There are three versions of this graph in the paper (check the supplemental materials for two of them), all showing about the same thing. It is supposed to be a graph of population size at different times in the past, and the most incredible thing is that for the past 100,000 years or so, the most numerically dominant populations in Africa were the Baka Pygmies, followed by various Bushmen (San) groups. The authors write:
To unravel the ancient demographic history of the African populations that are present in our data set, we used the Pairwise Sequentially Markovian Coalescent (PSMC) model that analyzes the dynamics of the effective population size over time [60]. We included at least one representative of each of the 15 African populations and two Eurasian samples in the analysis (Additional file 1: Figure S7.1) and considered both the classical mutation rate of 2.5 × 10−8 [61] and the 1.2 × 10−8 mutations per bp per generation reported in other analyses [62, 63]. The demographic trajectories of the sub-Saharan agriculturalist populations are very similar to each other; and only South African Bantu and Toubou individuals differ partly from the rest of sub-Saharan farmer samples; however, their considerable levels of admixture with other North African or hunter-gatherer populations (Fig. 2b) might explain this trend. Therefore, in order to ease visualization, we plotted a Yoruba individual (Yoruba_HGDP00936) and two Ju|‘hoansi individuals as representatives of the sub-Saharan agriculturalist and Khoisan populations, respectively (Fig. 3 and Additional file 1: Figure S7.2 considering a mutation rate of 1.2 × 10−8).
The authors note that the apparent large size of the pygmy groups could have been due to groups splitting and merging and thus getting more DNA variety than they would normally. It’s all very speculative. But still, the Baka Pygmies could have been the absolutely dominant group over central Africa for centuries.
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]
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.
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.
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.
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:
The ancestors of the Bushmen (aka the San/KhoiSan) once occupied a much wider area.
They contributed about 2/3s of the ancestry of ancient Malawi hunter-gatherers (around 8,100-2,500 YA)
Contributed about 1/3 of the ancestry of ancient Tanzanian hunter-gatherers (around 1,400 YA)
Farmers (Bantus) spread from west Africa, completely replacing hunter-gatherers in some areas
Modern Malawians are almost entirely Bantu.
A Tanzanian pastoralist population from 3,100 YA spread out across east Africa and into southern Africa
Bushmen ancestry was not found in modern Hadza, even though they are hunter-gatherers and speak a click language like the Bushmen.
The Hadza more likely derive most of their ancestry from ancient Ethiopians
Modern Bantu-speakers in Kenya derive from a mix between western Africans and Nilotics around 800-400 years ago.
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.
A small amount of Iranian DNA arrived more recently in the Horn of Africa
Ancient Bushmen were more closely related to modern eastern Africans like the Dinka (Nilotics) and Hadza than to modern west Africans (Bantus),
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.
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.
#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.
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.
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.
Welcome back to our discussion of recent exciting advances in our knowledge of human evolution:
Ancient hominins in the US?
Homo naledi
Homo flores
Humans evolved in Europe?
In two days, first H Sap was pushed back to 260,000 years,
then to 300,000 years!
Bell beaker paper
As we’ve been discussing for the past couple of weeks, the exact dividing line between “human” and “non-human” isn’t always hard and fast. The very first Homo species, such as Homo habilis, undoubtedly had more in common with its immediate Australopithecine ancestors than with today’s modern humans, 3 million years later, but that doesn’t mean these dividing lines are meaningless. Homo sapiens and Homo neandethalensis, while considered different species, interbred and produced fertile offspring (most non-Africans have 3-5% Neanderthal DNA as a result of these pairings;) by contrast, humans and chimps cannot produce fertile offspring, because humans and chimps have a different number of chromosomes. The genetic distance between the two groups is just too far.
Oldowan tool
The grouping of ancient individuals into Homo or not-Homo, Erectus or Habilis, Sapiens or not, is partly based on physical morphology–what they looked like, how they moved–and partly based on culture, such as the ability to make tools or control fire. While australopithecines made some stone tools (and chimps can make tools out of twigs to retrieve tasty termites from nests,) Homo habilis (“handy man”) was the first to master the art and produce large numbers of more sophisticated tools for different purposes, such as this Oldowan chopper.
