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inferred effective population size over time

inferred effective population size over time

600px-Namibian_Bushmen_Girls The Khoisan are not the oldest people on the face of this earth, they simply have been the lest impinged by population crashes over the past ~200,000 years. This is not a shocking assertion, but it is supported with greater robustness by a new paper in Nature Communications, Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Unfortunately the standard tropes that come to the fore whenever the Khoisan are the objects of genetic scrutiny have emerged fully formed. But the worst problem is that one of the authors seems to be contributing to the misleading perceptions. Here are the press release

“Khoisan hunter/gatherers in Southern Africa have always perceived themselves as the oldest people,” said Prof Schuster, an NTU scientist at the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and a former Penn State University professor.

“Our study proves that they truly belong to one of mankind’s most ancient lineages, and these high quality genome sequences obtained from the tribesmen will help us better understand human population history, especially the understudied branch of mankind such as the Khoisan.

Though I think I know what Dr. Schuster is saying, I also believe that it is important remember that both you and I are also descendants of one of mankind’s most “ancient lineages.” We’re all equally descended from ancient lineages, because we’re all descended from ancient proto-humans. The Khoisan are not fossils preserved from a bygone age, they’re a modern people who descend from those same archaic Africans that we descend from. The phylogenetic distinction of the Khoisan is that their ancestors seem to have diverged from other human beings rather early on. In fact, it is defensible to suggest that they departed from the family tree of other humans at the first fork in the road, with the ancestors of Nilotic and Bantu Africans separating from the ancestors of Eurasians rather later on (also, it seems that the lineage that led up to the Khoisan after their divergence from the proto-non-Africans/agriculturalist Africans diversified and are represented by the Hadza and Pygmies, in addition to the Khoisan).

So what is the figure at the top of this post telling us? It’s showing you the effective population in the past by using the variation within the genome of individuals. In any given generation only a fraction of the population reproduces, and among the fraction which reproduces there is variation in output (e.g., some have one offspring live to adulthood, others have four). This increases random genetic drift by reducing population size and increasing variance of the sampling outcome. Drift tends to remove variation as some alleles fix and others go extinct due to the fluctuations that it produces. What happens when populations go through a bottleneck is that a lot of the variation that was present in a population can be squeezed out of it, and it takes a long time for that variation to replenish itself through mutation alone. This is why the long term effective population of the Khoisan is so much larger than the Han Chinese, despite there being four orders of magnitude more Han Chinese in the world today than Khoisan. As you can see in the figure the Khoisan were not subject to nearly as strong a bottleneck in the past. The small long term effective population size of non-Africans, reflected in their relative genetic homogeneity in comparison to Africans, is due to the bottlenecks that occurred as the ancestors of non-Africans were migrating across the world. About ~30,000 years ago the effective population of the Khoisan was ~10,000, while that of the ancestors of Eurasians was ~1,000. Both groups were going through a bottleneck, but the proto-Eurasians were experiencing a much stronger one. The ancestors of agriculturalist Africans, the vast majority of Sub-Saharan Africans today, were also experiencing a bottleneck, but a milder one.

One major caveat with the time scale above is that it is sensitive to the mutational rate. The figure above uses ~2.5 X 10-8 value, while some estimates are close to ~1.25 X 10-8. Though the authors brush this problem off, arguing that paleoclimate models can fit both parameter values in terms of explanations for the demographic patterns, from what I know the paleonathropology more neatly fits the dates from the higher mutation rate. With the lower value the divergence between Khoisan and non-Khoisan is almost contemporaneous with the first fossil evidence of anatomically modern H. sapiens in Africa. But it is true that in either scenario non-Africans are subject to a strong bottleneck, long evident from the genetic data, and that the Khoisan have relatively large long term effective populations.

To put my cards on the table I do not accept the paleoclimatic explanation for why the Khoisan in particular had a large population while the ancestors of agriculturalist Africans and non-Africans did not. First, in Science Pontus Skoglund observes that “Many African populations are not included for comparison….” Yes. He also points out that the Khoisan could have gotten their diversity from interbreeding, something that has support in the literature. That being said, that’s not my biggest problem with the explanatory model outlined in the paper. In the blog post yesterday I reviewed results which imply that the Igbo of Nigeria have some admixture from a hunter-gatherer group genetically closer to the Khoisan than to to the Pygmies. This is peculiar because geographically the Igbo are far closer to the Pygmy populations. So what’s going on here?

