China.

        • Cloveoil says:

          Ceprano is interesting: its somehow erectus-like. Its still heidelbergensis, but leans back to the LCA of Asian erectus and the clade comprising H. saps and the neanderthal-related group. Look at fig. 1 and fig. 2.

          Steinheim is esp. sapiens-like, something I noticed before; Jinniushan is neanderthal, which is something else I speculated on before. The other heidelbergensis are between erectus and members of the ‘advanced’ clade. There might be evidence in that study for an Asian origin of H. heidelbergensis, or for hybridisation in ie. Hexian. The Denisova genome, believe it or not, is supposed to show admixture from an unknown source that is presumably Asian Homo erectus.

          • epoch2013 says:

            Eske Willerslev and a team have a paper out where they use proteins in teeth enamel to establish the phylogenetic relationships of a 1.77 million years old Rhinoceros found in Dmanisi. I certainly hope that means the hominins of Dmanisi will be analyzed just as well. It also would mean we have a tool to look at phylogentic relations that old. Maybe we are on the brink of solving a lot of these questions.


            • Cloveoil says:

              I’m not sure what to make of Dmanisi: probably a failed OOA event as they represent Homo ergaster, and – perhaps – H. rhodesiensis as well. Its a question how much variability can exist in a single species, or even a single population: something to bear in mind is that the koolakamba skulls turned out to be chimps rather than chimp x gorilla hybrids, a new ape, or small gorillas. I’m noncomittal but without aDNA I don’t think its possible to untangle early Homo species.

              At present it seems as though H. naledi and Au. sediba are H. habilis, or at least its close relatives. It also seems as though H. floresiensis is closer to mainline Homo than are they. But that’s all I will say based on the literature.

              Argue (2017) on the other hand, found evidence for a relationship of H. georgicus to H. naledi and (more weakly) Au. sediba as a true australopithecine; so even what I said above is not certain. It would be nice to add H. naledi and H. floresiensis to the Gonzalez-Jose (2008) dataset IMO.

              • Cloveoil says:

                Typo: “I’m not sure what to make of Dmanisi: probably a failed OOA event as they represent Homo ergaster, and – perhaps – H. rudolfensis as well.”

    • GAGCAT says:

      Yes, my initial thoughts are either that or experiment error. What are the chances of 1st gens? We need a border skirmish/fucking simulator model.

      If it is infertility then looking at that crossing over contig config vs other possible ones would be fruitful.

  6. Eponymous says:

    A local pop sink isn’t enough by itself. You need the fertility rate in the sink to be low enough, and its area large enough, that the genetic signal from the sink doesn’t propagate back to the main population.

    Even then there’s still a mystery: if interbreeding is happening regularly in some area, then if you dig there you should find a lot of hybrids, of which relatively few are 1st gen.

    No matter how you cut it, a 1st gen hybrid out of very few samples is a mystery. Unless the hybrids have something really wrong with them. That seems the simplest explanation.

  7. biz says:

    How many total Denisovan specimens are there? Is it highly improbable that out of that small number we have one is a (presumably infertile) hybrid?

    • TWS says:

      Why presumably infertile? They are more closely related to each other than to us, and they managed to interbreed with us.

    • Eponymous says:

      If most Denisovans lived in hot/wet places, like SE asia, then we wouldn’t expect to find many remains there. This is plausible, because it seems that Denisovans were widespread, but we haven’t been able to find many.

      But suppose that interbreeding occurred in a cold place in between their ranges, where population was low and death rates were high. But that might be just where we could recover remains.

      Thus it might not be inconsistent that hybrids are very rare, but we found one out of only a few samples; because we might be drawing our samples from one of the few places where hybridization occurs, because that’s where it’s cold enough to preserve remains.

  8. JRM says:

    Are caves population sinks?

  9. Cloveoil says:


    There is Denisovan admixture throughout India, and even (to a much lesser %) in Finlanders. East Asians get theirs from a population related to Denisova cave: South Asians & Papuans get theirs from another, more distantly related population.

    I think calling the southern source Denisovan might therefore be misleading? This sort of matches the zoogeographic barrier that would’ve affected gene flow among late archaic Homo. The southern group was, presumably, closer to Narmada and Maba than to typical Chinese fossils further north.

    • Cloveoil says:

      I might add: has anyone compared Maba’s neanderthal-type nasals to the convex, somewhat European-like (but broader) noses of some Papuans. Does one see regional continuity in the midface?

  10. Maybe they killed her and others of her kind because she was an abomination (No, I’m not serious.)

  11. David Chamberlin says:

    Astute conclusion

    They didn’t interbreed very often yet here we find the first generation of interbreeding. I doubt many people get the full ramifications of population sinks. Many walk in. Few walk out. No history to tell because just a few emerged. Why here? Extreme cold, the absolute far end of either Neanderthals or Denisovans range, so not many choices in mate selection Billions of Denisovans and Neanderthals lived and died but what’s left? Almost nothing. We are talking small populations but times all the generations they lived. But this cave was a very rare place, a perfect natural refrigerator, not a good place for hominids to survive but an ideal place for DNA preservation. So one pinky bone tells us a moment in a past that is almost completely lost.

    May the science of archaic DNA open up new vistas on worlds otherwise lost to time.