But we also group species based on moral or political beliefs–scientists generally believe it would be immoral to say that different modern human groups belong to different species, and so the date when Homo ergaster transforms into Homo sapiens is dependent on the date when the most divergent human groups alive today split apart–no one wants to come up with a finding that will get trumpeted in media as “Scientists Prove Pygmies aren’t Human!” (Pygmies already have enough problems, what with their immediate neighbors actually thinking they aren’t human and using their organs for magic rituals.)
(Of course they would still be Human even if they part of an ancient lineage.)
But if an ecologically-minded space alien arrived on earth back in 1490 and was charged with documenting terrestrial species, it might easily decide–based on morphology, culture, and physical distribution–that there were several different Homo “species” which all deserve to be preserved.
But we are not space aliens, and we have the concerns of our own day.
So when a paper was published last year on archaic admixture in Pygmies and the Pygmy/Bushmen/everyone else split, West Hunter noted the authors used a fast–but discredited–estimate of mutation rate to avoid the claim that Pygmies split off 300,000 years ago, 100,000 years before the emergence of Homo sapiens:
There are a couple of recent papers on introgression from some quite divergent archaic population into Pygmies ( this also looks to be the case with Bushmen). Among other things, one of those papers discussed the time of the split between African farmers (Bantu) and Pygmies, as determined from whole-genome analysis and the mutation rate. They preferred to use the once-fashionable rate of 2.5 x 10-8 per-site per-generation (based on nothing), instead of the new pedigree-based estimate of about 1.2 x 10-8 (based on sequencing parents and child: new stuff in the kid is mutation). The old fast rate indicates that the split between Neanderthals and modern humans is much more recent than the age of early Neanderthal-looking skeletons, while the new slow rate fits the fossil record – so what’s to like about the fast rate? Thing is, using the slow rate, the split time between Pygmies and Bantu is ~300k years ago – long before any archaeological sign of behavioral modernity (however you define it) and well before the first known fossils of AMH (although that shouldn’t bother anyone, considering the raggedness of the fossil record).
Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago.
260,000 years! Looks like West Hunter was correct, and we should be looking at the earlier Pygmy divergence date, too.
Fossil evidence points to an African origin of Homo sapiens from a group called either H. heidelbergensis or H. rhodesiensis. However, the exact place and time of emergence of H. sapiens remain obscure … In particular, it is unclear whether the present day ‘modern’ morphology rapidly emerged approximately 200 thousand years ago (ka) among earlier representatives of H. sapiens1 or evolved gradually over the last 400 thousand years2. Here we report newly discovered human fossils from Jebel Irhoud, Morocco, and interpret the affinities of the hominins from this site with other archaic and recent human groups. We identified a mosaic of features including facial, mandibular and dental morphology that aligns the Jebel Irhoud material with early or recent anatomically modern humans and more primitive neurocranial and endocranial morphology. In combination with an age of 315 ± 34 thousand years (as determined by thermoluminescence dating)3, this evidence makes Jebel Irhoud the oldest and richest African Middle Stone Age hominin site that documents early stages of the H. sapiens clade in which key features of modern morphology were established.
Hublin–one of the study’s coauthors–notes that between 330,000 and 300,000 years ago, the Sahara was green and animals could range freely across it.
While the Moroccan fossils do look like modern H sapiens, they also still look a lot like pre-sapiens, and the matter is still up for debate. Paleoanthropologist Chris Stringer suggests that we should consider all of our ancestors after the Neanderthals split off to be Homo sapiens, which would make our species 500,000 years old. Others would undoubtedly prefer to use a more recent date, arguing that the physical and cultural differences between 500,000 year old humans and today’s people are too large to consider them one species.
