Bantus, Pygmies, and Ghosts

 

Aka Pygmy Father and child, from “Why the Aka Pygmy People of Africa have the ‘best dads in the world‘”.

A paper has just been released on the first ancient DNA recovered from central African burials: Ancient West African Foragers in the Context of African Population History, by Lipson, Ribot, Reich, et al. This is exciting news because our ancient genetic coverage of central Africa has been, until now, completely nonexistent. The local climate tends to degrade human remains quickly, making it difficult to recover DNA, and most genetics researchers don’t live in Africa.

Researchers have recovered the remains of four people, two from about 8,000 years ago and two from 3,000 years ago, buried in Shum Laka, Cameroon. (Cameroon is the country right in the big turn in the curve of Africa’s coast; Shum Laka has been inhabited by humans for about 30,000 years.) The really interesting part is the “ghost population,” which we’ll get to soon.

The burials turned out to be Pygmy people, not Bantus, despite the belief among linguists that Cameroon is the Bantu homeland. From the paper:

One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region^12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

And then we hit the paywall. Thankfully, Science Magazine has a summary.

The Bantu language group is a branch of the larger Niger-Congo language family, one of the biggest (along with Indo-European and Sino-Tibetan) language families in the world. Niger-Congo contains about 1,740 languages (depending on how you count) with 700 million speakers. The Bantu branch accounts for half of them, or 350 million people.

The Bantu branch has clearly undergone a massive expansion over the past 3,000 years. 4,000 years ago, central Africa belonged to the Pygmies, Bushmen, and their relations. Today, those populations are tattered remnants of their former empires; the Bantus are dominant. The Bantu expansion is thus one of the great conquering events of recent history, comparable to the Indo-European expansion. The size of the Pygmy and Bushman population has consequently collapsed, though at what speed, we don’t know.

The presence of a significant Pygmy population in the supposed Bantu homeland back when the Bantu speakers were gearing up to conquer a huge chunk of the Earth’s surface indicates that Cameroon might not actually be the Bantu homeland. Of course there are easy fixes to this theory, like “the region just to the west of Cameroon is the Bantu homeland” or “there are still Pygmies in Cameroon today; researchers just happened to find some Pygmies,” but I propose a different possibility: the Bantu homeland is in the Sahara.

Lake Megachad and its tributaries in blue; modern day Lake Chad in green

Yes, the Sahara is an enormous desert–today. Before 3,500 BC, the Sahara was significantly wetter. The Niger-Congo speakers started as agriculturalists who farm along the edge of the Sahara. During the African Humid Period, 3,500 years ago and before, much of the Sahara was green, full of plants and animals, flowing rivers and giant lakes. I propose that the Bantu homeland was in the vicinity of lake “Megachad,” which aside from having a great name, was an enormous lake in central Chad, overlapping the borders of Nigeria, Cameroon, and Niger, fed by a suitably extensive network of tributaries. Today, only remnants of the lake remain.

The drying of the Sahara and Lake Megachad turned the Bantu’s homeland to dust; just based on the African topography and modern rivers, they probably headed into northern Cameroon, eastern Nigeria, and the Central African Republic. The area of Cameroon where these pygmy skeletons have been found looks a little harder to get to, cut off from the north/east by highlands. This area may have therefore been a bit of a refugia during the Bantu expansion.

I think it is common for people to think of African populations as relatively homogeneous because it is the origin point from which humanity spread to Asia, Europe, Australia, the Americas, etc. But Africa isn’t a point. It’s big, and people spread out and wandered around Africa for thousands of years before some of them headed north.

The oldest extant human splits aren’t between Africans and non-Africans, but between Pygmies/Bushmen and everyone else. This split happened around 250,000 years ago. This was followed by more splits within Africa, like the one between West and East Africans about 150,000 years ago, and the out-of-Africa event about 70,000 years ago. Here’s a mostly-accurate tree diagram, Bushmen and Pygmies on the right:

(The big inaccuracy in this diagram is the yellow line representing Eurasian back-migration leaving genetic traces in modern Bushmen/Khoisan peoples. That never happened; the results turned out to be a computer error.)

Before the Bantu expansion, Pygmies and Bushmen were among the biggest ethnic groups on the planet. The extremely high Baka Pygmy population on this graph is probably partially due to high genetic diversity due to the merger of multiple long-separated groups rather than a massive Pygmy boom and then genocide, but I think it is still fair to conclude that relatives of today’s Pygmies and Bushmen once controlled most of central and southern Africa.

source

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.

(Today, the biggest ethnic group is the Han Chinese.)

From the Science article:

In the new study, geneticists and archaeologists took samples from the DNA-rich inner ear bones of the four children, who were buried 3000 and 8000 years ago at the famous archaeological site of Shum Laka. The researchers were able to sequence high-quality full genomes from two of the children and partial genomes from the other two. Comparing the sequences to those of living Africans, they found that the four children were distant cousins, and that all had inherited about one-third of their DNA from ancestors most closely related to the hunter-gatherers of western Central Africa. Another two-thirds of children’s DNA came from an ancient “basal” source in West Africa, including some from a “long lost ghost population of modern humans that we didn’t know about before,” says population geneticist David Reich of Harvard University, leader of the study.

I spent a while trying to figure out what this is saying, because it isn’t clear. First, I doubt they found that the 8,000 year olds were cousins to the 3,000 year olds. The notes in the extended data section of the paper claim to have found a nephew/aunt or niece/uncle relationship between two of the children; the other two were less closely related–possibly cousins.

This doesn’t tell us which skeletons they got the DNA from, but it turns out that one of the good ones was 8,000 years old.

The article claims that 1/3 of their DNA came from ancestors related to the [Aka] Pygmies and 2/3s from “basal West Africans”, who are also closely related to the modern Bantus.

This is confusing because it makes it sound like these children were a cross between Aka Pygmies and Bantus, and that the’re 2/3s Bantu, in which case they’d be more Bantu than Pygmy and this really wouldn’t upset the idea of Bantus in Cameroon.

From Extended Data 6: Deep Ancestry Correlation  “An allele-sharing statistic sensitive to ancestry that splits more deeply than southern African hunter-gatherers … is shown as a function of ancestry related to the West African clade (from admixture graph results; the Mota individual, Yoruba and Lemande are shifted slightly away from the boundaries for legibility).

The thing they didn’t say–and I only figured out from looking at the extended data–is that the modern Aka are not 100% “ancestral pygmy.” They are also part “basal West African.” (41% pygmy ancestor and 59% BWA, to be exact.) This is actually quite similar to the 1/3 and 2/3s found in the burials in Shum Laka. So there probably was an event where people related to modern Bantus mixed with an ancient Pygmy population, and their descendants include both the modern Aka Pygmies and the Shum Laka children. 

The Aka Pygmies now live near the border between Cameroon and the DRC. (The “ba-” suffix, found in names like Bantu, Baka, and Batswana, means “people,” so “Baka” just means “Aka People.” Batswana means “Tswana people;” “bo-” means land, so Botswana is “Land of the Tswana.”)

The Mbuti Pygmies, whom you have probably also heard of, live much further from the Cameroonian border and have less Bantu DNA. The Mbuti Pygmies average only 4’6″, while the Aka Pygmies average a couple more inches. The average Aka man stands about 4’11”; the women a little less. Don’t fall into the trap of thinking that the Aka aren’t “real pygmies”–they’re still very short by modern standards, and as this paper shows, the mixing that created them occurred over eight thousand years ago. The Aka have been a distinct ethnic group for an extremely long time.

People always ask why the Pygmies are so small, but I think this question is backward. Bushmen are also short (compared to Dinka and Norwegians); I think our common human ancestors were only about 5′ tall. The pygmies got a little shorter, yes, but not by much; the rest of us got taller.

Schematic of first alternative admixture graph, (the primary admixture graph is here; it is just a more complicated image)

Now, the really interesting thing in this paper is the identification of three “ghost” populations.

First we have the Ghost Archaic:

The Ghost Archaic was a species similar to Neanderthals, but in Africa. We don’t have any skeletal remains from this species because of the aforementioned climate difficulties, but its DNA shows up in groups like the Mende and Yoruba of West Africa. Here’s the relevant paper, Recovering Signals of Ghost Archaic Introgression in African Populations:

Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population 15 that diverged prior to the split of Neanderthals and modern humans.

