Pygmies: Among the world’s most isolated peoples, or archaic hominin admixture?

Pygmies are interesting because:

1. They’re the world’s shortest peoples

2. They’re rainforest hunter-gatherers

3. They appear to have split off from the rest of humanity and have been relatively isolated for longer than almost anyone else on Earth.

4. They’re getting wiped out by their neighbors, so we’d better learn about them now.

First, Who are the Pygmies?

“Pygmy” does not refer (as far as we know) to one specific ethnic group, but to the members of any ethnic group in which adult men are, on average, 4’11” or shorter. In practice, people tend to only use the word Pygmy to refer to certain African groups; there are short-statured groups found outside of Africa, but we’ll discuss them in another post.

The principle African Pygmies are the Aka, Baka, Mbuti, and Twa. (Some countries and groups use different name; I am not an expert on Pygmies, so I’m sure there is much I’ve missed.) The Mbuti are probably the shortest, with an average height under 4’6″. There are about 250,000 to 600,000 Pygmies, scattered about the Congo rainforest:

Locations of some Pygmy groups
Locations of some Pygmy groups

We’ve known for a while that the Pygmies–especially the Mbuti Pygmies–and their more southerly neighbors, the San, appear to be the most genetically divergent people on Earth:

Average age of SNPs in different populations, from West Hunter
Average age of SNPs in different populations, from West Hunter

You might have to squint, but the Pygmies and San are on the far right.

In normal English, what does this mean? Here is my understanding:

There are parts of your (our) genome where random mutations won’t generally kill you. Random mutations tend, therefore, to accumulate there. Since have some pretty decent estimates for how often random mutations occur, comparing the mutations in two different populations lets us estimate how long ago they split. For example, let’s suppose you get one random mutation per hundred years, and we’re comparing two populations that split 300 years ago and haven’t seen each other since. Population A should have gotten 3 mutations during that 300 years, and Population B should have gotten 3 mutations. So if we look at a third population, C, and find that they have 5 mutations that they don’t share with A or B, then we conclude that C split off from some ancestral population 500 years ago. We can reconstruct this as: 600 years ago, there was a group called ABC, but 500 years ago, it split into Group AB and Group C. 300 years ago, Group AB split into Group A and Group B.

Anatomically Modern Humans (that is, Homo Sapiens Sapiens,) according to our best estimates, emerged around 200,000 years ago in central Africa. We’re used to talking about the Out of Africa event, when humans started wandering around the rest of the globe, but it looks like the first major migration event might have been toward the south:

Map of early diversification of modern humans according to mitochondrial population genetics
Map of early diversification of modern humans according to mitochondrial population genetics, from Wikipedia

Those guys who went south (Pygmies, Bushmen aka San,) look like they’ve been isolated down there for an awfully long time–much longer than, say, the Australian Aborigines, who got to Australia about 50,000 years ago.

A recent paper by PingHsun Hsieh et al, “Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection,” describes the results of sequencing 4 Biaka Pygmy genomes and comparing them to 3 Baka Pygmy and 9 Yoruba genomes. (The Yoruba are farmers.)

“Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested.”

That’s a long time ago!

(“Bi-directional asymmetric gene-flow” means that they have occasionally inter-married, but not equal numbers of men and women.)

BUT, and this is where I get speculative and may be saying things that a real scientist would tell me are just dumb, what if the Pygmies (and San) actually split off more recently, and just picked up some archaic hominin DNA on their way south?

It’s not so far-fetched an idea. Everyone outside of Sub-Sharan Africa seems to have some Neanderthal DNA, picked up around the time their ancestors left Africa (Northern Africa has had a lot of mixing with non-African populations over the years, so I assume North Africans have Neanderthal DNA, too.) Melanesians (eg, guys from Papua New Guinea and a bunch of tiny Pacific Islands,) and Australian Aborigines are about 4%-6% Denisovan, but it looks like no one else is. Wikipedia article on archaic admixture.

Less is known about potential hominin admixture in Sub-Saharan populations. This may just be because we’ve sequenced far more European genomes and all sorts of remains tend to rot really quickly in the rainforest, making it hard to uncover any archaic DNA to compare modern humans to. However, I can’t help but think that few scientists wanted to be the guy who announced archaic hominin admixture in Sub-Saharan Africans before it was announced in Europeans. That seems like the kind of finding that could quickly get your department defunded, not to mention a lot of people mad at you and a ton of nonsense on the internet.

But with archaic admixture showing up all over the place, no one need worry about the political implications anymore, and science can get on with its business.

So, anyway, what if, on their way into the rainforest, the Pygmies’ ancestors encountered–and bred with–some other group of archaic hominins? (No, not chimps or gorillas–they have a different number of chromosomes than we do, so you couldn’t get viable offspring with them, similar to how mules are infertile.) They would have been more like Neandearthals, though obviously probably shorter.

It seems to me that a more recent divergence from other human groups + archaic admixture could result in a similar number of different genetic mutations as a much more ancient divergence + no admixture.

