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."

---

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

Genetic diversity among the Chachapoyas

Online there are many sites promoting the theory that the Native American Chachapoya people of Peru are blond, fair, white skinned people who came from the Old World, Celts or maybe voyagers from Carthage (depending on the site). This theory has no scientific backing. It is just another quack theory found on the Internet.

I posted eleven years ago about these people (see: The Peruvian Chachapoyas or "white indians" - Aug. 2014). Todays post will explore some additional research that was conducted since then about their genetic makeup. We will follow several papers that have investigated the mtDNA and Y-chromosomes of modern Chachapoyans and their conclusions (Spoiler: No, they are not Caucasian, they are Amerindian).

The first is a paper published in 2017 (Guevara, E. K., Palo, J. U., Sajantila, A., and Guillén, S. (2018). Explorando dinámicas poblacionales ancestrales en el noreste peruano: marcadores uniparentales de ADN en los Chachapoyas modernos. Boletín De Arqueología PUCP, (23), 127–158. https://doi.org/10.18800/boletindearqueologiapucp.201702.004)

The authors studied the mtDNA and Y-chromosomes in different populations of Peru's northern region, the Chachapoya, Jivaro, Huanca and Cajamarca people. The highlights of this study are the following:

• Europeans admixed with these groups in an asymmetrical manner witht he Chachapoyas having only 11% of maternal European lineages (mtDNA) but a high proportion of paternal influx (43%) from Europeans.
• When looking exclusively at the Native American component, "the Chachapoya population displayed relatively high levels of genetic diversity and large Tajima’s D and Fu’s Fs values. Tis suggests that no drastic reduction in the effective population size has taken place in the past."

Before someone starts imagining that the high ratio of European Y-chromosomes is due to some mysterious ancient immigration of "White" people into the area, we should consider more credible options. The authors clearly state that this is very frequent among South American people:

"As in many other populations in the Americas, a higher proportion of the foreign component (mostly European) has been observed in Y-chromosome lineages (40%). This phenomenon of asymmetric gene flow, e.g. Chachapoya: mitochondrial = 11%, Y = 40%, is a well-known phenomenon reported in other Native American populations, which reflects the history of European conquest during the second half of the 16th century. These proportions tend to vary depending on the degree of interbreeding of the populations studied."

Maternal inherited mtDNA

As expected, 89% of the Chachapoya sample contains Native American haplogroups (A, B, C, and D). The remaining 11% is non-Native. This is higher than among the other people in the area. When looking at the Amerindian component, it displays a high diversity: "All populations studied have high levels of haplotype diversity. The Chachapoya population shows one of the highest indices (H = 0.9671 ± 0.0051). The Jívaro (H = 0.9343 ± 0.0178) and Huancas (H = 0.9286 ± 0.0325) groups exhibit intermediate levels, and the Cajamarca group (H = 0.9715 ± 0.0137) has the highest index."

Paternal Y-chromosome

The situation is different when it comes to the Y-chromosome, although the Native American haplogroup Q is present in 60% of the samples, the other 40% is non-Amerindian. Among other populations non-Amerindian haplogrups range from 4% among the Jívaros to 52% in Cajamarca. Like the maternal lineages, it is also very diverse: "High haplotype diversity was observed in all populations studied (H > 0.92). The Chachapoya and Cajamarca populations exhibited the highest values, with H = 0.9974 ± 0.0032 and H = 1 ± 0.0388, respectively."

Why is the genetic diversity so high?

The authors suggest several reasons for a high diversity in a population should have lost it as it underwent epidemics, war, and death due to exploitation, first by the Inca rulers and later by the Spanish conquerors:

1. The Incas between 1470 and 1532 AD applied the "mitmaq" policy to control the Cachapoyas, it was a forced resettlement that implanted people from other parts of the empire in a new territory to control it, and extirpation and resettlement in other parts of the empire of rebel populations (like the Cachapoyas). This paper says that up to 50% of the Cachapoyas were relocated elsewhere.
2. Spanish Conquest. European diseases provoked epidemics that exterminated the natives, an event known as "The Great Dying". Then, the Spaniards recruited the surviors, mostly men, and forced them to work in mines, fields, and enlisted them as soldiers and porters in their search for El Dorado, provoking a high death toll among males. Many people ran and hid in the jungles, escaping from Spanish opression.
3. Strife. War caused the collapse of the fortified Cachapoya citadel of Kuélap c.1570 where many young men and even children were massacred.