That’s a lot of archaic! Since the populations with the highest rates of ghost archaic live in far West Africa, I assume the Ghost Archaic did, too.

Next we have the Ghost Modern, which I regretfully did not realize is different from the Ghost Archaic when I first wrote about it.

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:

Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. … Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.

The Ghost Archaics were in the genus Homo, just like Homo erectus, Homo Neanderthalis, but they were not Homo sapiens. The Ghost Moderns were Homo sapiens. They split off from the rest at about the same time the Pygmies, Bushmen, and everyone else went their separate ways.

The Ghost Moderns later contributed to the ancestors of the Niger-Congo people of West Africa and the Mota burial, a 4,000 year old burial from Ethiopia. A branch later split from the Niger-Congo people, creating the “Basal West Africans” and carrying the Ghost Modern DNA (and a bit of the Ghost Archaic) with it. That branch eventually contributed to the Aka Pygmies, including the children found at Shum Laka.

The third ghost population is the Ghost North African.

GNA split from the West Africans well before the Ghost Moderns, shortly after they had split with the East Africans. They appear to be related to the folks buried at Toforalt, Morocco.

I don’t know anything about the Ghost North Africans, but apparently they also contributed to the Shum Laka people. We’ll have to leave that question open for later.

Perhaps it is this infusion of “ghost” DNA into the ancestors of the Aka Pygmies that that accounts for their apparent enormous population size around 20,000 years ago. In this case, their population probably wasn’t actually enormous so much as it had a lot of genetic variation, caused by the merger of several different groups.

All of these Ghost populations used to be full ethnic groups (or species) in their own right, but today they exist only as a trace of DNA in modern people; they no longer exist as a group. These ghost populations were most likely killed off by other human groups or completely absorbed into them. The Ghost Moderns, for example, were probably finished off during the Bantu expansion.

(Let’s remember that all of these numbers are estimates based on the genetic data we have so far, which is not very much. The numbers could change quite a bit as we uncover more information.)

The final interesting thing was the “deeply divergent Y chromosome haplogroup A00,” found in one of the children. The authors did not look into mtDNA (passed down from mothers to children,) but did investigate local Y-chromosome diversity. A00 is estimated to be around 270,000 years old and is relatively common in Cameroon and, as far as I know, nowhere else. (The relevant Wikipedia page unfortunately contains an error, claiming that the Shum Laka children are most closely related to the Mbuti. They are, as the paper actually says, most closely related to the Aka.)

That’s all for now, but here are a few related things if you want to read more:

Some thoughts on the ancient West African forager genomes paper (Nature). The reality is even more complex, as the next tweet will show… pic.twitter.com/mSZUA9zUwz

— Chris Stringer (@ChrisStringer65) January 22, 2020

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection:

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. … Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. … We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Insights into the Demographic History of African Pygmies from Complete Mitochondrial Genomes:

To investigate the demographic history of Pygmy groups, a population approach was applied to the analysis of 205 complete mitochondrial DNA (mtDNA) sequences from ten central African populations. No sharing of maternal lineages was observed between the two Pygmy groups, with haplogroup L1c being characteristic of the Western group but most of Eastern Pygmy lineages falling into subclades of L0a, L2a, and L5. Demographic inferences based on Bayesian coalescent simulations point to an early split among the maternal ancestors of Pygmies and those of Bantu-speaking farmers (∼70,000 years ago [ya]). Evidence for population growth in the ancestors of Bantu-speaking farmers has been observed, starting ∼65,000 ya, well before the diffusion of Bantu languages. Subsequently, the effective population size of the ancestors of Pygmies remained constant over time and ∼27,000 ya, coincident with the Last Glacial Maximum, Eastern and Western Pygmies diverged, with evidence of subsequent migration only among the Western group and the Bantu-speaking farmers. Western Pygmies show signs of a recent bottleneck 4,000–650 ya, coincident with the diffusion of Bantu languages, whereas Eastern Pygmies seem to have experienced a more ancient decrease in population size (20,000–4,000 ya).

Western Pygmies, ie the Mbuti, were killed by the Bantus during the Bantu expansion of the past 3,000 years.

Eastern Pygmies, ie the Aka, probably experienced a genetic diversification event about 20,000 years ago that makes it look like their population was much bigger back then than it is now. Their population probably has dropped over the years, but probably not as precipitously as the data shows.

Steve Sailor’s summary:

As I mentioned yesterday, Carl Zimmer’s article in the New York Times on the new ancient DNA paper with its ho-hum title, Ancient DNA from West Africa Adds to Picture of Humans’ Rise, is a model of how to construct articles upside down to bore complacent NYT subscribers with the opening paragraphs before revealing the unsettling details toward the end. Carl doesn’t mention the word “pygmy” until his 18th paragraph and the word “ghost” until the 24th paragraph.

 

 

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When Did Black People Evolve?

In previous posts, we discussed the evolution of Whites and Asians, so today we’re taking a look at people from Sub-Saharan Africa.

Modern humans only left Africa about 100,000 to 70,000 yeas ago, and split into Asians and Caucasians around 40,000 years ago. Their modern appearances came later–white skin, light hair and light eyes, for example, only evolved in the past 20,000 and possibly within the past 10,000 years.

What about the Africans, or specifically, Sub-Saharans? (North Africans, like Tunisians and Moroccans, are in the Caucasian clade.) When did their phenotypes evolve?

The Sahara, an enormous desert about the size of the United States, is one of the world’s biggest, most ancient barriers to human travel. The genetic split between SSAs and non-SSAs, therefore, is one of the oldest and most substantial among human populations. But there are even older splits within Africa–some of the ancestors of today’s Pygmies and Bushmen may have split off from other Africans 200,000-300,000 years ago. We’re not sure, because the study of archaic African DNA is still in its infancy.

Some anthropologists refer to Bushmen as “gracile,” which means they are a little shorter than average Europeans and not stockily built

The Bushmen present an interesting case, because their skin is quite light (for Africans.) I prefer to call it golden. The nearby Damara of Namibia, by contrast, are one of the world’s darkest peoples. (The peoples of South Sudan, eg Malik Agar, may be darker, though.) The Pygmies are the world’s shortest peoples; the peoples of South Sudan, such as the Dinka and Shiluk, are among the world’s tallest.

Sub-Saharan Africa’s ethnic groups can be grouped, very broadly, into Bushmen, Pygmies, Bantus (aka Niger-Congo), Nilotics, and Afro-Asiatics. Bushmen and Pygmies are extremely small groups, while Bantus dominate the continent–about 85% of Sub Saharan Africans speak a language from the Niger-Congo family. The Afro-Asiatic groups, as their name implies, have had extensive contact with North Africa and the Middle East.

Most of America’s black population hails from West Africa–that is, the primarily Bantu region. The Bantus and similar-looking groups among the Nilotics and Afro-Asiatics (like the Hausa) are, therefore, have both Africa’s most iconic and most common phenotypes.

For the sake of this post, we are not interested in the evolution of traits common to all humans, such as bipedalism. We are only interested in those traits generally shared by most Sub-Saharans and generally not shared by people outside of Africa.

detailed map of African and Middle Eastern ethnicities in Haaks et al’s dataset

One striking trait is black hair: it is distinctively “curly” or “frizzy.” Chimps and gorrilas do not have curly hair. Neither do whites and Asians. (Whites and Asians, therefore, more closely resemble chimps in this regard.) Only Africans and a smattering of other equatorial peoples like Melanesians have frizzy hair.

Black skin is similarly distinct. Chimps, who live in the shaded forest and have fur, do not have high levels of melanin all over their bodies. While chimps naturally vary in skin tone, an unfortunate, hairless chimp is practically “white.”

Humans therefore probably evolved both black skin and frizzy hair at about the same time–when we came out of the shady forests and began running around on the much sunnier savannahs. Frizzy hair seems well-adapted to cooling–by standing on end, it lets air flow between the follicles–and of course melanin is protective from the sun’s rays. (And apparently, many of the lighter-skinned Bushmen suffer from skin cancer.)

Steatopygia also comes to mind, though I don’t know if anyone has studied its origins.

