Khoisan and their epicanthic fold

As promised in my previous post, I decided to explore the similar eye-shape in Khoisan Africans and East-South Asians. The former are said to be the "oldest", most diverse group of humans, that split from the original Homo sapiens group and remained isolated in Southern Africa for ovre 150,000 years. Yet they have some particular features not found in other African groups, but common in Eurasia (pale pigmented skin, and a typical Asian feature in their eyes, the epicanthic fold).

Few papers on eye-shape genes

Unexpectedly, even though tens of thousands of papers have been published on genes and their effect on human health and features, there are just a handful dealing with the epicanthic fold, and none of them have identified the genes originating it.

I have found comments on the Internet stating that it evolved independently in Africa and in Asia. That is is the result of convergent evolution (like the one that shaped mammal dolphins, fish sharks, and reptilian ichtyosaurs, or mammalian bats, birds and flying pterodactyl reptiles) where bodies are shaped to forms that are best adapted to their environments. But no in-depth analysis of genes producing these eye-shapes.

Khoisan people.

I wonder if the lack of publications is due to some unconscious bias, where scientists don't want to look into an Asian feature found in a small allegedly "ancestral" population, a fact that seems to go against the established Out of Africa origin of humans.

Why is it prevalent among the "ancient" (150 ky old) Khoisan in southern Africa, and the modern Out of Africa humans in Eastern Asia (40 ky old) and South East Asia?

Its presence elsewhere is due to migrations from Asia, moving into northern Europe, America and Polynesia.

Epicanthal Folds

The inner corner of the eye, or medial canthus has a distinct appearance in some human populations. It is quite frequent among East Asians, and also among Tibetans, Central Asians, South East Asians, American Natives, and even North European groups with ancient Asian origins, like the Sami and Finish people. Interestingly, the Khoisan people also have this feature. The map below shows its global distribution (but the prevalence is lower in America, Europe and South Asia, highest in South Africa and East Asia (Source). The map also provides some genetics to the different regions, but since it came from Reddit, and I haven't found research to back it, I am doubtful. It mixes mtDNA and Y-chromosome haplogroups with the EDAR variant.

One paper (Peng et al., 2015) studied Uyghur people, and found that EDAR V370A may be related to the fold, but it only seemed to be statistically significant for the left eye fold, but not for the right one. The authors also note that EDAR V370 plays a role in embryonic development and therefore affects ectodermal-derived features like teeth and face shape, hair thickness, sweat glands, etc. I have posted about the EDAR gene and the peopling of America. Below is the data from this paper:

The Fold itself

What is the Epicanthal fold: it is a skin fold on the upper eyelid with an oblique or vertical alignment that covers the medial canthus (inner corner) and gives the eye a distinct external appearance. It has no effect on the zize of shape of the eye itself, but it makes it appear as almond shape, more "slanted" and smaller.

"The genetic basis for epicanthus is not well known" (Source), but I came across some interesting facts about the development of this feature: all human embryos: "in all races during foetal life" (Source). Most babies lose them by the time of birth, but other babies are born "with epicanthic folds, In some people the folds are retained into adulthood, while in some people they reduce at an early age... and often grow out of it as the bridge of their nose grows" (Source).

The lower nose bridge a common feature in Asians and Khoisan people influences the muscles on their faces, and the tensions produced by them which may be one of the causes of these folds.

" It is normally most prominent during childhood. As the bridge of the nose gains more height with age, it pulls the skin away from the eye, diminishing and reshaping the fold." Source

Kwon and Nguyen, 2015, in a paper on epicanthic eyes, confirm the uncertain origin of this trait: "the developmental mechanism of Asian epicanthus has not been defined clearly" and attribute the eye shape to the thickening of a muscle (the preseptal orbicularis oculi muscle) caused by an environmental factors such as ultraviolet radiation, cold weather, dust in the air leading to "excessive frowning, and repeated excessive frowning can induce orbicularis muscle hypertrophy ... There would be a strong repeated contraction of upper orbicularis muscle and depressor supercilii muscle in the Asian eyelid from frowning. Excessive muscle contraction would be an unavoidable action in the protection of eyes from environmental harshness. Hence, environmental adaptation would be a basic cause for the formation of the epicanthus"

Those born with this trait would have been better adapted in these harsh enviornments, and the feature could have been fixed in these populations by natural selection. As the Khoisan live in the Kalahari desert, dust there could have selected for this variant. However, why is it not present among people living in the Sahara or in Saudi Arabia, also dusty, desertic, UV-radiated regions?

