Genetics of white skin - The White Indians

Another post about white-skinned native people in America.

Today's post will look into what causes light-colored skin, and address the question of why people can have white skin without having European ancestry (like the Chachapoyas in Peru).

The color of the skin depends on the amount of melanin, a pigment that causes the skin to darken. Melanin plays an important role in protecting the skin from damage caused by ultraviolet (UV) rays from the sun, which can cause burns, and over the years, skin cancer.

Since humans seem to have evolved in the tropical and subtropical zones of Africa, which have high levels of solar radiation, the basal color of human skin was dark as more melanin was necessary to protect the skin in equatorial regions.

But, as our ancestors moved out of Africa and reached temperate and cold areas, which due to their latitude receive lower levels of solar radiation, the dark skin became a problem. Sunlight is necessary to help the body convert a provitamin called 7-dehydrocholesterol, into previtamin D3. This process requires ultraviolet radiaton, and takes place in the skin.

Low levels of vitamin D3 can cause health problems such as ricketts in children, poor calcium absorption (leading to fragile bones), lower immunity, and impaired muscle development. Those who lived in regions with little sunlight and had pale skin produced more vitamin D3 than their dark-skinned counterparts, and had a selective advantage. They survived, mated, and passed this trait to their offspring.

>> Read our Vitamin D fact sheet

So, people who live in Northern Europe inherited a genetic trait that favors sunlight absorption and vitamin D3 production in the overcast, long-winters, short-summers, region they live in which also receives sunlight with a low incidence angle (that weakens it). Their skin is pale.

Now we know that it is due to a mutation unique to European people in the genes SLC24A5, TYR, OCA2, and SLC45A2.

The people living in northern Asia also have pale skin, for the same reasons, but they developed it through a different mutation. This is known as convergent evolution. The same outcome through different genes and adaptations (think about dolphins, and sharks or bats, birds and pterosaurs).

The East Asian gene is still unknown, but rs885479 a site inside the OCA2 gene is thought to play a role in their white skin. But there may be other genes involved. In fact, a paper suggests that this is the case, white skin among Asians may be polygenic, this means that several genes work together to produce this effect.

Below we cite a paper reporting the whitening effects of another gene, the MFSD12 gene in East Asians and Amerindians.

The people who left Africa and lived in areas with high levels of solar radiation (New Guinea, Australia, Tropical India, and also in the Amazon region of South America, all retained the dark-skinned genes, due to selection, as it protects them from sunburns and cancer.

Native Americans

Since Amerindians are said to have originated in Eastern Asia and Siberia, they too should carry the Asian variant in low levels (due to bottle necks and founder effects).

But, as mentioned previously, European discovery and conquest brought diseases that exterminated nearly 90% of the Native Americans, then they introduced millions of African slaves and all groups intermingled causing a genetic mixture that impacted on skin color of the modern populations.

A study conducted in 2023 (by Ang et al.) analyzed the genetics of a group of people known as Kalinago in the Island of Dominica in the Caribbean. These people have a high level of African and Native American ancestry (~87%) so the white skin effect added by their European background is minimized, this helps eliminate it as a confounding factor. It found that European ancestry with the SLC24A5 and SLC45A2 genes reduced skin darkness by only 5 and 4 melanin units while "Native American ancestry had the highest effect on pigmentation and reduced it by more than 20 melanin units." The authors checked the genetics but were not able to identify the genes involved in causing this light-skinned effect (hypopigmentation) in the Amerindians.

The authors used a Melanin Index to classify skin color by measuring the amount of light reflected by the skin on the inside of the upper part of the arm of the subjects. The average value ranged between 20.7 and 79.7 units.

The authors conclude that "Additional Native American hypopigmenting alleles of significant effect size remain to be identified. Previously characterized variants do not explain this difference. It is possible that multiple hypopigmenting variants of small effect sizes are together required to reach Native American and/or East Asian levels of hypopigmentation, individually having insufficient effect to detect in the Kalinago, given our power limitations."

