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Not Separate, But Not Equal

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Human Brangle

A new paper in Nature fleshes out some details about the relationships between Denisovans, Neanderthals, and modern humans, as well as possible others. I believe the figure above gives the flavor of the general findings in terms of phylogenetics, though if you want more I recommend Carl Zimmer in The New York Times. It has to be noted that it’s incredible that such high resolution sequencing could be done on these ancient fossils, when ~10 years ago we were excited about one modern genome. Also, I am struck by, though not surprised, that it doesn’t seem to be that modern humans (our lineage) had too many distinctive major genetic differences from our cousins. Finally, it does seem that the human phylogeny is more properly defined as a graph than a tree. But don’t forget that it doesn’t seem like all the edges were weighted the same. We’re a whole lot more Neo-African than we are Neanderthal or Denisovan.

• Category: Science • Tags: Evolution, Human Evolution 

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  1. That pretty figure leaves out the recent finding that, apparently, progenitors of modern humans had gene flow with Eurasian heidelbergensis/ Neanderthals that resulted in the latter to have a shared mtDNA branch, but not the former (closely aligned with Denisovans, instead).

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  2. The latest Neandertal DNA showing a high level of inbreeding has me wondering if this may have played a major role in why anatomically modern humans won out.

    Look at what we’re aware of inbreeding causing. Lower intelligence. Smaller height. Reduced fertility. More miscarriages and deaths in infancy. Slower growth rates. Weaker immune systems. More genetic disorders. All of these are deleterious to survival and reproduction. Eventually in some isolated species (like island populations) the worst traits get bred out through natural selection, but notably this merely means the population is good enough to survive in the absence of competition. It says nothing about fitness overall – and indeed insular populations, all things considered, are far less resilient to changes than mainland populations.

    I could see a scenario where repeated waves of hominin expansion leave Africa. As they move into less productive climates, population density drops considerably. Eventually the individual bands may be so distant from one another that regular outbreeding becomes impossible (either because no one else is nearby, or the neighbors are so culturally alien). The populations manage to eke on – for a time. But when non-inbreed populations come into conflict with them, they inevitably win, and either annihilate the latter or push them to the margins.

    The “Great Leap Forward” of cultural modernity might even be partially a response to the end of widespread inbreeding. Perhaps populations in Africa genetically admixed to a large degree, resulting in hybrid vigor – a new group of geniuses. But they were in favorable enough environmental conditions they could spread far and achieve higher densities, which got them out of the winnowing trap which caused earlier human populations to decline into inbrededness. Once a critical mass of normal intelligence, healthy people established itself, cultural innovations began to be spread through the realm, which only deepened the ability to achieve high (for a hunter-gatherer) populations.

  3. This seems congruent with the finding that mtDNA from Sima de los Huesos clades with Denisovan mtDNA. Just swap “potential unknown hominin” with “Homo heidelbergensis” (or however you classify the Sima de los Huesos specimens).

    Of course the picture could be more complicated — are they working on getting nDNA from Sima de los Huesos?

  4. Why is the Denisovan introgression into Asians considered distinct from the introgression into Oceanians? Isn’t it possible that there was one period where ancestors of Asians and Oceanians mixed with Denisovans, and that Denisovan DNA was later swamped out on the mainland more than in Oceania?

  5. Whatever happened to the RRM2P4 pseudogene stuff which may hint at some additional archaic admixture in East Asians? Is it part of the Denisova?

  6. “The latest Neandertal DNA showing a high level of inbreeding has me wondering if this may have played a major role in why anatomically modern humans won out.”

    The Altai Neanderthal specimen would have been at the very farthest fringe of the Neanderthal range, not so many thousands of years before Neanderthals went extinct. The European Neanderthal DNA samples imply an effective population size that while small was no where near incestuous. The inbreeding in this sample was probably because they were a tiny relict or exiled population, something that may have been as much of an effect as a cause of the decline of the European Neanderthals.

  7. How possible is it still that the supposed Denisovan introgression really represents an introgression from H. Floresiensis? This seems very plausible on a right-place/right-time basis.

    I could imagine the Denisova remains being a mixture of late Heidelbergensis, Neanderthals, and Asian Erectus, while the Floresiensis would be (mostly) independently derived from Asian Erectus. This doesn’t seem completely crazy to me, since the branching between the Denisova genome and the Denisova related introgression in Oceanians seems quite deep (paper says 276000-403000 years.) With a branching that deep it doesn’t seem like there’d be much linking D.I with Denisova (to the exlusion of ordinary Neanderthals, which seems to have mixed with everything) other than the shared introgression of the mystery hominin.

  8. Ray,

    I partially addressed that at Dienekes’ blog, because I had a similar suspicion that perceived Neanderthal admixture into humans is really (or partially) W Eurasian heidelbergensis. 276–403ky (138-202ky with the higher mutation rate, which IMO here fits better for numerous reasons) is actually a good fit for heidelbergensis, but a very poor one for Asian erectus. This paper thus is consistent with Denisovans being part of the heidelbergensis branch – which their mtDNA appears to indicate, as well.

    On a grand scale, it seems Neanderthals and Denisovans aren’t really all that far removed, and where they are, the authors could quantify this as additional introgression from another hominin (likely Asian erectus). Also their Neanderthal contribution could be quantified. In other words, the Denisovan genome seems to be too well-defined to allow its measured introgression into Asian populations to be caused by yet another, substantially different hominin.

  9. “How possible is it still that the supposed Denisovan introgression really represents an introgression from H. Floresiensis? This seems very plausible on a right-place/right-time basis.”