According to Wikipedia, additional traits common to Sub-Saharan Africans include:

In modern craniofacial anthropometry, Negroid describes features that typify skulls of black people. These include a broad and round nasal cavity; no dam or nasal sill; Quonset hut-shaped nasal bones; notable facial projection in the jaw and mouth area (prognathism); a rectangular-shaped palate; a square or rectangular eye orbit shape;^[21] a large interorbital distance; a more undulating supraorbital ridge;^[22] and large, megadontic teeth.^{[23] …}

Modern cross-analysis of osteological variables and genome-wide SNPs has identified specific genes, which control this craniofacial development. Of these genes, DCHS2, RUNX2, GLI3, PAX1 and PAX3 were found to determine nasal morphology, whereas EDAR impacts chin protrusion.^{[27] …}

Ashley Montagu lists “neotenous structural traits in which…Negroids [generally] differ from Caucasoids… flattish nose, flat root of the nose, narrower ears, narrower joints, frontal skull eminences, later closure of premaxillarysutures, less hairy, longer eyelashes, [and] cruciform pattern of second and third molars.”^[28]

The Wikipedia page on Dark Skin states:

As hominids gradually lost their fur (between 4.5 and 2 million years ago) to allow for better cooling through sweating, their naked and lightly pigmented skin was exposed to sunlight. In the tropics, natural selection favoured dark-skinned human populations as high levels of skin pigmentation protected against the harmful effects of sunlight. Indigenous populations’ skin reflectance (the amount of sunlight the skin reflects) and the actual UV radiation in a particular geographic area is highly correlated, which supports this idea. Genetic evidence also supports this notion, demonstrating that around 1.2 million years ago there was a strong evolutionary pressure which acted on the development of dark skin pigmentation in early members of the genus Homo.^[25]…

About 7 million years ago human and chimpanzee lineages diverged, and between 4.5 and 2 million years ago early humans moved out of rainforests to the savannas of East Africa.^[23][28] They not only had to cope with more intense sunlight but had to develop a better cooling system. …

Skin colour is a polygenic trait, which means that several different genes are involved in determining a specific phenotype. …

Data collected from studies on MC1R gene has shown that there is a lack of diversity in dark-skinned African samples in the allele of the gene compared to non-African populations. This is remarkable given that the number of polymorphisms for almost all genes in the human gene pool is greater in African samples than in any other geographic region. So, while the MC1Rf gene does not significantly contribute to variation in skin colour around the world, the allele found in high levels in African populations probably protects against UV radiation and was probably important in the evolution of dark skin.^[57][58]

Skin colour seems to vary mostly due to variations in a number of genes of large effect as well as several other genes of small effect (TYR, TYRP1, OCA2, SLC45A2, SLC24A5, MC1R, KITLG and SLC24A4). This does not take into account the effects of epistasis, which would probably increase the number of related genes.^[59] Variations in the SLC24A5 gene account for 20–25% of the variation between dark and light skinned populations of Africa,^[60] and appear to have arisen as recently as within the last 10,000 years.^[61] The Ala111Thr or rs1426654 polymorphism in the coding region of the SLC24A5 gene reaches fixation in Europe, and is also common among populations in North Africa, the Horn of Africa, West Asia, Central Asia and South Asia.^[62][63][64]

That’s rather interesting about MC1R. It could imply that the difference in skin tone between SSAs and non-SSAs is due to active selection in Blacks for dark skin and relaxed selection in non-Blacks, rather than active selection for light skin in non-Blacks.

The page on MC1R states:

MC1R is one of the key proteins involved in regulating mammalianskin and hair color. …It works by controlling the type of melanin being produced, and its activation causes the melanocyte to switch from generating the yellow or red phaeomelanin by default to the brown or black eumelanin in replacement. …

This is consistent with active selection being necessary to produce dark skin, and relaxed selection producing lighter tones.

Studies show the MC1R Arg163Gln allele has a high frequency in East Asia and may be part of the evolution of light skin in East Asian populations.^[40] No evidence is known for positive selection of MC1R alleles in Europe^[41] and there is no evidence of an association between MC1R and the evolution of light skin in European populations.^[42] The lightening of skin color in Europeans and East Asians is an example of convergent evolution.

However, we should also note:

Dark-skinned people living in low sunlight environments have been recorded to be very susceptible to vitamin D deficiency due to reduced vitamin D synthesis. A dark-skinned person requires about six times as much UVB than lightly pigmented persons.

PCA graph and map of sampling locations. Modern people are indicated with gray circles.

Unfortunately, most of the work on human skin tones has been done among Europeans (and, oddly, zebra fish,) limiting our knowledge about the evolution of African skin tones, which is why this post has been sitting in my draft file for months. Luckily, though, two recent studies–Loci Associated with Skin Pigmentation Identified in African Populations and Reconstructing Prehistoric African Population Structure–have shed new light on African evolution.

In Reconstructing Prehistoric African Population Structure, Skoglund et al assembled genetic data from 16 prehistoric Africans and compared them to DNA from nearby present-day Africans. They found:

1. The ancestors of the Bushmen (aka the San/KhoiSan) once occupied a much wider area.
2. They contributed about 2/3s of the ancestry of ancient Malawi hunter-gatherers (around 8,100-2,500 YA)
3. Contributed about 1/3 of the ancestry of ancient Tanzanian hunter-gatherers (around 1,400 YA)
4. Farmers (Bantus) spread from west Africa, completely replacing hunter-gatherers in some areas
5. Modern Malawians are almost entirely Bantu.
6. A Tanzanian pastoralist population from 3,100 YA spread out across east Africa and into southern Africa
7. Bushmen ancestry was not found in modern Hadza, even though they are hunter-gatherers and speak a click language like the Bushmen.
8. The Hadza more likely derive most of their ancestry from ancient Ethiopians
9. Modern Bantu-speakers in Kenya derive from a mix between western Africans and Nilotics around 800-400 years ago.
10. Middle Eastern (Levant) ancestry is found across eastern Africa from an admixture event that occurred around 3,000 YA, or around the same time as the Bronze Age Collapse.
11. A small amount of Iranian DNA arrived more recently in the Horn of Africa
12. Ancient Bushmen were more closely related to modern eastern Africans like the Dinka (Nilotics) and Hadza than to modern west Africans (Bantus),
13. This suggests either complex relationships between the groups or that some Bantus may have had ancestors from an unknown group of humans more ancient than the Bushmen.
14. Modern Bushmen have been evolving darker skins
15. Pygmies have been evolving shorter stature

Automated clustering of ancient and modern populations (moderns in gray)

I missed #12-13 on my previous post about this paper, though I did note that the more data we get on ancient African groups, the more likely I think we are to find ancient admixture events. If humans can mix with Neanderthals and Denisovans, then surely our ancestors could have mixed with Ergaster, Erectus, or whomever else was wandering around.

Distribution of ancient Bushmen and Ethiopian DNA in south and east Africa

#15 is interesting, and consistent with the claim that Bushmen suffer from a lot of skin cancer–before the Bantu expansion, they lived in far more forgiving climates than the Kalahari desert. But since Bushmen are already lighter than their neighbors, this begs the question of how light their ancestors–who had no Levantine admixture–were. Could the Bantus’ and Nilotics’ darker skins have evolved after the Bushmen/everyone else split?

Meanwhile, in Loci Associated with Skin Pigmentation Identified in African Populations, Crawford et al used genetic samples from 1,570 people from across Africa to find six genetic areas–SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2–which account for almost 30% of the local variation in skin color.

Bantu (green) and Levantine/pastoralist DNA in modern peoples

SLC24A5 is a light pigment introduced to east Africa from the Levant, probably around 3,000 years ago. Today, it is common in Ethiopia and Tanzania.

Interestingly, according to the article, “At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations.”

These are the world’s other darkest peoples, such as the Jarawas of the Andaman Islands or the Melanesians of Bougainville, PNG. (And, I assume, some groups from India such as the Tamils.) This implies that these groups 1. had dark skin already when they left Africa, and 2. Never lost it on their way to their current homes. (If they had gotten lighter during their journey and then darkened again upon arrival, they likely would have different skin color variants than their African cousins.)

This implies that even if the Bushmen split off (around 200,000-300,000 YA) before dark skin evolved, it had evolved by the time people left Africa and headed toward Australia (around 100,000-70,000 YA.) This gives us a minimum threshold: it most likely evolved before 70,000 YA.

(But as always, we should be careful because perhaps there are even more skin color variant that we don’t know about yet in these populations.)