In plain English: they could't identify any genes among the Native ancestry that could account for the skin whitening effect. So, if it is a gene that has a big effect, it hasn't been found, or, if it is the cummulative small effects of many genes, the individual impact is too small to be detected by their methods.

The "previously characterized variants" mentioned above may refer to an earlier paper from 2019 by Adhikari et al., that analyzed sampled of 6,357 Latinamericans and identified a gene linked to lighter-colored skin tone, MFSD12. It is also found in East Asians. The authors suggest that positive selection for this variant began some 10,834 year ago (CI: 5,266–33,801 years ago). Below is the average frequencies of this variant in Asian and Amerindian people, in Africa and West Eurasia it is zero.

The mutation is the SNP rs2240751 on the "the third exon of the major facilitator superfamily domain containing 12 (MFSD12) gene".

Worldwide allele frequencies of rs2240751 (MFSD12). See Fig. 11 in paper Suppl. Info.

The frequency is high in America roughly 30% on average and peaks at 55% among the Quechua. In East Asia it is lower,~18% on average and 37% among Japanese.

Perhaps it was higher among some natives in America leading to whiter skin (like those reported by the Spanish chroniclers in the 1500s as we will see in tomorrow's post).

Dark Skin variants

The 2019 paper also reports a skin-darkening variant: "The derived allele for the index SNP (rs11198112) is associated with darker skin pigmentation, in contrast to the effect of the majority of variants associated with skin pigmentation... The derived allele is segregating at low to moderate frequency across many populations, but reaches its highest frequency (>50%) in Native Amazonians and Melanesians."

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

Early European and African Presence in South America? (Chachapoyas)

Today I will follow up on the "third component" of the Cachapoyas mentioned in a recent post-

I read a paper cited in by Guevara et al. (2020) in their references, which discussed this component (Barbieri C, Barquera R, Arias L, Sandoval JR, Acosta O, Zurita C, Aguilar-Campos A, Tito-Alvarez AM, Serrano-Osuna R, Gray RD, Mafessoni F, Heggarty P, Shimizu KK, Fujita R, Stoneking M, Pugach I, Fehren-Schmitz L. The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast. Mol Biol Evol. 2019 Dec 1;36(12):2698-2713. doi: 10.1093/molbev/msz174. PMID: 31350885; PMCID: PMC6878948.)

I came across some interesting facts which I share below.

The paper also looked into post-Columbian (after 1492) introgression of European (conquest) and African (slave trade) genes into the native Amerindians. The chart below is from this paper, it gives the admixture dates based on different analytical tools.

Admixture dates between European and African sources. Estimates of admixture are calculated with the MALDER and WAVELETS methods. Dates are expressed in generations ago and converted to calendar years using a generation time of 29 years.. Source

As expected most dates are located between the late 1500s and mid 1700s, but a few fall way earlier, even before the discovery of America! around 1380 AD.

The authors explain this oddity as follows:

"Finally, studies of ancient DNA have shown that as much as one third of the ancestry in modern Native Americans could be traced to western Eurasia (Raghavan et al. 2014). Similarly, modern-day Europeans were found to be a mixture of three ancestral populations, one of which was a population deeply related to Native Americans (Lazaridis et al. 2014). These findings imply that European (or more accurately, Eurasian) ancestry found in modern-day Native Americans may not have been acquired exclusively through admixture during the post-Columbian period, but instead may reflect a much deeper origin. It is therefore possible that the WT method is picking up this signal of shared ancestry, which predates European colonization, and hence infers dates for some populations that are too early to be consistent with the first appearance of the conquistadors in the Americas, only after 1492."

I am skeptical, a signal of ancient pre-Beringian Eurasian genetic material shared by Western Europeans and Native Americans? Far fetched. Perhaps the method is wrong, the generation times are shorter, or there was some type of pre-Columbian contact with Europeans (Genoese, Venetian, Viking, or evern older like Romans, Carthaginians, Greek, Minoans, and why not, Phoenicians).