According to the Atlantic:
[The Jebel Irhoud] people had very similar faces to today’s humans, albeit with slightly more prominent brows. But the backs of their heads were very different. Our skulls are rounded globes, but theirs were lower on the top and longer at the back. If you saw them face on, they could pass for a modern human. But they turned around, you’d be looking at a skull that’s closer to extinct hominids like Homo erectus. “Today, you wouldn’t be able to find anyone with a braincase that shape,” says Gunz.
Their brains, though already as large as ours, must also have been shaped differently. It seems that the size of the human brain had already been finalized 300,000 years ago, but its structure—and perhaps its abilities—were fine-tuned over the subsequent millennia of evolution.
No matter how we split it, these are exciting days in the field!
Note: This post still contains a lot of oversimplification for the sake of explaining a few things.
Welcome back to our discussion of the geographic dispersion of humanity. On Tuesday, we discussed how two great barriers–the Sahara desert and the Himalayas + central Asian desert–have impeded human travelers over the millennia, resulting in three large, fairly well-defined groups of humans, the major races: Sub-Saharan Africans (SSA), Caucasians, and east Asians.
Of course, any astute motorist, having come to a halt at the Asian end of our highway, might observe that there is, in fact, a great deal of land in the world that we have not yet explored. So we head to the local shop and pick up a better map:
Our new map shows us navigational directions for getting to Melanesia and Australia–in ice age times, it instructs us, we can drive most of the way. If there isn’t an ice age, we’ll have to take a boat.
The people of Melanesia and Australia are related, the descendants of one of the first groups of humans to split off from the greater tribe that left Africa some 70k ago.
As the name “Melanesian” implies, they are quite dark-skinned–a result of never having ventured far from the equatorial zone.
Today, they live in eastern Indonesia, Papua New Guinea, Australia, and a smattering of smaller islands. (Notably, the Maori of New Zealand are Polynesians like the Hawaiians, not Melanesians, descendants of a different migration wave that originated in Taiwan.)
Fijian mountain warrior with curly, “African” style hair
There is some speculation that they might have once been wider-spread than they currently are, or that various south-Asian tribes might be related to them, (eg, “A 2009 genetic study in India found similarities among Indian archaic populations and Aboriginal people, indicating a Southern migration route, with expanding populations from Southeast Asia migrating to Indonesia and Australia,”) but I don’t think any mainland group would today be classed as majority Melanesian by DNA.
They may also be related to the scattered tribes of similarly dark-skinned, diminutive people known as the Negritos:
Males from the Aeta people (or Agta) people of The Philippines, are of great interest to genetic, anthropological and historical researchers, as at least 83% of them belong to haplogroup K2b, in the form of its rare primary clades K2b1* and P* (a.k.a. K2b2* or P-P295*).[7] Most Aeta males (60%) carry K-P397 (K2b1), which is otherwise uncommon in the Philippines and is strongly associated with the indigenous peoples of Melanesia and Micronesia. Basal P* is rare outside the Aeta and some other groups within Maritime South East Asia. …
Two Melanesian girls from Vanatu (blond hair is common in Melanesian children.)
A study of blood groups and proteins in the 1950s suggested that the Andamanese were more closely related to Oceanic peoples than African Pygmies. Genetic studies on Philippine Negritos, based on polymorphic blood enzymes and antigens, showed they were similar to surrounding Asian populations.[13]
Negrito peoples may descend from AustraloidMelanesian settlers of Southeast Asia. Despite being isolated, the different peoples do share genetic similarities with their neighboring populations.[13][14] They also show relevant phenotypic (anatomic) variations which require explanation.[14]
In contrast, a recent genetic study found that unlike other early groups in Malesia, Andamanese Negritos lack the Denisovan hominin admixture in their DNA. Denisovan ancestry is found among indigenous Melanesian and Australian populations between 4–6%.[15][16]
Australian Aboriginal man
However, the Negritos are a very small set of tribes, and I am not confident that they are even significantly related to each other, rather than just some short folks living on a few scattered islands. We must leave them for another day.