MFSD12 is common among Nilotics and is related to darker skin.

And according to the abstract, which Razib Khan posted:

Further, the alleles associated with skin pigmentation at all loci but SLC24A5 are ancient, predating the origin of modern humans. The ancestral alleles at the majority of predicted causal SNPs are associated with light skin, raising the possibility that the ancestors of modern humans could have had relatively light skin color, as is observed in the San population today.

The full article is not out yet, so I still don’t know when all of these light and dark alleles emerged, but the order is absolutely intriguing. For now, it looks like this mystery will still have to wait.

 

Two Exciting Papers on African Genetics

Nǃxau ǂToma, (aka Gcao Tekene Coma,) Bushman star of “The Gods Must be Crazy,” roughly 1944-2003

An interesting article on Clues to Africa’s Mysterious Past appeared recently in the NY Times:

It was only two years ago that researchers found the first ancient human genome in Africa: a skeleton in a cave in Ethiopia yielded DNA that turned out to be 4,500 years old.

On Thursday, an international team of scientists reported that they had recovered far older genes from bone fragments in Malawi dating back 8,100 years. The researchers also retrieved DNA from 15 other ancient people in eastern and southern Africa, and compared the genes to those of living Africans.

Let’s skip to the article, Reconstructing Prehistoric African Population Structure by Skoglund et al:

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago.

Paths of the great Bantu Migration

The San are also known as the Bushmen, a famous group of recent hunter-gatherers from southern Africa.

We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions…

This is most likely the Great Bantu Migration, which I wrote about in Into Africa: the Great Bantu Migration.

…and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist…

Whereas the two individuals buried in ∼2,000 BP hunter-gatherer contexts in South Africa share ancestry with southern African Khoe-San populations in the PCA, 11 of the 12 ancient individuals who lived in eastern and south-central Africa between ∼8,100 and ∼400 BP form a gradient of relatedness to the eastern African Hadza on the one hand and southern African Khoe-San on the other (Figure 1A).

The Hadza are a hunter-gatherer group from Tanzania who are not obviously related to any other people. Their language has traditionally been classed alongside the languages of the KhoiSan/Bushmen people because they all contain clicks, but the languages otherwise have very little in common and Hadza appears to be a language isolate, like Basque.

The genetic cline correlates to geography, running along a north-south axis with ancient individuals from Ethiopia (∼4,500 BP), Kenya (∼400 BP), Tanzania (both ∼1,400 BP), and Malawi (∼8,100–2,500 BP), showing increasing affinity to southern Africans (both ancient individuals and present-day Khoe-San). The seven individuals from Malawi show no clear heterogeneity, indicating a long-standing and distinctive population in ancient Malawi that persisted for at least ∼5,000 years (the minimum span of our radiocarbon dates) but which no longer exists today. …

We find that ancestry closely related to the ancient southern Africans was present much farther north and east in the past than is apparent today. This ancient southern African ancestry comprises up to 91% of the ancestry of Khoe-San groups today (Table S5), and also 31% ± 3% of the ancestry of Tanzania_Zanzibar_1400BP, 60% ± 6% of the ancestry of Malawi_Fingira_6100BP, and 65% ± 3% of the ancestry of Malawi_Fingira_2500BP (Figure 2A). …

Both unsupervised clustering (Figure 1B) and formal ancestry estimation (Figure 2B) suggest that individuals from the Hadza group in Tanzania can be modeled as deriving all their ancestry from a lineage related deeply to ancient eastern Africans such as the Ethiopia_4500BP individual …

So what’s up with the Tanzanian expansion mentioned in the summary?

Western-Eurasian-related ancestry is pervasive in eastern Africa today … and the timing of this admixture has been estimated to be ∼3,000 BP on average… We found that the ∼3,100 BP individual… associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant … These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East. We fit the remaining approximately two-thirds of Tanzania_Luxmanda_3100BP as most closely related to the Ethiopia_4500BP…

…present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age …and in ancient Egypt by the Iron Age …

There is then a discussion of possible models of ancient African population splits (were the Bushmen the first? How long have they been isolated?) I suspect the more ancient African DNA we uncover, the more complicated the tree will become, just as in Europe and Asia we’ve discovered Neanderthal and Denisovan admixture.

They also compared genomes to look for genetic adaptations and found evidence for selection for taste receptors and “response to radiation” in the Bushmen, which the authors note “could be due to exposure to sunlight associated with the life of the ‡Khomani and Ju|’hoan North people in the Kalahari Basin, which has become a refuge for hunter-gatherer populations in the last millenia due to encroachment by pastoralist and agriculturalist groups.”

(The Bushmen are lighter than Bantus, with a more golden or tan skin tone.)

They also found evidence of selection for short stature among the Pygmies (which isn’t really surprising to anyone, unless you thought they had acquired their heights by admixture with another very short group of people.)

Overall, this is a great paper and I encourage you to RTWT, especially the pictures/graphs.

Now, if that’s not enough African DNA for you, we also have Loci Associated with Skin Pigmentation Identified in African Populations, by Crawford et al:

Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

I’ve had an essay on the evolution of African skin tones sitting in my draft folder for ages because this research hadn’t been done. There’s plenty of research on European and Asian skin tones (skin appears to have significantly lightened around 10,000 years ago in Europeans,) but much less on Africans. Luckily for me, this paper fixes that.

Looks like SLC24A5 is related to that Levantine/Iranian back-migration into Africa documented in the first paper.

Locations of the African Ethnic Groups in Haak et al’s dataset

This is the small version, which does not show all the groups. The larger version, with all the groups, is below.

Continuing my quest to produce a handy guide to the many obscure ethnic groups found in Haak et al’s dataset, here are all of the African groups I could fit on a map. Since many of these groups are extremely small and live near each other, it was impossible to fit them into their exact locations, but I hope my approximations are sufficient.

Here’s the more detailed map:

Note that there’s a ton more genetic data in the actual study; this is just a reference map. Also, “Bedouins” have an extremely broad range, from Morocco to Oman,  but I think these are the locations where these two samples were taken. Please ask if anything is unclear.

Anthropology Friday: Still a Pygmy (pt 3) Bantus, Mobutu, and Witchcraft

Continuing with our review of Still a Pygmy, by Isaac Bacirongo and Michael Nest

 “All happy families are alike; each unhappy family is unhappy in its own way.” — Tolstoy

One of the things I find interesting (and reassuring) when reading about other peoples and places is discovering that they have problems, too–it’s not just us. This is a bit of a personal life philosophy–when the going gets tough, I tell myself “Other people have been through this. You are not the only one. They got through it and so will you.” It is always useful to have some perspective on life.

These days, the biggest source of trouble in Pygmies’ lives isn’t leopards, but the Bantus. Of course this must be taken with a grain of salt, since the book was written by a Pygmy; perhaps Bantus have a whole list of their own grievances–maybe Pygmies “hunt” their livestock and “gather” their crops. I should try to be at least a little cautious of accepting uncritically a single account of relations between two groups of people I have no personal experience with.

Thankfully there is a lot of other evidence on the subject, and it looks like the Pygmies are generally on the losing end of Bantu violence, and the Bantus are not generally on the losing end of Pygmy violence. The Wikipedia: article on Pygmies quotes a BBC report:

In 2003, Sinafasi Makelo, a representative of Mbuti pygmies, told the UN’s Indigenous People’s Forum that during the Congo Civil War, his people were hunted down and eaten as though they were game animals. In neighbouring North Kivu province there has been cannibalism by a group known as Les Effaceurs (“the erasers”) who wanted to clear the land of people to open it up for mineral exploitation.^[23] Both sides of the war regarded them as “subhuman” and some say their flesh can confer magical powers.^[24] Makelo asked the UN Security Council to recognise cannibalism as a crime against humanity and an act of genocide.^[25]

It’s sad that we have to add “cannibalism” to the list of “things people have to be explicitly told not to do.”

Since the world of Pygmy activists is pretty small, it’s not surprising that Isaac also mentions Sinafasi Makelo. “My position in APDMAC [A pygmy rights group] was Founder and Coordinator. Sinafasi, a Pygmy from the Mangurejipa Forest in North Kivu, was the Secretary.”