    • gcochran9 says:

      Last time I made a guess about total # of Neanderthals, more like hundreds of millions.

      • David Chamberlin says:

        Denisovans had the greener pastures, Larger populations? I assume so but who knows. Southeast Asia seems a whole lot more hospitable to me than than the Neanderthal range. Damn it, too much is lost. One friggin pinky bone and a few genes is all we have left from Denisovans, it’s frustrating.

        • epoch2013 says:

          “Damn it, too much is lost. One friggin pinky bone and a few genes is all we have left from Denisovans, it’s frustrating.”

          We don’t know yet. We might have skulls but not realize it. If, as some suggest, Denisova is a chronospecies H. Heidelbergensis we quite a lot.

          By the way: A new way of researching relations and the phylogenetics of early hominims may have come around, looking at proteins in teeth enamel rather than DNA which enables research of far older samples. This has been successfully done on 1.77 million year old Rhino’s:

          • Cloveoil says:

            The southern Denisovan might be Maba-Narmada paleodeme: the northern is more likely to descend from Xuchang and Xujiayao. The caveat is no one knows for sure, or understands the full pattern or extent of ancient migration or hybridisation in the Middle Paleolithic of China.

            Collagen studies are accurate in your instance but they create mismatch with other molecular data.

      • David Chamberlin says:

        I do not trust the low estimates of average Neanderthal population, nobody knows. It was low at times of population bottlenecks, presumably caused by hellacious drops in average temperature caused by the north Atlantic current slowing down and stopping periodically.The only estimates that have been made on Neanderthal populations are based on population low points and nobody knows what the average population was during warmer periods when the population rebounded. The Neanderthal range presumably held a much smaller population than that of the Denisovan population. It was damned cold. If it wasn’t for limestone caves and the colder dryer temperatures in their range our fossil evidence of Neanderthals would be as skimpy as it is for Denisovans.

  12. crew says:

    Possible explanation: hybridization was happening in a population sink.

    Wait. They had cities?

  13. David Chamberlin says:

    Question while we are on the subject of Denisovans. Denisovans had to have developed their own mutations to protect against diseases. Are any of the mutations protecting against malaria originally Denisovan? Has anyone looked? Great lecture on Youtube by John Hawks on malaria.

  14. iffen says:

    God is an enthusiastic supporter of interbreeding. He had left this sign for the doubters.

    • Coagulopath says:

      He tried it out for Himself in Nazareth this one time.

      • JP says:

        I have always wondered what Christ’s genome would have looked like, ancestry-wise. Half Palestinian and half….well I don’t know. Or 100% Palestinian? It’s a mystery, as they say.

        • Toddy Cat says:

          A once-famous “All in the Family” exchange:
          Meathead; (responding to a mildly anti-Semitic remark by Archie) “Jesus was Jewish!”
          Archie; “Yeah, but only on His Mother’s side…”

  15. Darwin often gets accused (eg by Ernst Mayr) of not having a theory of speciation. This isn’t really fair. He didn’t think reproductive isolation was essential to defining species, because he was aware of many cases of hybridization across species lines. But he did think there is a puzzle of why natural variation seems so often to come in discrete lumps rather than smooth continua, e,g species A here, species B there, with only a narrow hybrid zone in between. His proposed solution was that there is a positive feedback between population size and rate of evolution, because favorable variants are more likely in large populations (a point made by Cochran and Harpending discussing accelerated human evolution with the Agricultural Revolution).

    From Origin of Species, Chapter 6:
    During the process of modification, by which two varieties are perfected into two distinct species, the two which exist in larger numbers … will have a great advantage over the intermediate variety, which exists in smaller numbers in a narrow and intermediate zone. For forms existing in larger numbers will always have a better chance … of presenting further favourable variations for natural selection to seize on, than will the rarer forms which exist in lesser numbers. Hence, the more common forms, in the race for life, will tend to beat and supplant the less common forms, for these will be more slowly modified and improved.

    In other words, he thought that hybrid zones were likely to be population sinks.

    Here’s me from my blog with further thoughts:

  16. David Chamberlin says:

    Both anatomically modern man and Neanderthals rarely bred with Denisovans with one exception, Melanesia. I wonder why.

  17. J says:

    The reduced fitness of Homo hybrids may have been caused by zygotic incompatibility, and by sexual selection. Each population has its ideal male and females avoid getting pregnant by strangely looking males.

  18. Samo Burja says:

    What kind of population sink do you think it might be?

  19. A Layman says:

    if not, the two groups could not have accumulated lots of neutral-genome differences, which they did.

    How is it authoritatively known that the differences were in fact neutral?

    Googling, I came across:

    With regard to the ‘The “neutralist–selectionist” debate’ section: I take it you view evidence for the neutralist side as compelling?

    Over the time frame of a few thousand years*, would highly-intensified selection in certain genome areas (based e.g., on the after-effects of encountering closely related species and their new pathogens) swamp (i.e. postpone/minimize) selection on slightly deleterious mutations, thus making those mutations appear neutral (when in actuality they were not)?

    *Time frame proposed based on how long it took lactose tolerance to reach near-fixation in Euros. I understand this is considered a rather dramatic selective effect.

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