The vast majority of Aborigines and Melanesians live in Australia, Papua New Guinea, and nearby islands. They resemble Africans, because they split off from the rest of the out-of-Africa crew long before the traits we now associate with “whites” and “Asians” evolved, and have since stayed near the equator, but they are most closely related to–sharing DNA with–south Asians (and Indians.)
So we have, here, on the genetic level, a funny situation. Melanesians are–relatively speaking–a small group. According to Wikipedia, thee are about 12 million Melanesians and 606,000 Aborigines. By contrast, Tokyo prefecture has 13 million people and the total Tokyo metro area has nearly 38 million. Meanwhile, the Han Chinese–not a race but a single, fairly homogenous ethnic group–number around 1.3 billion.
Of all the world’s peoples, Melanesians/Aborigines are most closely related to other Asians–but this is a distant relationship, and those same Asians are more closely related to Caucasians than to Aborigines.
As I mentioned on Tuesday, the diagram, because it is 1-dimensional, can only show the distance between two groups at a time, not all groups. The genetic distance between Caucasians and Aborigines is about 60 or 50k, while the distance between Asians and Caucasians is around 40k, but the distance between Sub-Saharan Africans and ALL non-SSAs is about 70k, whether they’re in Australia, Patagonia, or France. Our map is not designed to show this distance, only the distances between individual pairs.
Some anthropologists refer to Bushmen as “gracile,” which means they are a little shorter than average Europeans and not stockily built
Now if we hopped back in our car and zoomed back to the beginning of our trip, pausing to refuel in Lagos, we’d note another small group that has been added to the other end of the map: the Bushmen, aka the Khoi-San people. Wikipedia estimates 90,000 San and doesn’t give an estimate for the Khoi people, but their largest group, the Nama, has about 200,000 people. We’ll estimate the total, therefore, around 500,000 people, just to be safe.
The Bushmen are famous for being among the world’s last hunter-gatherers; their cousins the Khoi people are pastoralists. There were undoubtedly more of them in the past, before both Europeans and Bantus arrived in southern Africa. Some people think Bushmen look a little Asian, due to their lighter complexions than their more equatorial African cousins.
Various Y chromosome studies show that the San carry some of the most divergent (oldest) human Y-chromosome haplogroups. These haplogroups are specific sub-groups of haplogroups A and B, the two earliest branches on the human Y-chromosome tree.[48][49][50]
Mitochondrial DNA studies also provide evidence that the San carry high frequencies of the earliest haplogroup branches in the human mitochondrial DNA tree. This DNA is inherited only from one’s mother. The most divergent (oldest) mitochondrial haplogroup, L0d, has been identified at its highest frequencies in the southern African San groups.[48][51][52][53]
The late Nǃxau ǂToma, (aka Gcao Tekene Coma,) Bushman star of “The Gods Must be Crazy,” roughly 1944-2003
In a study published in March 2011, Brenna Henn and colleagues found that the ǂKhomani San, as well as the Sandawe and Hadza peoples of Tanzania, were the most genetically diverse of any living humans studied. This high degree of genetic diversity hints at the origin of anatomically modern humans.[54][55]
Recent analysis suggests that the San may have been isolated from other original ancestral groups for as much as 100,000 years and later rejoined, re-integrating the human gene pool.[56]
A DNA study of fully sequenced genomes, published in September 2016, showed that the ancestors of today’s San hunter-gatherers began to diverge from other human populations in Africa about 200,000 years ago and were fully isolated by 100,000 years ago … [57]
So the total distance between Nigerians and Australian Aborogines is 70k years; the distance between Nigerians and Bushmen is at least 100k years.
When we zoom in on the big three–Sub-Saharan Africans, Caucasians, and Asians–they clade quite easily and obviously into three races. But when we add Aborigines and Bushmen, things complicate. Should we have a “race” smaller than the average American city? Or should we just lump them in with their nearest neighbors–Bushmen with Bantus and Aborigines with Asians?
I am fine with doing both, actually–but wait, I’m not done complicating matters! Tune in on Monday for more.
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.
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.
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:
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.
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.
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:
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
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, 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.
“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.
evolutionistx 
