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.

 

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Two Exciting Papers on African Genetics

I loved that movie
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.