Continuing with Wikipedia:

According to Minority Rights Group International there is extensive evidence of mass killings, cannibalism and rape of Pygmies and they have urged the International Criminal Court to investigate a campaign of extermination against pygmies. Although they have been targeted by virtually all the armed groups, much of the violence against Pygmies is attributed to the rebel group, the Movement for the Liberation of Congo, which is part of the transitional government and still controls much of the north, and their allies.^[26]

The Pygmy population was also a target of the Interahamwe during the 1994 Rwandan Genocide. Of the 30,000 Pygmies in Rwanda, an estimated 10,000 were killed and another 10,000 were displaced. They have been described as “forgotten victims” of the genocide.^[27] The current Rwandan Pygmy population is about 33,000, and is reportedly declining.^[28]

By one estimate, the total number of Pygmies killed in the civil wars in Congo and Rwanda is 70,000.^[27]

I am not sure that the Pygmies are actually being targeted anymore than everyone else in the area–the Tutsis have a pretty good claim to have been victims of genocide as well, and the Tutsis got back at the Hutus by massacring them. And plenty of ordinary Bantus living in the area have been raped, shot, massacred, and probably eaten, too. The only difference is that you never hear of the Pygmies being the victors (or aggressors) in these conflicts. Not that Pygmies are peace-loving forest hippies or something like that, but they are a tiny group of hunter-gatherers and therefore don’t have the numbers nor the weapons to attack their neighbors.

Regardless, the situation in the Congo is not good. As Reuters reports (2014):

KINSHASA— A militia leader accused of kidnap, rape and cannibalism in Democratic Republic of Congo was killed on Monday alongside four other people during a firefight as he sought to escape his army captors, the government said. … U.N. experts said in December he switched his focus from poaching elephants to attacking gold mines. They accuse him and his men of kidnapping people to carry looted goods and of forcing women into being sexual slaves for militia members.

They said in another report last July that former captives had told them the group, known as “Mai Mai Morgan”, had engaged in cannibalism on several occasions.

From the Toronto Star, in a report about “child soldiers” (children kidnapped by the Congolese militias and forced into service):

“When you kill a Tutsi, you remove his heart and mix it with special potions, like a medicine,’’ explains Popy Matenda, rather blandly. “Other parts of the body can be eaten too but the heart is special. It gives you the strength of the person you killed, like you are sucking in his spirit. It’s a kind of magic.’’ … “It didn’t make me sick or anything, eating humans,’’ continues 15-year-old Matenda as he slurps up a cola, when what he’d really wanted was a whiskey. “You couldn’t even taste the flesh because it was all ground up with the medicine.”

From Worldcrunch, In Congo, A Tribal Chief Forced to Flee Cannibalistic Militia:

“Since 2003, 40 chiefs have been killed by the Mai-Mai, who ate their flesh, which they believe can strengthen their power and make them invulnerable to bullets. This has happened to the leaders Musumari, Mwele, Lwalaba, Dilenge, Kawama Mubidi, Kiyombo, Ntambo, Kileba …”

As I have noted before, the belief that eating people (or animals) can give you magic powers leads quickly down a very bad path. If you want an historical view, I recommend Cannibalism in the African Congo.

Isaac Bacirongo does not actually dwell much at all on the specific targeting of Pygmies for cannibalism and genocide. However, he does say:

The owners of the forest became those who had guns. If APDMAC went there and said, ‘Pygmies are the owners of the forest,’ they would put us in prison. In the past, pygmies id not worry about the future. Life was easy because it was easy to find something to eat and thee was only one need: meat. … Many had fled deep into the forest because of the fighting but life was hard because militias operated there as well. They might be killed or raped. there was no medicine in the forest and many people died because of this, including my papa. …

A lot of people are suffering back home and there is nothing I can do about it. In the north-east of Congo, a rebel militia went into the Ituri Forest to hunt Pygmies because they thought they could get magic powers from them. One of my aunts was also killed by rebel forces. They found out she was a Pygmy and wanted to learn about Pygmy magic because they thought it would help them in the forest. he told them she knew nothing, so they buried her alive. Sinafasi, one of the founders of APDMAC,went to the Unted Nations in New york to petition to include cannibalism as a crime against humanity, because other militas were eating Pygmies. The militas thout this would help them in the forest.

… In 2005, Kabungulu from Herieters de la Justice, the man who convinced me to become an activist, was murdered, probably because of his activist work. After that I got the news that 56 people in Bunyakiri were killed by a Hutu milita fighting the Congolese government. Among the dead were my sister’s husband, Josephine’s [his wife’s] nephew, the father of Akili (the nephew I brought to Australia,) and many other neighbors. …

The Pygmies’ reputation for magical powers, which earned them a special position in Bantu religious rituals (see last week’s Anthropology Friday,) definitely backfires when people decide they can get those same magic powers for themselves by eating you.

But enough sensationalism–let’s get back to the mundane, because the day-to-day lives of Congolese Pygmies obviously isn’t invading armies or cannibals.

As a small child, Isaac lived on the banana plantation where his parents worked and attended the local school. He was the only Pygmy at the school, for the simple reason that school cost money, which Pygmies generally could not afford, and because Pygmies tend to prefer living their lives and not worrying about school. But Isaac wanted to be like all of the other kids on the plantation, so he bugged his parents until they somehow scraped up the cash and sent him to school.

I first became aware of politics when I was at this school, because every morning we had to stand in assembly and sing praises to our president, Joseph Mobutu. The government forced shops to put up President Mobutu’s picture and some people even had a picture of Mobutu in their homes, although we didn’t in our hut made of sticks and leaves. … Mama and Papa knew about Mobutu but were not interested in politics and paid no attention to any of it.

Having to pay homage to Mobutu as part of a fake religion was pretty dumb, but a lot better than getting shot by invaders. Unfortunately, the kinds of people who set up fake religions about themselves are often idiots who do things like not pay their armies, which leads to your people getting shot by invaders.

My teacher at the school was Mr. Enoch. ‘Which tribe are you from?’ he asked me, as all the other students in the whole school were Shi. I told him ‘BaTembo.’ ‘That,’ he replied, ‘means you are a Pygmy.’ … Mr. Enoch despised me. He made a point of calling me a ‘Pygmy’ in a way that told the other students I was inferior. …

After three months at the Kabuga school I had a very bad experience. One day I wet my pants, and Mr Enoch hit me very hard with his fists and kicked me. Mr Enoch shouted, ‘that’s what I think of Pygmies!’ as he punched me… I remember bleeding from my ears and nose…

(Remember that Isaac was, at this time, only in the equivalent of kindergarten or first grade.)

My parents were not surprised to see me beaten half-dead by my teacher. They had told us that Bantu always treat Pygmies badly. But I did not understand Mr. Enoch when he told me that Pygmies are not human! …

After I arrived home my body started to swell up. My parents massaged me with hot water and herb from the forest. … The police asked my parents to pay 5 makutas–what they called the ‘arrest fee’–to arrest Mr. Enoch, but where could they get 5 makutas? … ‘Will you insist on going to school again?’ Papa asked. … ‘School is not for us. Now you see for yourself why we don’t go to school.’

Eventually Isaac does go back to school, after his parents move to a different area.

Isaac also recounts the story of a time when his mother was selling firewood, and a Bantu man did not like the price she asked for her wood, so he just hit her and stole her wood.

When Bantu cheat Pygmies or refuse to honor a promise of payment, they do not want the Pygmies to react badly. For example, most Pygmies work at times on the farms of Bantu villagers. The villager might promise to give them two or three measure of beans as payment, but then only give one. …

There are Pygmies who have had their lands sold to Bantu. If we complain, the territorial administrator or the lawyers will be given a cow by the person who bought the land, and because they have bee bought off, they do nothing for the Pygmies.

Anyway, Isaac finishes 10 years of schooling (plus part of year 11,) and sets out to get a job. He has more than enough education to become a teacher, but it is very tough to find people willing to hire a Pygmy teacher. He ends up going into business, leading to his successful pharmacy chain. Eventually he gets married to a town girl, Josephine. Unfortunately, Josephine and Isaac’s mom don’t get along:

Mama was not happy. ‘Look,’ she said, ‘you are marrying someone from a rich family. Town girls don’t know how to look for crabs or firewood…’ Mama wanted me to marry a girl from the forest. …

Mama also blamed Papa for me wanting to stay in town. ‘I told you not to send your son to school,’ she said, ‘because he will want to live in town. It will change his thinking and he won’t want to live in the forest.’ But Papa hadn’t sent me to school.