    Given that we have no ancient H. Floresiensis DNA, it is entirely possible. Despite the fact that they are very different morphologically from Erectus or Heidelbergensis or Neanderthals, there are modern human populations that differ profoundly in appearance despite even living reasonably close to each other geographically (e.g. African Pygmies v. Maasi Nilo-Saharans) who are reasonably similar genetically (e.g. both of those groups would be on the African rather than Eurasian side of the k=2 divide within modern human autosomal DNA).

    My personal belief is that H. Heidelbergensis

    The hard question is whether (1) the Denisovan DNA was once widespread in mainland Asia from Siberia to Indonesia, or (2) was instead always in isolated niches and islands distinct from the dominant Erectus derived population of Asia.

    The former scenario (i.e. scenario (1)) would require subsequent dilution of first contact modern human populations on the mainland by later waves by a factor of about 40 with a large part of that dilution taking place at the time of a second wave sometime towards the early end of a the period between 45 kya and 20 kya or so – for example, if humans who had domesticated dogs had a decisive edge for a while over first wave modern humans who had not. This is because the estimated original admixture rate of Denisovans and Melanesians was about 8%. So, the 0.2% Denisovan trace in modern mainland Asians could be consistent either with massive dilution over multiple waves that had no archaic Denisovan admixture, or with back migration from Melanesian populations, e.g. via the Austronesians. But, the apparent lack of difference in Denisovan admixture between modern Asian populations that probably represent different waves of modern human migration into Asia, however, suggests that this dilution was front-loaded.

    The latter scenario (i.e. scenario (2)), would fit what I think of as a Heidelbergensis exile scenario, in which Neanderthals emerge in Heidelbergensis’s European homeland and drive Heidelbergensis out to Asia in folk migrations that take some to Siberia by a Northern route and others to marginal niche habitats in Asia by a Southern route that are unfavorable to H. Erectus but which more intellectually advanced Heidelbergensis either can’t survive in or can’t get to (e.g. Siberia and Flores) – because exiled Heidelbergensis are unable to displace already well established and locally adapted H. Erectus in their prime habitats.

    In a variant on the Heidelbergensis exile scenario, Heidelbergensis emerges in Europe and displaces Erectus there, and then expands until they encounter biogeographic barriers and well established H. Erectus populations. They end up again in scattered niches which H. Erectus can’t thrive in or can’t get to (e.g. Siberia and Flores). This scenario looks like the first archaeologically, but puts Heidelbergensis presence in Asia several hundreds of thousands of years earlier than the latter scenario. Of course, the possibilities aren’t inconsistent. Flores, e.g., might be settled in an initial Heidelbergensis expansion ca. 800,000 years ago, while the Siberian Denisovans might have migrated ca. 200,000-300,000 in the face of displacement by Neanderthals (whose presence in West Asia might have rendered the Southern route no longer viable as a Heidelbergensis exile route).

    We have be able to resolve the relatively likelihood of these three scenarios soon. A good estimate of Denisovan admixture in the Japanese might be helpful in understanding the facts – if Jomon peopels had none, it should be about half of the Chinese level. If Jomon people had similar amounts to later East Asian waves, the Japanese should have about the same level of Denisovan admixture as the Chinese. Similarly, one would expect elevated Denisovan admixture in SE Asian Negritos if there was mainland Denisovan admixture but below average Denisovan admixture in SE Asian Negritos if back migration accounts for the levels seen in mainland Asia.

    The Denisovan Siberia remains at 40,000 kya favor a Heidelbergensis exile scenario. The Flores investigators claim stone tool from 800 kya on Flores in continuity with the later skeletal remains of H. Floresiensis, which favor an expansion around the time of Heidelbergensis’s appearance in the archaeological record as part of an initial expansion.

    The archaeological evidence available to date IMHO favors an isolated niche expansion of Heidelbergensis over a widespread mainland Asian distribution, because the hominin tool remains from Asia show a much more static Acheulean industry than areas where Heidelbergensis thrived. But, given the fact that hominins don’t really seem to advance beyond the Acheulean until Neanderthals and modern humans (who may share a common ancestor more recent than Heidelbergensis), this may not count for much and the hominin skeletal fossil record from mainland Asia from ca. 800kya to 100kya is very thin, it would be easy to miss something. Fortunately, a lot of this gap probably has more do with less intense exploration for geopolitical reasons rather than purely for preservation condition issues, so it isn’t unreasonable to home that this could change in the next couple of decades as more exploration is conducted.

  10. Oops. Where I started “My personal belief is that H. Heidelbergensis . . .” I meant to say “My personal belief is that H. Heidelbergensis is indeed the ancestor of H. Floresiensis, and is also an ancestor of an ancestor of the Denisovans who later in turn admixed with Neanderthals in Central Asia or Siberia. But, that neither were very widespread in mainland Asia, occupying only marginal habitats and not displacing or replacing H. Erectus in Asia.” But, I hit the delete button my accident and then the post button in quick succession.

  11. Eurologist: “276–403ky (138-202ky with the higher mutation rate, which IMO here fits better for numerous reasons) is actually a good fit for heidelbergensis, but a very poor one for Asian erectus.”

    Just to be clear: In my speculative scenario, The distinctiveness (from Neanderthals) of both Denisova and D.I. would largely be explained by independent introgression events from populations derived from Asian Erectus. So the 276-403ky number, if anything, would represent the split time between H. Floresiensis and whatever Erectus-derived population contributed to the ancestry of the remains at Denisova. This doesn’t seem that implausible to me, since we’re not talking about the Erectus/Heidelbergensis split time, which I agree is likely to go further back than 400ky, but rather the time when Floresiensis became distinctive from the Erectus populations on the mainland.

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