The Tumbes signal indicates Yoruba (African) input around 1380! Could these have been slaves of European mariners? But, why would these genes appear among people living along the Pacific coast of South America, and not along the Atlantic coast? Wouldn't an early contact with Europeans or Africans have brought the same catastrophic Old World diseases to America and wiped out the native population?

Further studies could answere these questions.

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

Chinchorros, Europe and their tetanus strain...

A paper published in Nature in Sept. 2023, reported about different Clostridium tetanus (tetanus) strains found in ancient archaeological remains, some of which included Chinchorro mummies. Their findings are interesting and may shed some light on the European DNA found in Chinchorro remains.

The authors studied the Clostridium tetani a microbe which produces a potent neurotixin that causes tetanus or "lockjaw" disease (the tetanus neurotoxin or TeNT). They identifed TeNT variants in South American archaeological remains, and one TeNT variant, extracted from a 6000-year-old Chinchorro mummy was still active, and provoked paralysis in mice.

Their data included samples from Japanese (3000 BP), Egyptian (3900 BP), Chinchorro remains (5900 BP). And modern samples too.

Normally you'd expect more divergence to be associated with older lineages, that evolved separately from others, over longer periods of time. The study reported "five strains (Sanganji-A2-Tooth, Chinchorro-Mummy-Bone, SLC-France-Tooth, Karolva-Tooth, Chincha-UC12-24-Tooth) were identified ... as possessing higher estimated levels of strain variation."

They measured the DNA damage in the bacteria samples to use it as an indicator of antiquity (more damage implies an older sample which has had more time to degrade), this also affects the human DNA and mtDNA.

But the researchers noticed that bacterial DNA had less damage than the mtDNA in the human tissue they came from. The authors interpreted this by assuming that less damage meant less age, implying that the tetanus and the humans carrying them were not contemporary: "damage rates were generally lower than the corresponding human mtDNA rates, especially for some samples (e.g., Tenerife-004, Tenerife-013, Chinchorro-Mummy-Bone), which may suggest that a subset of the archeological samples have been colonized by C. tetani at later dates." Notice it includes two samples from the Canary Islands, and the Chinchorro bone sample.

Phylogenetic Tree. From the paper

The ancient lineages are highlighted in bold font. And as expected, certain lineages cluster together, the "1H" lineage is found in ancient American samples while "2" lineages were Old World ones, and the "X" clade was found exclusively in Europe. We marked the Chinchorro samples with red arrows in the image above.

The authors point out that "Notably... the Sanganji, Tenerife, Chinchorro, and Chincha samples do not show evidence of branch shortening in the tree indicative of ancient genomes, and instead cluster with modern strains. These... tend to have higher rates of strain variation, which could affect branch lengths, or low damage rates potentially indicative of a more recent origin."

When they focused on the "tent" gene sequences they found that "The largest number of unique substitutions occurred in tent/Chinchorro... which is the oldest sample in our dataset [with] 18 unique substitutions not found in modern tent, and 12 of these are shared with tent/El-Yaral and 10 with tent/Chiribaya. The three associated acBins also cluster as neighbors in the phylogenomic tree ... and the three associated archeological samples originate from a similar geographic region in Peru and Chile ... suggest[ing] a common evolutionary origin for these C. tetani strains and their unique neurotoxin genes and highlight tent subgroup 3 as a distinct group of tent variants exclusive to ancient samples."

This is, in my opinon, proof of an ancient origin (hichly diverse, unique), and associated with variants that are found in ancient samples from the same geographical region in Peru and Chile.