… Mama tried everything she could with witchcraft to kill Josephine.

Mama thought Josephine was controlling me, and told me the reason I did not return to the forest was because Josephine had used witchcraft to make me change my mind and beliefs… So Mama went to a witchdoctor to ask for magic herbs more powerful than those she thought Josephine had given me, to kill the power of Josephine’s magic. Mum tried to get me t eat these herbs and she placed others where I was sitting or stepping. The herbs did not work…

Mama then went to a woman who was known to be a sorceress, Nagabushu… Mama said that if Josephine were to die while pregnant with Deborah, people would think it was because of the pregnancy and would not suspect witchcraft. Nagabushu got upset and started fighting with Mum. ‘I’m not a sorceress!’ she shouted. ‘I’ve never killed anyone!’ …

In 1991, ten years after we married, Mama went to a different witchdoctor… He was an older man in his forties. … The witchdoctor told mama how powerful he was. ‘It will be very simple to kill your daughter-in-law,’ he said. ‘I have the power to bring storms, such as lighting storms… Someone died a few months ago from a lightning strike, and it was me who did that. … If you give me your youngest daughter, Sibaruzi, to be my wife that would be enough payment…’

Mama told Sibaruzi that if she refused to be the witchdoctor’s wife, everyone in our family would be killed. … mama escorted her to the witchdoctor and when they arrived he showed them teeth of wild animals, herbs and bottles of liquids. Sibaruzi was afraid. … She was twelve at the time and had not even had her first period. I still do not know how Mama could do this. What a bad heart!

Obviously the witchdoctor failed and Josephine is still alive and well. Eventually Sibaruzi figured out what was up and left, saying she never wanted to see him again. (What a creep.)

Amusingly, sometime I get witchdoctor spam, but being an idiot, I didn’t save the part I wanted to quote for you and my spam folder auto-deleted it. Oh, well. It was funny.

Well, Josephine, if it’s any consolation, I’ve heard lots horrible mother-in-law stories here in the US, too. I guess this means that “horrible mothers-in-law” may be a true human universal.

South Africa, democracy, and the dangers of demographics (part 1)

(Remember, creatives are psychotic.)
People have been bugging me to write a post on South Africa ever since I started this blog, more or less, so here you go.

I regard South Africa (SA) as one of the most misunderstood countries in the world, so I’m going to start with the history and try to clear up some potential misconceptions.

Disclaimer: I am not a South Africa scholar. This is what I’ve cobbled together by reading first and second hand accounts on the internet, Wikipedia, talking to friends who’ve lived in SA, etc. Since I’ve never been there myself, there’s always a chance that I’ve trusted the wrong people or come to some incorrect conclusions, but as always, I’ve tried to present an accurate picture.

The most common misconception I run across is that whites arrived recently in SA, conquered and oppressed the natives via apartheid and after years of righteous struggle, the native people of South Africa have finally gotten the right to vote and run their own country.

History, as usual, tells a slightly different story.

The dominant group in South Africa today is the Bantus. Nelson Mandela, for example, was a Bantu.

When the first Europeans arrived at the Cape of Good Hope (later site of Cape Town and most of the economic development of the state of South Africa,) most of the people there were Bushmen, (aka San aka KhoiSan,) who were hunter-gatherers. Not Bantus.

Distribution of ancient paintings and engravings attributed to the San

Modern distribution of African languages–Bantus in orange. Note the isolated pocket of KhoiSan speakers up in Tanzania

If you believe that ancestrality determines a person’s right to a country, then the KhoiSan have a right to the Cape, and the Johnny-Come-Latey Bantus do not.

If you haven’t been reading along, you might think that the Bushmen and the Bantus are probably closely related, and that I am merely splitting hairs.

No. The Bantus are more closely related to Koreans, Australian Aborigines, and even Europeans than they are to the Bushmen.

As we’ve discussed before, the Bushmen are one of the world’s most isolated peoples, having split off from the rest of the human population, (or perhaps the rest of the humans split off from them,) 100,000 years or more ago. The Out-of-Africa event only happened 70,000 years ago, so only 70,000 years separates the Bantus from all non-Africans, but 100,000 years separate the Bantus from the San.

So. The original inhabitants of the area, who’d been there for about 100,000 years, were the San. Most of them were hunter-gatherers, which means their population density was really low; much of the area appears to have been uninhabited, given regions with names like “Nomansland”. Some of the Khoi peoples, though, had adopted animal herding.

The Bantus came originally from somewhere up near Nigeria, but by the relevant time period, occupied the north east part of South Africa, which they’d conquered from the San. (The Cape of Good Hope, where the Europeans settled, is in the south west corner. Hardly anyone has ever lived in the north west corner, because it’s desert.)

The first European in the area was Portuguese sailor Bartolomeu Dias, (and, obviously, his crew,) way back in 1488. In 1647, the Dutch built a small fort in the area, and in 1652, the Dutch East India Company (which I wrote about recently,) set up a supply station and fortifications on the Cape. By 1659, the Dutch were producing corn, wine, and babies.

Most of the KhoiSan people were probably killed, either outright by warfare or by diseases they had no resistance to, but I have no numbers and am just speculating. There are still KhoiSan people in SA and neighboring places, so they are not all dead.

By 1800, some of the mixed-race children/descendants of the Dutch and the locals, KhoiSan, former slaves*, and the like decided they’d had enough of the Dutch and migrated northward, establishing Griqualand in an apparently uninhabited area. They migrated around a bit, and eventually Griqualand got moved to the region formerly known as Nomansland.

*The slaves were imported from elsewhere in Africa, since the Dutch considered it a bad idea to enslave the locals.

The British took possession of the Cape during the Napoleonic Wars. They promptly set about outlawing slavery and the Dutch language, so a lot of the Dutch decided to leave, too. By the 1830s, they were leaving by the hundreds, a migration known as the “Great Trek.” (There is some debate about whether outlawing slavery was actually a big deal to the Trekkers, as they tended to be the poorer folks who would have been less likely to own slaves in the first place, but I don’t know anywhere near enough history here to weigh in on the debate.)

Paths of the Great Trek–note the locations of the Cape Colony in the south east, and the Zulu kingdom in the north west.

The Dutch population by this point also included a lot of Germans, French, etc., and so would be more accurately called Afrikaners.  These Trekkers, or Voortrekkers, or Boers, or Trekboers, or Afrikaners, whatever we want to call them.

These Afrikaners are an interesting people, who endured considerable hardship to go live in the middle of nowhere with nothing but what they could carry in small wagons, their family, faith, and a few guns. They trekked toward the north east, until they ran smack into the southern end of the Great Bantu Migration. The Bantus (Zulus) massacred about 500 Boers–men, women, and children–in the middle of the night. Shortly after, approximately 30,000 Zulu soldiers attacked 460 Boers, at the Battle of Blood River. This time the Boers were awake, and since they had guns and the Zulus had pointy sticks, 3,000 Zulus died and 3 Boers were injured. (December, 1836.)

Long story short, the Boers established several small, independent republics up in north east South Africa, the details of which are too complicated for our current discussion, but you may want to remember the names Orange Free State, Transvaal, and Natal.

The British-controlled Cape Colony is in blue; Boer Transvaal in Green; Boer Free Orange State in orange; Zulu state, Natal (aka Natalia,) is in red.

In 1866, diamonds were discovered on the banks of the Orange River. The diamond-rich territory was eventually awarded to Griqualand, which was subsequently annexed by Britain in 1874. In 1886, gold was found in Transvaal. The British had tried to conquer Transvaal in 1877, but did not succeed until the Second Anglo-Boer War, 1899-1902, which ended with the annexation of both Transvaal and the Orange Free State.

Boers forced to watch their home burned to the ground

Lots of people were killed, but eventually the British got the upper hand and, having decided they were sick of the Boers, herded them into concentration camps and tried to kill them all:

“This was not the first appearance of internment camps. … But the Boer War concentration camp system was the first time that a whole nation had been systematically targeted, and the first in which some whole regions had been depopulated.

“Eventually, there were a total of 45 tented camps built for Boer internees and 64 for black Africans. Of the 28,000 Boer men captured as prisoners of war, 25,630 were sent overseas. The vast majority of Boers remaining in the local camps were women and children. Over 26,000 women and children were to perish in these concentration camps.