These events would have reduced Cachapoyan diversity and introduced new genetic variants in the area. But, are there other factors that could have increased the local diversity?

The paper offers several possibilities:

They were alreeady highly diversified on a genetic level before Incaic conquest. Their location in an area that forms corridors linking the Andean mountain ranges with the Pacific coast and the Amazon jungles could have promoted the movement of different ethnic groups through the area, enriching its genetic pool.

During the Colonial period, the Spaniards searched for El Dorado using the Cachapoya area as a base for their expeditions. They brought many indians from different areas to support these expeditions, many could have stayed here later. There is also a record of 300 Tupi natives from Brazil that reached Cachapoya territory in 1549, coming from the Atlantic seabord of Brazil along the Amazon and Marañon Rivers. They too could have added variety to the local genes.

The Spaniards imitated the Inca tactics and "reduced" the natives (reducciones) it was similar to the mitimaq; natives from a wide area were relocated and concentrated forcibly in villages to make it easier to tax, control, and christianize them.

So after the original collapse of the primitive inhabitants of this region between 1470 and 1550, the inflow of new stock altered the local genome, increasing its diversity.

Another paper published in 2020 (Guevara EK, Palo JU, Översti S, King JL, Seidel M, Stoljarova M, Wendt FR, Bus MM, Guengerich A, Church WB, Guillén S, Roewer L, Budowle B, Sajantila A. Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru. PLoS One. 2020 Dec 31;15(12):e0244497. doi: 10.1371/journal.pone.0244497. PMID: 33382772; PMCID: PMC7774974.) also reported the efect of the Inca and Europeans on the Cachapoyas during the 1400s and 1500s, stressing the impact it had on the men: "This would suggest that the severe male-biased population contraction may be associated with post-European contact events."

See table in the paper, replicated in the image below:

Y-chromosome haplogroups in Cachapoyas. Source

The "Third Component"

The 2020 paper didn't only find the two expected components in the Cachapoyas: The European and the Native American component, which is what is found in mestizo, admixed populations in America. The study "showed a third unknown component present in much higher proportion in three study populations, Chachapoyas, Awajún and Wampís; but nearly absent in the reference Hispanic population (HIS). The 3rd unknown component was consistently observed with increasing number of K in plots including also other continental datasets."

The authors conclude that the "Chachapoyas harbour an autosomal variation component of undetermined origin" and that this "third autosomal component ... could not be readily associated to any modern source population. WRithin Chachapoyas, inter-subgroup differences in the commonness of this component was observed especially in odríguez de Mendoza, but nearly absent in e.g. Chillao, La Jalca and Uchucmarca. On the regional level... the synthetic '3rd component group' showed no obvious affinity to reference datasets of African, European or Asian origin, nor to the populations included from the Americas.... The exact origin of this variation component remains thus elusive; it could derive from a yet unsampled ancient or modern population, for example representing assemblages that have developed locally in semi-isolated populations with no distinctive cultural features. On this note, a recent study of South American populations has shown the existence of two autosomal components of alleged Amazonian origin: 1) The first one, distributed along the eastern slopes of the Northern Andes in Ecuador and Colombia, and 2) the second one, observed mostly in populations from the Peruvian rainforest. Due to geographic proximity and the commonness of the 3rd unknown component among the Amazonian Jívaro, we could suggest ties to the second component, although this cannot be tested with our current resolution."

Not European

Just in case someone thinks it is a Celtic, Carthaginian or Phoenician signal, the paper is clear: "although the origin of this component could not be clarified, we speculate it may be of Native American origin as it remains distant to African, European and Asian populations."

Guevara, co-author of the 2020 paper gave a dissertation in 2022 (Guevara, E. K. (2022). Genetic insights on old riddles: the Chachapoyas from the Northeastern Peruvian cloud forests. Helsingin yliopisto. https://helda.helsinki.fi/bitstream/handle/10138/342172/guevara_evelyn_dissertation_2022.pdf?sequence=1&isAllowed=y) ratifying these findings and suggesting that analysis of ancient pre-conquest and pre-Inca remains can help shed more light on this matter. Guevara states that her team was analyzing the remains of 82 ancient Chachapoyans and would publish the results. To date the otucome of this analysis is not available.