Asia, Africa and human origins

Interestingly, Yuan, 2019 proposing an Out of Asia and Into Africa theory, suggests an Asian origin for the distinct features of the Khoisan: "Fossils or traits indicating AMH [Anatomically Modern Humans] migration from East Asia into Africa or Europe have been noted before. First, native Africans such as Khoisans are well known to have certain East Asian features such as shoveling teeth, epicanthic fold, and lighter skins"

But how did this trait, so common in Asia reach South Africa and leave no traces in the intermediate regions (Iran, Middle East, South Asia, Caucasus, North Africa, Central Africa, Western Africa)?

Maybe the answer lies in the findings of a paper published by Krishna R Veeramah et al., 2001: the Khosian or people linked to them once occupied a much larger territory:

"Conventional thinking has tended toward a model where KhoeSan initially diverged from the ancestors of all other AMH groups and remained relatively isolated. However, the KhoeSan demonstrate deep genetic connections with other click-speaking peoples in Tanzania (Henn et al. 2011), with proposed time to the most recent common ancestor (TMRCA) estimates ranging from 35 to 110 kya (Chen et al. 2000; Knight et al. 2003; Gonder et al. 2007; Tishkoff et al. 2007). In addition, a genetic link with contemporary Ethiopian populations has also been proposed (Cruciani et al. 2002; Salas et al. 2002; Semino et al. 2002). This, along with linguistic evidence, suggests that the KhoeSan territory once covered a much larger area, extending further northwest toward the Great Rift Valley (Cavalli-Sforza et al. 1994; Blench 2006; Scheinfeldt et al. 2010). Recent autosomal-based analyses show a tendency for KhoeSan and Pygmies to cluster together and away from other sub-Saharan Africans (Zhivotovsky et al. 2003; Tishkoff et al. 2009; Sikora et al. 2011), leading to the hypothesis that the ancestors of these two populations may have once formed a proto-KhoeSan–Pygmy hunter-gatherer group that was geographically widespread before being encroached upon by expanding agricultural populations."

If their homeland reached further north, it is possible that a migration from Asia could have reached Eastern Africa and admixed with the ancestors of modern Khoisan. Then, other African groups, with archaic admixture advanced and pushed them into their current territory, closing the door for furhter mixing. These dark-skinned Africans erased the ancestral San people in East Africa.

Perhaps the Hadza and Sandawe people from Tanzania are a relict of the old San click-speaking people of East Africa

The EDAR gene mentioned further up also influences the shape of teeth, and in this, the teeth of Homo erectus and modern East Asians share the same shape! Research on the EDAR 1540C variant states that "the continuity of shovel-shaped incisors between Homo erectus and modern humans in East Asia was a rationale for the multiregional evolution theory of modern humans, although this theory is not generally supported at present" (Kimura et al., 2009).

So, a bolder alternative to its distribution could be that the ancestral origin is found among the Homo erectus, who originated in Asia, back-migrated into Asia and passed it on to the Khoisan people, with their click language. It entered the continent along a southern Asian route, leaving no trace in Southwestern Asia or North Africa. They entered Africa from the East, settling there, later modern humans picked it up from these erectus in China and in Africa, leading to its current distribution.

Let's see what further research brings.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

EDAR in ancient Amerindians and modern ones - 2025 update

The ectodysplasin A receptor (EDAR) gene, which is also known as rs3827760; 370V/A (where the V and the A represent Valine and Alanine, two aminoacids) or 1540T/C (where T and C are two nucleotides Thymine and Cytosine respectively) has an impact on tooth shape, hair thickness, sweat glands, and milk production and breasts in women. It is also found almost exclusively in Asian and Native American populaitons. It is extremely rare in Africa and Europe who carry the "ancestral" variant the 370V. The derived or mutated allele, where the Alanine was replaced for Valine in the protein or Thymine for Cytosine in the DNA strand, is a "recent" mutation known as 370A.

I have posted about it, when I mentioned that an ancient Amerindian from Brazil, a the Lapa do Santo individual who died over 6,000 years ago, carried the ancestral variant. Which is odd, since his ancestors came from Asia, and the derived variant is predominant there. This variant is also predominant among current Native Americans.

The question is: How could he have the original ancestral unmutated version while the other natives have the derived version? What about the bottle necks and founder effects, the Beringian standstill and so forth? These "filters" are supposed to have narrowed down the genetic variability in America, only a few mtDNA and Y-Chromosome haplogroups managed to enter America. So, with these limiations, wouldn't we expect all ancient Native Americans to carry the mutated Asian variant with them into America?