However, the authors suspect that the tetanus varieties found in these samples are recent and came from the researchers who handled the remains or from the soil that was in contact with them. It is a good point:

"...a variety of environmental factors and mechanisms may account for the presence of toxigenic clostridia in aDNA samples. These include the possibility of their introduction by human handling of archeological samples by researchers, their introduction from human handlers during ancient mummy preparation practices, or post-mortem colonization by environmental (e.g., soil) clostridia. Regarding our identification of C. tetani in numerous mummy samples, it is worth mentioning that although today mummies are manipulated taking in consideration cross-contamination, during the 1990s when some of these mummies were first discovered, fieldwork procedures were different. Thus, it is notable that the Chinchorro mummy sample from which we identified the TeNT/Chinchorro toxin, was not always handled by researchers using nitrile gloves during digging; also, these mummies have been manipulated by many researchers since their initial discovery (B. Arriaza, Personal communication)."

But, how could have the samples from El Yaral and Chiribaya have a similar strain? Were the same researchers handling all of these bones? And, why aren't these strains of tetanus found in modern samples in the countries from which these researchers of the 1990s came from?

This 1H strain is a singularity, and the authors find it strange they note that only one modern sample (you can see it in the tree, in gray, as 2017.061) clusters with the American strains of Chichorro. It was found in France. How could an ancient Amerindian tetanus microbe appear in France?

The scientists explain this incongruity as follows: (aDNA = ancient DNA)

"Lineage 1H in particular has undergone the greatest expansion through the newly identified aDNA-associated C. tetani genomes, from one known sample derived from a patient in France in 2016 10, to 9 additional draft genomes assembled from ancient DNA. This suggests that a broader diversity of 1H strains may exist in undersampled environments. Interestingly, these newly identified lineage 1H strains share a common pattern of originating from the Americas, which suggests that a lineage 1H C. tetani strain specific to (or abundant within) this region may have colonized these samples at some point in the past."

Nevertheless, the ancient Amerindian samples "revealed novel variants and lineages of TeNT, including the newly identified “subgroup 3” toxins: TeNT/Chinchorro, TeNT/El-Yaral toxins, and TeNT/Chiribaya-Alta. Not only do these toxins share a similar mutational profile, but they are derived from a similar geographic area (regions of Peru and Chile in South America) and their associated C. tetani genomes also cluster phylogenetically as the closest neighbors... the tent/Chinchorro gene also happened to be most divergent from modern tent sequences by possessing the greatest number of unique substitutions. Despite being the most divergent tent, [it]... did not show strong patterns of DNA damage, and the damage level was weaker than that for human mtDNA. This indicates that, despite originating from the oldest sample in our dataset and possessing a unique tent variant, it is possible that the Chinchorro mummy-associated C. tetani strain may be a relatively “newer” strain that colonized the sample post-mortem."

Another paper, the one that identified the H1 variant in France, includes a tree (see its Figure 1), as can be seen, the only H1 sample detected is located on a separate branch that is distinct from all other branches A to G in Clade 1. This means an ancient origin, close to the root from which all these tetanus variants originated.

A recent paper, published this year studying botulism and tetanus, also reported "DNA damage patterns" and also found "that human mitochondrial DNA (mtDNA) exhibited significant damage ... consistent with expectations for degraded ancient DNA. However, the majority of toxin genes displayed minimal damage... This discrepancy suggests that most toxin genes in our dataset have undergone less degradation than the endogenous host DNA. "

They say that human handling, scavengers or soil contamination could have included younger bacteria into the samples, but also add a new suggestion: that the bacteria are more resistant to degradation. They stat that: "This may be due to differential DNA preservation (Clostridium spores may be more resistant to environmental degradation, leading to better long-term DNA preservation)." They suggest ways by which further studies could prove which factor causes this different degradation.

This 2025 study also indicates that TeNT "was also identified in aDNA from horses, wild bears, gorillas, and chimpanzees." However, I must add, that these animals were not found in Pre-Hispanic America, so they couldn't act as natural sources..

Let's hope that further research clarifies the degradation issue, and more information is gathered on the 1H variant and its distribution around the world.

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