---

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

The Peruvian Chachapoyas or "white indians"

The Spanish conquistador Pedro Cieza de León (1520 - 1554) wrote a chronicle in which he described Peru at the time of Spanish conquest. His "Crónicas del Perú" also recorded the history of the local native groups and, of course, the Incas and the tribes that they had subjected.

See this 2025 update: Genetic Diversity Among Chahapoyas (published 03.Oct.20225).

He mentions a certain group of Indians, The "Chachapoyan" natives [1], that lived in the Andes, in what is now Northern Peru, right next to Ecuador, in the Cachapoyas District of the Department of Amazonas. Theirs was an area with high mountain ranges: the Calla-Calla range in the south reaching 4,300 m (14,100 ft.) and the Cordillera Oriental to the east with 3,500 m. (11,500 ft.), with forests. The Marañon River flows through the area, draining towards the Amazon. (See map below).

The Chachapoyan region has been inhabited for over 8,000 years, but the group we know as Chachapoya, arrived much later: their most relevant cultural remains date back to 800 C.E. and their society peaked during the eleventh century C.E. (Their buildings at Olán, Yálape, Congó and especially Cuélap are monumental). They were subdued by the Inca around 1470 and incorporated as a province of their Empire after a though campaign. Many Chachapoyans were uprooted and sent to Cuzco and other parts of the Empire, where they were resettled and given new land to grow their crops on (This was a usual practice of the Incas, to dilute local resistence). [4]

After the Spanish conquistadors arrived, they too dominated the Chachapoyans (1535), it was during this period that Pedro Cieza de León visited the region and recorded his encounter with them. He described them as:

"These Indians that live at Chachapoyas are the most white and good looking of all those that I have seen in my travels through the Indies [America] , and their women were so beautiful that merely due to their good nature, many of them deserved to be women of the Incas and be taken to their temples of the sun; and so we see nowadays that the remaining Indian women of this lineage are extremely pretty, because they are white and very well built..." [1]

Text quoted above. From [1]

The "White" natives, true or false?

I have read some posts and articles that imply that these people have a Pre-Hispanic European origin, that is, that they somehow reached America long before Columbus did. And that is why they were "white skinned". I am skeptical about this, because trans-Atlantic communications probably did take place (I have posted about possible Phoenician, Greek, Micenian and Carthaginian navigators reaching the eastern coasts of America), but from there to the Andean foothills of Peru there is quite a distance and a long stretch of inhospitable Amazonian jungle. I doubt that the Chachapoyans were stray Phoenicians or similar sailors.

The official version is that they were a Native American group of people: The symbols that they used to decorate their buildings and the manner in which they mummified their dead suggests that the ancestral Chachapoyas may have reached their territory from the coastal areas of Peru or, from the northern mountain ranges [4].

Little is known regarding their pre-Inca or pre-Hispanic history. The oldest written reference about them dates back to January 14, 1538 in a letter from Alonso de Alvarado to the Spanish leader, Francisco Pizarro after his campaign to conquer the region.

The meaning of the word "Chachapoyas" is uncertain, and it is definitively not a Quechua or Aimará word, (which is what the Incas spoke). Little is known about the language spoken by the Chachapoyas before their conquest by the Inca, so we cannot shed any light on the matter from that angle.

There are of course many theories regarding its meaning: the local chronicler, Garcilaso de la Vega wrote in the 1600s that a Jesuit priest who accompanied the Spanish invaders in 1535 said it meant "Land of strong men", Lecuanda in 1792 suggested that it meant "Mountain of clouds", but these are only conjectures. [3]

They, like most of the American Natives suffered a dramatic population drop after the initial contact with the Spanish conquerors (they were decimated by the epidemics of measles, small pox, and plague that took place in 1546, 1558-59, 1585-91, 1614, 1618-19 and 1721). The population which in 1549 was nearly 88,000 strong, fell to 2,200 by 1793. Many Chachapoyans ran away into the junges to avoid being subjected to the forced-labor of the Spaniards. [3]

This must have bottlenecked the population considerably. Add to this the fact that many of them had been transplanted to other parts of the Inca empire after their defeat in 1470, and that other groups were placed in their homeland. The consequences of this dispersal and impantation plus massive population loss is that the original aboriginal Chachapoyan stock has been seriously diluted since 1470.