“… 93,940 Boers and 24,457 black Africans were reported to be in “camps of refuge” and the crisis was becoming a catastrophe as the death rates appeared very high, especially among the children.

“A report after the war concluded that 27,927 Boers (of whom 24,074 [50 percent of the Boer child population] were children under 16) had died of starvation, disease and exposure in the concentration camps. In all, about one in four (25 percent) of the Boer inmates, mostly children, died.

“Improvements [however] were much slower in coming to the black camps.”^[51] It is thought that about 12 percent of black African inmates died (about 14,154) but the precise number of deaths of black Africans in concentration camps is unknown as little attempt was made to keep any records of the 107,000 black Africans who were interned.” —Wikipedia

Her name was Lizzie Van Zyl. She was 7 years old.

“[Hobhouse] describes Lizzie as “a frail, weak little child in desperate need of good care”, who was placed on the lowest rations and, after a month, was moved to the new hospital about 50 kilometres (31 miles) away from the concentration camp, suffering from starvation.

According to Hobhouse, she was treated harshly in the hospital. Unable to speak English, she was labelled an “idiot” by an English-speaking doctor and her nurses, who were unable to understand her. One day she started calling for her mother; a lady went over to comfort her, but “was brusquely interrupted by one of the nurses who told her not to interfere with the child as she was a nuisance.” Lizzie died in 1901 at 7 years of age.”

As a mother, I look at Lizzie and feel like someone has torn my heart out and stomped on it.

To add insult to murder,

“The photo [of Lizzie] was used as propaganda, author Hélène Opperman Lewis states, to convince the British public that Boer children were neglected by their parents. The image was released with the detail that it was taken when van Zyl and her mother entered the camp. Chamberlain was quoted in The Times on 5 March 1902, saying that Lizzy’s mother was prosecuted for mistreatment.^[4]

Hobhouse investigated the case and was unable to find any evidence of the case or prosecution of Lizzie’s mother. She located the photographer, a man named Mr. de Klerk, who confirmed that the photograph was taken two months after Lizzie arrived at the camp.^[4]”

And people accuse the Afrikaners of being racist.

I count about 62,000 people dead in this war. Certainly it was no WWII, but then, South Africa didn’t have that many people to start with, so percentage wise, it’s pretty significant.

Now, I want to pause and look at some demographic issues that contributed to the Anglo-Boer War. Note that the Boers had been pretty much going along, minding their own business, running their own country, for several decades before this war started. They’d gone through quite a bit of effort to get away from the British, successfully defeated the Zulus (and other tribes,) and weren’t even the worst people in the area.

“But wait,” I hear you saying, “Didn’t the Boers have slaves? Or at least Apartheid?”

I actually don’t remember if they had slaves; if they did, they are still better than the Congolese, who are not only enslaving the Pygmies right now, but also literally eat other humans. As for apartheid, do you think the Zulus were letting their conquered subjects vote? (Or live?)

For the most part, the Boers just wanted to be left the fuck alone–they didn’t conquer the Griquas, they abandoned their colony after the British took it over rather than fight for it, and I don’t think they were even messing with Natal. They just had the bad luck to have gold and diamonds, and the British decided they wanted gold and diamonds.

“In 1866 Erasmus Jacobs discovered diamonds at Kimberley, prompting a diamond rush and a massive influx of foreigners to the borders of the Orange Free State. Then in 1886, an Australian discovered gold in the Witwatersrand area of the South African Republic. Gold made the Transvaal the richest and potentially the most powerful nation in southern Africa; however, the country had neither the manpower nor the industrial base to develop the resource on its own. As a result, the Transvaal reluctantly acquiesced to the immigration of uitlanders (foreigners), mainly from Britain, who came to the Boer region in search of fortune and employment. This resulted in the number of uitlanders in the Transvaal potentially exceeding the number of Boers, and precipitated confrontations between the earlier-arrived Boer settlers and the newer, non-Boer arrivals.” —Wikipedia [Bold mine]

The British then demanded voting rights for their citizens in Transvaal, the Boers realized that they were outnumbered and that letting the Brits vote would result in their country becoming part of the British Empire and so refused, and so the war began.

Once you are a demographic minority, there is absolutely nothing to stop the majority from herding you into concentration camps and murdering you and your children, except for how much they pity you.

And nobody pities you, my friend.

At any rate, South Africa was thus forged from the Cape Colony, Natal, the Orange Free State, and Transvaal. (I still don’t know why Lesotho is independent. Perhaps no diamonds, or maybe just the fact that it’s on top of some mountains.) The British instituted the system of apartheid, perhaps because they felt like it, perhaps because they felt like making some concessions to the conquered Afrikaners.

SA became an independent country again in 1960. In 1966, UN resolution 2202 A (XXI) declared apartheid “A Crime Against Humanity.” (Of course, the UN also criticized the Vietnamese for kicking the Khmer Rouge out of Cambodia and decided to let the deposed Khmer Rouge gov’t continue holding its seat in the UN despite being one of the most genocidal regimes the earth has ever seen, so who gives a shit what the UN thinks?)

Deaths under apartheid:

“By mid-1987 the Human Rights Commission knew of at least 140 political assassinations in the country, while about 200 people died at the hands of South African agents in neighbouring states. The exact numbers of all the victims may never be known. …

“Between 1960 and 1994, according to statistics from the Truth and Reconciliation Commission, the Inkatha Freedom Party was responsible for 4,500 deaths, South African Police 2,700, and the ANC about 1,300.^[135]” —Wikipedia

3,100+ murders attributed to the SA government, and 5,800 murders attributed to the anti-apartheid fighters.

The ANC (African National Congress,) Nelson Mandela’s party, is a communist organization that received direct funding and training by the Soviet Union. (I strongly suspect that the vast majority of anti-colonialist movements were funded by the Soviets, as colonialism has strong capitalist ties, eg, the Dutch East India Company, and so Communism morphed into an anti-colonialist ideology by the 50s or 60s.)

The ANC engaged in a brutal execution method called necklacing:

Necklacing Victim, burned alive

“In 1986 Winnie Mandela, then-wife of the imprisoned Nelson Mandela, stated “With our boxes of matches and our necklaces we shall liberate this country. …

The first victim of necklacing, according to the South African Truth and Reconciliation Commission, was a young girl, Maki Skosana, on 20 July 1985.^[10]

Moloko said her sister was burned to death with a tire around her neck while attending the funeral of one of the youths. Her body had been scorched by fire and some broken pieces of glass had been inserted into her vagina, Moloko told the committee. Moloko added that a big rock had been thrown on her face after she had been killed.^[11]” —wikipedia

As you know, nothing makes your country productive like electing communists who make their points by shoving broken glass into little girls’ vaginas.

Inkatha seems a little more into tribal pride and less communist; they’ve recently lost a bunch of parliamentary seats to the explicitly communist Economic Freedom Fighters. The EFF’s leader, Julius Malema, is a lovely person who admires Mugabe, advocates Mugabe-style seizure of mines and other economic resources in SA, and likes to lead the SA parliament in rousing choruses of “Shoot the Boer,” an old anti-apartheid war song.

You mean you can just print more of these things? Mugabe is brilliant!

SA president Jacob Zuma, a guy who gets 1.2 million pounds per year to support his four wives, is also fond “Shoot the Boer”:

“We are going to shoot them with machine guns, they are going to run… The cabinet will shoot them, with the machine gun… Shoot the Boer, we are going to hit them, they are going to run.”

Don’t worry; South Africans are very good at killing Boers, and getting better. Here’s what Genocide Watch has to say:

“Cape Town – Social media buzzed on Monday over a picture of a banner allegedly shown at the Economic Freedom Fighter (EFF) launch in Marikana.

A picture showing a red banner with the words “A revolutionary must become a cold killing machine motivated by pure hate” was quickly shared on various social networks on Monday.

Another picture shows a banner saying “Honeymoon is over for white people in South Africa”.

“I also saw ‘we need to kill them like they killed us’ banners yesterday,” User Qaanitah Hunter said in a Tweet.”

Gulags are a feature of communism, not bugs

From the second PDF:

“Over 3,000 white farmers have been murdered since the end of apartheid, according to Genocide Watch. Twenty years ago, there were 60,000 farmers. Today there are 30,000.

