I just want to highlight this graph I came across yesterday while trying to research archaic introgression in the Igbo:


From Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations, by Lorente-Galdos et al.

There are three versions of this graph in the paper (check the supplemental materials for two of them), all showing about the same thing. It is supposed to be a graph of population size at different times in the past, and the most incredible thing is that for the past 100,000 years or so, the most numerically dominant populations in Africa were the Baka Pygmies, followed by various Bushmen (San) groups. The authors write:

To unravel the ancient demographic history of the African populations that are present in our data set, we used the Pairwise Sequentially Markovian Coalescent (PSMC) model that analyzes the dynamics of the effective population size over time [60]. We included at least one representative of each of the 15 African populations and two Eurasian samples in the analysis (Additional file 1: Figure S7.1) and considered both the classical mutation rate of 2.5 × 10−8 [61] and the 1.2 × 10−8 mutations per bp per generation reported in other analyses [6263]. The demographic trajectories of the sub-Saharan agriculturalist populations are very similar to each other; and only South African Bantu and Toubou individuals differ partly from the rest of sub-Saharan farmer samples; however, their considerable levels of admixture with other North African or hunter-gatherer populations (Fig. 2b) might explain this trend. Therefore, in order to ease visualization, we plotted a Yoruba individual (Yoruba_HGDP00936) and two Ju|‘hoansi individuals as representatives of the sub-Saharan agriculturalist and Khoisan populations, respectively (Fig. 3 and Additional file 1: Figure S7.2 considering a mutation rate of 1.2 × 10−8).

The authors note that the apparent large size of the pygmy groups could have been due to groups splitting and merging and thus getting more DNA variety than they would normally. It’s all very speculative. But still, the Baka Pygmies could have been the absolutely dominant group over central Africa for centuries.

What happened?


7 thoughts on “Pygmy-pocalypse?

  1. Here’s a theory: The Pygmies evolved small bodies to use less sodium, which is extremely scarce in a tropical rain forest. When the Bantus established trade routes to bring in salt from deserts and oceans, the Pygmies’ main survival advantage suddenly disappeared.

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  2. I don’t know much more than appears in this comment (actually, I know less — there may be errors here!), but Effective Population Size isn’t the same thing as, or even very similar to, a census count.

    This post by someone who is familiar with the concept points out an estimate for the effective population size of humans (everywhere) in 2012 at 10,000 people. It can’t increase very quickly because, although there are a lot more humans than that, they are mostly similar to each other, being descended from a bottleneck somewhere back in the past.

    And your graph shows basically the same thing; the y-axis is marked in units of ten thousand. The pygmies appear to shoot up to about 23,000 during the period you’re wondering about.

    One unit of Effective Population Size represents the amount of genetic diversity that would be present in one census individual of a population that mated at random, which actual humans don’t do. That’s why “pygmy tribes interbred with each other at the jump” is the explanation the authors suggest — that, and not census size, is what’s being measured by the statistic.

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  3. I have no doubt that all of the above as stated by Mr. Watts is true, but there is also evidence of a dramatic contraction of Pygmy and San territory as the great Bantu expansion began, and this trend has continued almost to the present day; the Mbuti Pygmies are almost extinct. I’d be surprised, knowing my fellow human beings, if this contraction of territory was not accompanied by a contraction of population. The two explanations are most certainly not mutually exclusive.

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  4. I first read about ‘The Forest People’ in Colin M. Turnbull’s 1974 book. I found it to be a fascinating perspective, although perhaps somewhat narrow, but I would recommend it.

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