Below is a photograph from a book [5] which puts forward the theory that the Carthaginians escaped the destruction brought upon them by Rome after the Punic wars and reached America, and their descendants are... the Chachapoyans! The fair children among the Chachapoyans are known as "gringuitos", diminutive for "gringo" which is the way that Americans (from the U.S.A) are given in Latinamerica. But, wouldn't Carthaginians look like North Africans or Middle Eastern People (darker skinned, dark eyes, dark hair) instead of being blonde?

I posted about this in February 2011, so it does not surprise me. But, as I said above, it is hardly probable that they would have reached the western shores of South America.

To assume that contemporary fair haired children living in that region as "white" caucasoids with a pre-Columbian origin is an over simplification of complex facts. There may have been considerable European admixture during the Colonial period and later, as the population recovered during the nineteenth and twentyeth centuries. Only by studying the genes of their ancestors may we glean some useful information on their origins.

Fortunately the Chachapoyas mummified their dead, so we have plenty of material with a potential to yield useful genetic sequences.

The Mummies

Samples taken from seven Chachapoyan mummies were sequenced in a genetic study; only three yielded viable mtDNA which were assigned to haplogroups B2, M and D1, the others had insufficient coverage. [2]

The haplogroups B2 and D1 are a clear indication that the maternal lineage was American. Haplogroup M is quite strange because it is not one of the founding lineages of American Natives. It is found in Asia and only one other study mentions haplogroup M in the New World. Perhaps future studies will find more cases of it.

Anyway all three haplogroups are of a East Asian origin. This is ratified by a principal component analysis of SNPs overlapping between modern populations and the Chachapoyans which places them clearly in the "Amerindian" group together with the Aymara and Mayas, far from the Europeans and admixed hispanics (Colombian, Puerto Rico and Mexicans from Los Angeles) and closer to the East Asian groups. These people were definitively not "white" Europeans, they were Native Americans with ties to Eastern Asia. Below is an example of two of the samples that were sequenced:

Of course the alleged European origin is sustented by the fact that some of the mummies exhibit, as one blog states: "... Chachapoyas had curly brown or red Caucasoid hair, and not stiff black Mongoloid Amerindian hair.... the individual had red or reddish-brown Caucasoid hair". Below is a photo and some links to photographs of these mummies, so you can see them and decide for yourself:

Photo 1, Photo 2, Photo 3, Photo 4, Photo 5.

The hair is indeed wavy not straight. The color... well it seems to be brown, not the usual jet-black of the Amerindians. But, does this necessarily imply pre-Columbian European admixture?

The mummies are not dated. Are they older than 1535 or more recent? If older then we can assume that their brown hair is not due to post-discovery admixture. But even then it does not imply European ancestry.

I have posted extensively on Red Haired Native Americans during January 2014 and as I posted in my criticism to the Paracas cone heads, I believe that Neanderthal genes may be responsible for red or brown hair among pre-Hispanic Native Americans.

Red hair is a feature found in several Native mythical hominins (This post links to several posts on red haired hominins). and the reason for this, I believe is some ancient memory of their interaction with Neanderthals in America.

So maybe Europeans and Chachapoyans share a similar origin for their hair color: a common Neanderthal ancestry.

Sources

[1] Pedro Cieza de León, Obras Completas 1984, Cavileño, Madrid, pp. 104
[2] Meredith L. Carpenter, et al., (2013) Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. The American Journal of Human Genetics, Volume 93, Issue 5, 7 November 2013, Pages 852–864. doi: 10.1016/j.ajhg.2013.10.002
[3] Inge Schjellerup, (2005). Incas y españoles en la conquista de los chachapoya. Fondo Editorial PUCP.

[4] Kauffmann Doig, Federico. (2000). Primera expedicion arqueologica a los mausoleos chachapoya (s) de la laguna de las momias (Dpto. de Amazonas, Perú). Chungará (Arica), 32(1), 49-54. Recuperado en 06 de agosto de 2014, de http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-73562000000100009&lng=es&tlng=es. 10.4067/S0717-73562000000100009.
[5] Hans Giffhorn, Wurde Amerika in der Antike entdeckt?: Karthager, Kelten und das Rätsel der Chachapoya, C.H. Beck. 2013.
Further Reading on Chachapoyans: An Overview of Chachapoya Archaeology and History, by Adriana von Hagen.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©