On August 8, two men were convicted of killing a 77-year-old man and his wife on their farm in Somerset. The husband was hacked to pieces. The wife was tied up, thrown in a freezer, and buried in frozen meat. She suffocated to death.

According to the police, the motivation was robbery.

On August 11, four men broke into 57-year-old Vivien Ponté’s home. She was tied to her bed, raped and lit on fire. Her house was ransacked, but it is unclear if anything was stolen.

Just another robbery gone bad.

On August 15, an 83-year-old Volksrust woman was assaulted, raped and left for dead, lying naked on the floor.

The list of “robberies” goes on. …

Beginning in 2003, the government began disbanding the rural commando units used to protect the remote farming communities that did not have police protection. The government said the commandos were unconstitutional and promised special police units to replace them. In 2008, the last commando unit was disbanded.

To this day, the special police forces still haven’t arrived.

Then in 2010, the government passed gun-control laws mandating that all guns be re-registered. In the process of registration, more than half the applicants were turned down and their weapons were seized.”

Various sources estimate the murder rate of SA farmers at about 100 per 100,000.

But you know, the Afrikaners are the racists.

Oh, let me include a bit from the Wikipedia page on Malema:

“Malema visited Zimbabwe in October 2012… “He said the youths in South Africa were calling for whites to surrender land and minerals resources they hold because when they came from Europe they did not carry any land into South Africa.”

“‘What we are asking is for them to surrender our minerals because they did not come with any minerals. We want that land and those minerals for free because they never paid for those minerals.’

“Malema told the youth he was in Zimbabwe to gain inspiration and wisdom, so that when he returned home he could “double the spirit of fighting against imperialist forces”.^[77] He called on black South Africans to have as many children as possible so as to increase dominance of ‘our ideas’ in the world at large and help catalyze world revolution.^[78][79]

“‘We want to see many kids, why? Because we must reproduce ourselves. For our ideas to be sustainable, we have to reproduce ourselves. In the whole of Africa, we are not more than one billion and the world has seven billion people. In Africa we have not more than one billion people… facing more than six billion. We have to be half of that so that our ideas can dominate. I know that in some instances size does not matter… but when it comes to a revolution, size matters.^[79]‘” (bold mine)

Malema is descended from Bantus, so he is no more entitled to the mines than anyone else is, and certainly no one was mining those minerals before the Boers and English got there. If they were precious to Malema’s people, they would have been mining them, but they weren’t.

This is getting long, so I am going to continue with Part 2 tomorrow.

Into Africa: The Great Bantu Migration

As I’ve mentioned before, the famous Out of Africa (OoA) migration was likely preceded by an Into Africa migration, or at least, a Moving Through Africa migration.

Near as we can tell, based on the science at our disposal, H sapiens (humans, us,) evolved in Africa and then spread out from there.

But genetics (and other evidence) suggests that the oldest human split lies not between Africans and non-Africans, but between the San (aka Bushmen or KhoiSan) people of southern Africa and pretty much everyone else in the world.

But hold on. One frequently sees comments to the effect of “All modern humans descended from the San” or “The San are the most ancestral population alive today.” Bollocks. Look, you and your cousin are both descended from your grandparents. Your cousin is not ancestral to you, your grandparents are ancestral to both of you. You did not descend from the San because the San are living right now in southern Africa. They are not an ancient people known only from the architectural record, like the Yamnaya or Minoans. (Unless, of course, your parents actually are San. Then of course you are descended from the San.)

So what does this mean?

Humans–H Sapiens–arose around 200,000 years ago, somewhere or other in Africa. Around 100,000 years ago, the San split off from everyone else, and stayed isolated for almost 100,000 years.

The San look like this:

Some anthropologists refer to Bushmen as “gracile,” which means they are a little shorter than average Europeans and not stockily built

And their homeland is down in the green:

Modern distribution of major African language groups

Their historic range was probably much larger than it currently is–note the little green dot over in Tanzania.

Here’s a different map’s opinion on the subject:

And here’s a map showing the locations of art attributed to the San / their ancestors:

Whether the San started in southern Africa, and everyone else left for northern Africa, leaving them behind, or the San started in northern Africa and then left for the south, leaving everyone else behind, I have no idea. Either way, one group left the other, and the split persisted, more or less, for almost a hundred thousand years.

I’ve mentioned before that the San are notably lighter-skinned than Africans from closer to the equator, like the Bantus:

Bantu mother and child

Probably because the sun is just really harsh at the equator. You can see the current distribution of Bantus in orange on the brightly-colored map above.

Now, back to the story. Shortly after, the Pygmies split off, which I’m not going on to natter on about here because you can read the post I wrote about it. Around 70,000 years ago, some guys left Africa to explore the rest of the world. Around 40,000 years ago, some of those guys split, more or less, into Asians, Europeans, and their descendants.

Among other things, this means that the Batus are more closely related to Koreans, Australian Aborigines, and Native Americans than to the KhoiSan peoples. This is because the ancestors of the Bantus and the ancestors of everyone-not-from-Africa split up around 70,000 years ago, whereas the ancestors of the Bantus and the ancestors of the KhoiSan split 100,000 years ago.

If this is confusing, think about it like this: you and your brother are closely related, because you are only one generation away from your common ancestor, your parents. (In this case, Europeans and Asians are like siblings.) You are related to your cousins, but less closely–you share half your DNA with a sibling, but only 12.5% with a cousin. You and your cousin are two generations away from your common ancestor, your grandparents. In this case, Bantus are cousins to siblings Europeans and Asians. Your second-cousins are descended from your great-grandparents. (If you have cousins, and you both have kids, those kids are second-cousins.) Second cousins share only a quarter as much DNA again–3.13%. The San are like your second-cousins. They are also second-cousins to your brother, and also second cousins to your cousins. All of the siblings are more closely related to each other than to their cousins; all of the cousins are more closely related to each other than to their second cousins; Bantus are more closely related to Koreans than to the San.

And just in case you are still confused:

vs

If you’re still confused, here’s the Wikipedia page on kinship coefficients.

Please note that this is all a massive, massive over-simplification–obviously there are lots of groups in Africa other than the Bantus and the San–like the Yoruba. But “everyone in Africa other than the San and the Pygmies and people who’ve had Arab and other admixture” gets really clunky.

If you’ve been paying attention, you may have noticed that the green and orange regions on the map above look awfully close together. How have the San been so isolated for so long if they’re living right next to the Bantus?

About 3,500 years ago–96,500 after they split–the Bantus did this:

Paths of the great Bantu Migration

1 = 2000–1500 BC origin 2 = ca.1500 BC first migrations      2.a = Eastern Bantu,   2.b = Western Bantu 3 = 1000–500 BC Urewe nucleus of Eastern Bantu 4–7 = southward advance 9 = 500 BC–0 Congo nucleus 10 = 0–1000 AD last phase (from Wikipedia)

The Great Bantu Migration.

Why? I don’t know.

With their larger builds, superior weapons, and more complex social systems, the Bantus appear to have dominated the shit out of everyone they met, until they massacred the wrong guys:

Battle of Blood River

Yes, they ran right into the Afrikaneer (Dutch) Boers, trekking northward from Cape Town, South Africa. And the Boers had guns.

Never bring a spear to a gun fight.

In the end, though, the Bantus won. They have the overwhelming numbers, after all.

Nelson Mandela

The San are still around, but their territory has dwindled severely; some managed to survive in the Kalahari desert, a place just too harsh for anyone else, but even this has not protected them, as farmers and ranchers have moved in and they’ve been forced into more sedentary lifestyles.

I’ve mentioned The Harmless People before; it’s an ethnography of the Bushmen. It has the whole, “primitive people have so much less crime than we do” thing going on, (hence the title,) but it’s still an interesting account of a quickly-disappearing lifestyle.

The book’s epilogue describes efforts to force the Bushmen onto reservations, where they have been encouraged to take up farming and herding. The account is depressing; the Bushmen seem to have been perfectly happy with their lives before, and ill-suited to agricultural toil. Alcoholism is rampant, as it is among everyone whose ancestors haven’t been distilling alcohol for thousands of years, and violent crime appears to be taking more lives.

Whether the San will continue existing or be completely absorbed by the unstoppable Bantu migration remains to be seen.