The pruned tree

By Razib Khan | September 3, 2012 10:45 pm

Dienekes Pontikos has a long post up on how reticulation within phylogenetic trees may distort our perception of human natural history when we force the data into a more conventional tree (i.e., bifurcation after bifurcation). The concrete reason for this rethinking is the high probability of “archaic admixture” into the dominant genetic signal of anatomically modern African humanity, both within Africa and outside of it.

Dienekes proposes that when ancient DNA from early modern Eurasians is analyzed then a large portion of the portrait will be unmasked. For example, if high levels of admixture were present very early on then you would see very divergent regional populations because of persistence and continuity of local hominin population substructure. The pre-African Eurasians from each given region would have contributed substantially to the genetic makeup of the first modern humans who flourished in Europe and East Asia. On the other hand, if admixture was minimal, then the early Europeans and Asians would be far less distinct than their modern descents.

This is where I want to highlight one aspect of Dienekes’ model which is implicit, but I think needs to be strongly emphasized. The ancestors of modern Europeans and East Asians may not, and in fact I do not believe they are, predominantly descendants of the first settlers of Europe or East Asia. There are already hints of this as late as the Bronze Age, and I think it must have been substantial during the Ice Age as well. Perhaps less due to demographic replacement as meta-population dynamics, as local demes may have regularly gone extinct, so the “periphery” may have been settled more the denser “core” repeatedly.

A few years ago the model was that modern humanity replaced archaic lineages ~50,000 years ago. Part of that replacement was due to the emergence of ‘behavioral modernity,’ as distinct from ‘anatomical modernity,’ which predated the former by tens of thousands of years. That behavioral modernity was most clear in evidence in western Europe, in the artistic explosion of the early Upper Paleolithic. There is now a high probability that genetic contribution of these “First Europeans” is found only in residual levels across Europe.

The situation in eastern Asia is less clear in the archaeology, but I suspect similar dynamics are at play. Why? There is a strange result out of evolutionary genomics where the divergence between Europeans and East Asians post-dates the first settlement of these regions by moderns by 10-20 thousand years (depending on the result). My initial skepticism was toward the methods, because they were out of sync with archaeology. Now I suspect that there are two explanations. First, gene flow between these two regions is decreasing genetic distance, and the inferred time since the last common ancestor. Second, the first settlers may have had only a marginal genetic impact, in which case the archaeology remains valid, but not as relevant to the genetics.

MORE ABOUT: Human Evolution

Comments (8)

  1. There is a strange result out of evolutionary genomics where the divergence between Europeans and East Asians post-dates the first settlement of these regions by moderns by 10-20 thousand years (depending on the result)

    IMO almost entirely due to using a 2.5×10-8/b/generation mutation rate.

    The fast rate leads to recent splits between Europeans and East Asians, 60ky Out-of-Africa and Neandertals-Humans “splitting” hundreds of thousands of years after the appearance of Neandertal traits in Atapuerca.

    The slow rate (it’s unclear yet how slow it will eventually be) will make European East Asian split at the same time as the appearance of UP Europeans and modern humans in East, Asia, Out-of-Africa pre-100ka, and will also harmonize with the evidence for the appearance of the Neandertal lineage.

  2. I think that a tree as the one you post is simply impossible or most unlikely.

    First: there should always be a remnant, available for us to detect. If someone as extremely distant as Neanderthals or H. erectus (totally different species, even if remotely related) left a remnant, “Aurignacians” must have done as well and we shoul be able to detect it in the current genomes of at least Europe.

    Second: Neolithic is clearly overrated. Early Neolithic was surely less productive than Epipaleolithic and it’d take quite a time to reach levels of effectivity when it would be clearly superior, by then the Neolithic was widespread in much if not all Europe, albeit still with major importance of hunting and gathering.

    Also “behavioral modernity” is totally overrated. Almost always someone talks of “behavioral modernity” next says “God”, go figure! As if being superstitious would be a sign of cleverness, c’mon!

    Incidentally now we know that archaeological evidence of “behavioral modernity” long pre-dates Aurignacian and is found all around the World.

  3. Actually, I don’t know which post you are referring to. In my two latest posts


    I am actually talking about different things. In [2], I am arguing that populations may have grown closer over time due to gene flow: modern humans may have emerged out of the mixing of very divergent archaics that left all living humans very homogeneous but with a little regional-specific archaic admixture remaining on the margins. In [1], I am saying that greater archaic admixture in ancient H. sapiens (*cough* Oetzi) may in part be a technical artifact of the fact that they’re older.

    I like to argue both sides of the fence, because I really have no idea what actually happened. More data is needed.

  4. I would amplify this for East/Southeast Asia, where we have additionally to explain the lack of substantial Denisovan ancestry in present peoples.

    I agree with Dienekes that the slow mutation rate will push things back, but we will still have a discordance between early modern settlement in South and Southeast Asia and that in Europe.

  5. #2, you basically misunderstood lots of points of my post by being too literal. language barrier i’d guess.

  6. iron0037

    Maybe a better diagram than a tree would be a branching river. Each branch would be a different color. The width of the branch would represent the population size. There could be straight-lined “canals” representing periods of time where admixture is thought to have occurred. Of course, the canals can offer bidirectional flow…

    Forgive my uneducated, layman’s perspective, but perhaps you could clear something up for me. Why is that we find small percentages of Y chromosomes and mitochondrial DNA from early human settlers in modern populations, and yet we find no such markers from Neanderthals and Denisovans? Is it assumed that genetic drift has wiped them from our collective genome? If that’s the case, then why hasn’t genetic drift eliminated all genetic evidence? How does this 4% Neanderthal in us linger?

  7. #6, three was meant to be coarse. i was in a hurry 😉 but yeah, i think the ‘bush’ is really a ‘bramble.’

    re: Y & mtdna

    1) sex biased admixture. so denisovan male + modern female = no denisovan mtDNA. then imagine that hybrids are attacked by moderns, who kidnap hybrid females. then no denisovan Y left.

    2) selection, so that the markers are not neutral and representative of overall genealogy.

    3) y & mtdna turnover faster because of smaller effective pop sizes. so you ‘coalesce’ back to a common ancestor, and exclude the others. if the time depth is shallow there’s a high probability that you’re going to miss most lineages, and if there was a population size skew, no surprise if low number archaic lines go extinct

  8. Mark D

    If people insist on using trees, let me suggest the Banyan of which you may be familiar.


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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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