It also seems like you could have a third scenario: Pygmies (and San) have experienced recent selective pressure on parts of their genomes that no one else has. Maybe the parts of the genome that for everyone else have been just been accumulating random mutations have been important for the recent evolution of the San and Pygmy peoples, and so they’ve been accumulating changes faster than everyone else.


At any rate, the Pygmies are still genetically unique among humans.

Unfortunately, the Pygmies are not doing so well. The Batwa got kicked out of their homes in order to make a gorilla reserve. As hunter gatherers with no title deeds to the land they lived on, the government (Uganda) didn’t bother to give them new land or homes. In other words, the Batwa Pygmies were treated worse than the gorillas. (Today, some NGOs have helped the Batwa get new land and set them up as a living ethno-theme park for tourists, which I guess isn’t the worst fate in the world.)

The Bantus (who, despite living in Africa, are probably more closely related to Koreans than Pygmies,) use the Pygmies as slaves.

The Congolese (Democratic Republic of the Congo) have been literally eating the Pygmies, especially the Mbuti Pygmies, whom they regard as sub-human. Astoundingly, one of the reasons cited for genocidal cannibalism is that they want to open up Pygmy lands for mineral exploitation.

70,000 Pygmies have been killed in the civil wars in the DRC and Rwanda.

While I caution against idolizing the Pygmy villages as non-violent Edens (I have no idea what their violence rates are, but past experience suggests that it’s probably actually pretty high,) at least they aren’t cannibals. The Pygmies are smaller than everyone else and have only stone-age technology, so they tend to get defeated easily.

Pretty soon, there might not be any Pygmies left to talk about.

Some photos:

Pygmy village
Pygmy village


Women of the Batwa Pygmies
Women of the Batwa Pygmies


Batwa Pygmies
Batwa Pygmies singing and dancing

11 thoughts on “Pygmies: Among the world’s most isolated peoples, or archaic hominin admixture?

  1. […] Child-Rearing Norms vs. African American Norms, The Genghis Khans of Europe, Germans, (Gypsies), Pygmies: Among the world’s most isolated peoples, or archaic hominin admixture? Are the Pygmies Retarded? Some Notable Nigerians, Into Africa: The Great Bantu Migration, Why do […]


  2. You said “The Bantus (who, despite living in Africa, are probably more closely related to Koreans than Pygmies”. Explain, please.


    • Sure. I understand it’s not exactly intuitive.
      Modern humans evolved in Africa about 200,000 years ago. This initial group then split in two around 90,000 to 150,000 years ago, with the Pygmies and Bushmen heading south and the other group heading north. Everyone else on earth is descended from the other group. About 70,000 years ago, the other group split when part of it left Africa. So the Bantus and Koreans share a common ancestor about 70,000 years ago, whereas the Bantus and Pygmies share a common ancestor about 100,000 years ago.

      If you think of it in terms of a family, you and your siblings share a common ancestor one generation back–your parents–while you *and* your siblings share a common ancestor 2 generations back with your cousins. Bantus and Koreans here are like siblings, while Pygmies are like cousins.

      Of course, since the Bantus moved back into Pygmy/Bushmen territory over the past 3,000 years, there are now populations that are fairly mixed.

      Hope that helps!

      Liked by 1 person

  3. […] Mainly because Mbuti are the smallest Pygmies, with height in that region being correlated with Pygmy ancestry versus Bantu, and Biaka pygmies have been shown to be only 18.5% to 30% “pygmy”, if assuming Mbutis are pure and Bantus are the outside group. Though the latter point explains the overall association they have with West Africans, there is still the remote position of the Mbuti. According to Cavalli Sforza, the San and Bushmen don’t necessarily share a particularly close relationship but both their lifestyles and apparent divergence from Bantus makes the idea rather convincing. […]


  4. Nice article and interesting pictures. The theory that instead of an early divergence there could be admixture with hominids, a comment. Some Africans had admixture with early hominids, I do not remember if it was Pygmis. But the early divergence is shown not by aDNA but best by Y-DBA and mtDNA. The base types Y-DNA A, next B, and the base mtDNA L0 are at these groups Khoisan and Pygmi. For timing one uses nonsense parts of DNA, which do not code proteins and therefore cannot be under selection, so higher selection of some genes does not influence timing. But timing by DNA is still uncertain and the mutation rates are different for different parts and may not be stable if the environment changes.

    thanks for the article

    Liked by 1 person

  5. Since I was unable to edit my message submitted earlier today, here is some additional information.

    Here is the video pertaining to my message. Please watch the talk by Michael Hammer (Univ of Arizona) on ‘Interbreeding with Archaic Humans in Africa’. The main information begins around 30:53 and ends around 35:50 that discusses an African tribe interbreeding with ‘archaic’ humans approx. 35,000 years ago:

    Video: Human Origins ~ Interbreeding Within and Outside of Africa Fossils Modern Humans

    Liked by 1 person

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