Human populations move. Paleoclimate models are often predicated on the idea that populations were geographically fixed for eons. But there’s a fair amount of circumstantial evidence that Khoisan-like people were extant as far north as Ethiopia in the recent past. The major element of the ancestry of the Bantu speaking majority in South Africa was resident in Cameroon ~3,000 years ago. A hybrid Eurasian-Sub-Saharan African populations in the highlands of Ethiopia only emerged in the past 3,000 years. And so on. We don’t know that the ancestors of agriculturalist Africans were resident in the northern fringe of Sub-Saharan African ~100,000 years ago. We don’t if the ancestors of the modern Khoisan have such deep time history in southern Africa.

In light of evidence of Eurasian back-migration into Sub-Saharan Africa in deep antiquity it is quite reasonable to suggest that the intermediate population dynamics of the agricultural Sub-Saharan populations in this paper is simply due to the fact that they are a hybrid between long resident hunter-gatherer populations with some affinity with Khoisan and Pygmies, and descendants of the original Out of Africa migration. The blogger Dienekes Pontikos has been proposing a flavor of this model for a long time. Initially I thought it was a cranky fixation of his which had little basis in reality, but over the years I’ve come around to the position that it’s a plausible theory. At least as plausible as the myriad attempts to reconcile genetic patterns with paleoclimate models.

Citation: Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.

• Category: Science • Tags: African Genetics 
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  1. Why would they use that mutation rate? No actual measurement comes close to agreeing with it.

  2. #1, i’m wondering if a constant mutation rate assumption is robust.

  3. I see you describe that figure as using a mutation rate of 2.5 ^ -8. Do you actually mean 2.5 ^ -8 (~0.000655), or 2.5 * 10^-8 (0.000000025), and if it’s the second one, does my browser have a display issue I should be looking into?

  4. With the 5-6 papers currently published on human mutation rate tending towards a rate of around 1.2E-08 having derived this rate from hundreds of Trios using several different methodologies. I find it odd that papers such as this continue to use a much higher mutation rate.
    Scally & Durbin’s ( ) look at the implications of this in 2012 seem to suggest that a lower rate is not incompatible with other evidence.

    Now there are still questions around the exact accuracy of the NGS studies (see Determinants of Mutation Rate Variation in the Human Germline, Ségurel et al 2014, though solving some of the problems might lower the rate further) and it is likely that either the mutation rate or generation time has changed over time. As such using a rate of 2.5E-08 without question has issues that should be discussed in more detail. As it seems to me that if they are assuming the average rate is 2.5E-08 and the current rate is 1.2E-08 then there must have been a time when the rate was higher than 2.5E-08 or that they believe the current rate is the result of a change in the very recent past.

  5. #3, typo. fixed. #4, i accept the lower pedigree estimate as being accurate. so yes, there has to be an explanation of what’s going on….

  6. The evolutionary biology theory around mutation rate also adds some interesting questions to this. If the mutation rate should evolve towards zero until it reaches the limits imposed by the increasing cost of lowering the rate further. Then the rate must have started higher and evolved downwards towards the current rate. But something must have allowed the initial high rate to evolve.
    Or if Lynch is correct and the minimal rate is limited by the effective population size and thus the power of genetic drift. Then the rate has likely fluctuated with each of the population bottlenecks that has occurred and the mutation rate may vary between human sub populations.

  7. #6, doesn’t seem to vary in the major world populations. i’ve seen pedigree analysis with good coverage genome with lots of samples from different groups. comes to 1.2 x 10^-8 all

  8. #7, most of the published studies I’ve seen had been within European populations. Have any of the studies your’ve seen had a decent numbers of Khoisan or Yoruban pedigrees in them?

    Also one other interesting thing is when we look at the pedigree based rates for Human, Chimpanzee and Cattle (Bos Taurus) they’re all very similar (within the margin of error of the human studies) even though the current effective population sizes for each differ noticeable (though how historical Ne varies I’m not sure).

  9. #8, ashg had a presentation with a huge sample which included lots of asians. i think african amerians too. same rate.

  10. The phylogenetic distinction of the Khoisan is that their ancestors seem to have diverged from other human beings rather early on.

    Based on the data here, do you think would it be correct in saying that it was actually the Afrasians who were the outgroup to the Khoisan, and not the reverse? Which would imply that somewhere other than East Africa would be the source of the first anatomically modern humans.

    Also, how likely do you think earlier back-to-Africa migrations are? IE other hominids crossing back into Africa in small numbers prior to or simultaneous to the emergence of anatomically modern humans.

  11. #10, yeah, close to what i have in mind.

  12. The out of Africa theory has penetrated so deeply into even the best minds that it appears to be impossible for the best minds to follow their own logic elsewhere. If Homo Erectus was present on three land masses one million years ago there is no reason to believe that he did not evolve differently on those land masses.

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