Posth et al. (2018) were the first to point out this anomaly:

"EDAR gene Variant. Our data show that a variant in EDAR that affects tooth shape, hair follicles and thickness, sweat, and mammary gland ductal branching and that occurs at nearly 100% frequency in present day Native Americans and East Asians was not fixed in USR1, Anzick-1, a Brazil Lapa do Santo 9600 BP individual and a Brazil Laranjal 6700 BP individual, all of whom carry the ancestral allele. Thus, the derived allele rose in frequency in parallel in both East Asians and in Native Americans."

These ancient American remains mentioned by Posth are old: the USR1 baby was 11,500 years old, Anzic-1 ~12,900 years old, the Brazilian dates are given above.

Yet the derived (mutated) form was present in the ancient site of Los Rieles "(12.0 kya) from coastal Chile of South America." (source), and the same source states that the mutated form increased to a frequency of 90% by the Early Holocene in both East Asia and America (11.6 - 5.0 kya). Posth et al. give the Los Rieles site a younger age of 10.9 kya, and confirms it had a mutated variant (See the Table 7 in Posth's Supplementary Material with a site by site detail).

Posth explains this anomaly by suggesting that the derived EDAR was not yet fixed at that time and that it evolved later, in some kind of convergent evolution on both sides of the Pacific. Probably promoted by natural selection.

A newer paper by Xiaowei Mao et al., (2021) from which the following image was taken, discusses ancient remains from the Amur River region, it also mentions EDAR.

Fig 4B. EDAR alleles. Source

The image above is captioned "(B) Allele counts for adaptive mutations of EDAR V370A in Tianyuan, ancient populations in the Amur region, and recently published ancient northern East Asians (Yumin, Bianbian, Boshan, Xiaogao, and Xiaojingshan) (Yang et al., 2020) from 40–6 ka. Purple shading represents the period of the LGM. Dots represent genotype calls (blue, ancestral alleles; red, derived alleles; gray, missing alleles). The number at the top of the bar (separated by a comma) shows the allele coverage for the derived and ancestral allele, and the number in parentheses at the bottom of the bar shows the number of individuals included in that time column. Genotypes were called using a maximum-likelihood-based method (snpAD) that takes into account possible errors in the covered alleles."

The text adds that "here we show that mutation V370A in the EDAR gene appeared in all ancient East Asians (including AR19K), except for AR33K and Tianyuan, the only two individuals in our sample predating the LGM stadial in East Asia." So it was not present in the 34.3-32.4 cal BP AR33K specimen from the Amur River area or the older Tianyuan man (40 ky old). It developed later. Remember that it was not found in ancient Amerindians either.

The paper adds that "our direct observation demonstrated that this allele emerged as early as ∼19 ka, as observed in the AR19K individual (Figure 4B), providing an older and more accurate upper boundary for the allelic age estimate." Then it spreads quickly reaching 93.7% in Asia nowadays.

Prevous estimates from 2008 (online source) reported a later date of fixation of 370A, some 10,740 years ago, it also suggested that "370A was likely at high frequency before the colonization of the Americas 10,500–14,000 years ago. Thus, the high frequency of 370A in Native Americans is most likely due to positive selection prior to migrations from Asia to America."

These explanations suggest that the derived allele was already present in the people who populated America.

But why is it not found in the other old remains? Some would argue that the first people to reach America carried the ancestral and the derived variants, and that eventually the later replaced the former. I believe that these people came from a group that carried the Ancestral allele, so this places them before the LGM, say 30 or 40 kya. Then came the post LGM migration with the mutated allele and erased all of the previous original Americans.

Another explanation lies with the Australasians: A 2021 paper on the genetics ancient Asians reported that none of the 7 ancient Jomon samples (Jomon hunter-gatherers lived in Japan) dated to ~2500–800 BC carried the derived allele. The Jomon were assimilated by the a later wave of people who now make up the Japanese population. The Ainu of Northern Japan are realated to the Jomon, and these, in turn, seem to have reached Japan using a coastal route, linking them to Southeast Asian people like tue Taiwan aborigines (Ami, and Atayal) and the Igorot, all of which are Austronesian minorities. (source). This coastal migration from ASEAN to Japan could also link them with the Onge, who only carry the ancestral allele.

Could Onge-related people have carried the ancestral allele into America in a first peopling wave, and in the process leave their genetic imprint there?

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall ©