A comparison among ancient mutations

In this article we are going to make some comparison among ancient mutations for red and blond hair and blue eyes.

Red hair in Neanderthals

Over the past years, some websites about red hair claimed that Europeans inherited red hair from interbreeding with Neanderthals. A website like Eupedia even writes  that Europeans inherited from Neanderthals light-coloured eyes and hair too, but, as a matter of fact, there is no evidence for that. 

It is true that an MC1R mutation (mutations are also called variants) has been found on two Neanderthal individuals, but this mutation (Arg307Gly) is not among those we modern humans have. The two Neanderthals are one from the Sidròn Cave (Asturias, northern Spain), dating back to 43,000 years ago, and the other from the Lessini Mountains, near Verona (Veneto region, north-east of Italy), dating back to 50,000 years ago. Here’s a short article about them and the original study 

Also, as of now, neither the mutations for blond hair nor those for light-coloured eyes have been found in Neanderthals. 

This 2017 study argues that Neanderthals may have contributed to pigmentation in Europeans, but in a minor way.

Anyway, it’s interesting that Neanderthals had a different mutation for red hair, because it means that the same result can be reached through different evolutionary paths. Something similar happened with blond-haired Melanesians. Around 5-10% of Melanesians, particularly in the Solomon Islands and Vanuatu, display naturally blond hair, arising from a unique homozygous mutation in the TYRP1 gene (R93C, Rs387907171), which impairs melanin production in hair follicles without affecting skin pigmentation. This variant is absent in Europeans, which means in this case too the same result (blond hair) has been reached through two different paths.

Blond hair in fossils

Afontova Gora ("Afont Mountain") is a Late Upper Paleolithic and Mesolithic Siberian complex of archaeological sites located on the left bank of the Yenisey River, near the city of Krasnoyarsk, Russia. The complex was first excavated in 1884. 

In 2014, during salvage excavation before the construction of a new bridge over the Yenesei River, the mandible and five lower teeth of a teenage girl (named Afontova Gora 3) were found: she was estimated to be around 14–15 years old. In 2017, the remains were dated to around 16,090 BC.

Phenotypic analysis shows that Afontova Gora 3 carries the derived rs12821256 allele on KITLG gene associated with, and likely causal for, blond hair colour, making Afontova Gora 3 the earliest individual known to carry this derived allele.

If you are a follower of this blog, you probably know the Yenisei river from this article on the Yenisei Kyrgyz. 

Blue eyes in fossils

If you search online for the first appearance of blue eyes, you’ll probably get dates such as 6000, 7000 or 8000 years ago. Truth is that blue eyes appeared much earlier and the two most ancient skeletons with this mutation have been both found in Italy.

The first skeleton was found in Ripari Villabruna. Veneto region, north-east of Italy (the same where the “red-haired” Neanderthal was found).

Ripari Villabruna  is a small rock shelter with Mesolithic burial remains. It contains several Cro-Magnon burials, with bodies and grave goods dated to 14,000 years ago. The rock shelters were named by their discoverer "Ripari Villabruna" (ripari = shelters).

A grave that contained a well-preserved skeleton (named Villabruna 1) was discovered at the base of the archaeological layers in 1988: it was the skeleton of an adult male, about twenty-five years old, characterized by a relatively tall stature for the time period.

The genomic analysis revealed that this individual carried alleles like the derived HERC2 variant for light eye pigmentation (genotype rs12913832 GG), which means he probably had blue eyes.

This individual is also the oldest documented example of haplogroup R1b found anywhere. 

The second blue-eyed individual has been found in Apulia region, in a cave called Grotta Le Mura, near the city of Monopoli. The individual is an infant boy, aged around 17 months and dating back to 17,000 years ago. Here’s the link to the study. He too has got the homozygous mutation on HERC2 gene for blue eyes. 

Strangely enough, this finding is not as famous as the one in Ripari Villabruna and, as a matter of fact, it doesn’t even have a page on Wikipedia in English. 

MC1R mutations are harder to find in fossils

The most ancient MC1R mutation found so far was found… on dogs! It is called R301C and was found on archeological dog specimens over 10,000 years of age, although we don’t know if the mutation was functional. Many modern dog breeds carry this mutation, especially some Spitz breeds and Hound breeds. Here’s a short article on the subject, along with the link to the original study. 

Another interesting finding concerns… an ancient frog! As you can read here, the pigment phaeomelanin was found in the fossil of a 10-million-year-old frog, an extinct species called Pelophylax pueyoi, but we don’t know whether the frog was really reddish/yellow or not. Since pheomelanin is considered phototoxic, meaning it can contribute to cellular damage under intense UV exposure, it’s interesting it already existed 10 million years ago in a frog. Probably, in some way, this species of frogs found it useful. Today, phaeomelanin can still be found in certain reptiles and amphibious, but it’s rarer than it is in mammals and birds.

Pelophylax pueyoi

As for humans, unfortunately the situation is not as clear as with blond hair and blue eyes, for several reasons. 

Both blue eyes and blond hair can be predicted even with incomplete DNA data, as it often happens with ancient fossils. Their genetic signals are more stable and are better covered in datasets, so modern modelings can predict these pigmentations quite easily. Blue eyes, for example, are one of the traits that can be predicted more reliably. As for blond hair, all the genes involved (such as  KITLG, SLC24A4, SLC45A2, etc) have strong lightening effect. On the contrary, MC1R (as we have seen in a previous article) has many mutations, but not all of them result in red hair and some of them only result in red hair in combination with others. These mutations, in order to be detected, require a good coverage, which is not always possible in ancient fossils. For this reason, many scientific papers don’t mention the MC1R gene. It also seems that the MC1R gene is more susceptible to post-mortem damage (PMD), such as deamination, which alter the read of the sequencing. 

For example, in this study there is a whole chapter about this problem with the MC1R gene in ancient samples. 

So, as of now, archaeogeneticists don’t have fossil remains for which they can say “Probably this indivudual had red hair”.  

There are many amateur blogs and websites, run by genetics enthusiasts, that report that such and such an ancient individual had red hair because the remains carried such and such a variant of the MC1R gene, but these data cannot be taken seriously.

Egyptian mummies

Now, probably some of you might wonder “What about Egyptian mummies with red hair?” As a matter of fact, it seems that some Egyptian pharaohs had natural red hair, like Ramesses II and his father Seti I. Actually, more mummies exhibit red hair, but it’s not clear whether it is natural or not (although it shouldn’t be very difficult to find out: you only need to check hair roots). So, what about the MC1R gene of these mummies? Well, truth is that Egyptian mummies (especially the embalmed ones) are not the best for a DNA analysis. Most of the embalming techniques included evisceration (and internal organs are the best place for extracting DNA), desiccation with natron and resin coatings, and all of this can destroy the DNA. The bodies look well-preserved, but their DNA is gone. Besides, most of these mummies underwent recent contamination, for example because their tombs have been opened several times, or because they have been touched and manipulated by people not wearing gloves or face masks. 

The same problem arises with the so-called Gebelein mummies, seven naturally preserved human bodies dating to approximately 3400–3200 BC, One of these mummies, a young adult male, exhibits red hair, but although the body still has internal organs, including the brain and muscles, ancient DNA analysis has been limited by the degraded state of organic material, caused by prolonged exposure and natural mummification processes.

Tarim mummies

Other famous mummies with red hair are the so-called Tarim mummies. In 2021, a first genomic analysis was performed on 12 of these mummies, but it’s not clear whether some of the red-haired ones were included. Here’s the study of the genomic analysis,  but as you can see it only focuses on the individuals’ ancestry, since the team’s aim was to prove they were not from Europe (as if being from Europe were a mortal sin). If you want to learn something about the mummies’ phenotype, you have to scroll the page and download the file from the link Supplemetary Data 1. Here, on the last page, you can find the phenotypic traits. 

From what I could understand, 10 out of 12 individuals had the mutation rs885479 (V92M), which today is present especially in South Asia. However, it is considered a weak mutation, so, probably, if alone, it doesn’t result in red hair. Also, for some of the individuals analysed this mutation is heterozygous, while in order to have red hair you need for the mutation to be homozygous. However, one of the mummies has two more mutations: rs2228479 (V60L) and rs1805008 (R160W). The former is another weak one, while the latter is considered strong and is one of the most common, but this individual carries the “normal” allele, not the mutated one. So, to cut a long story short, some of these mummies did have one or more mutations for red hair, but probably none of them had this hair colour. 

It is important to notice that the mummies chosen for the 2021 analysis were among the oldest ones, so, hopefully, a new analysis will be done in the future, choosing more recent mummies and maybe some of the red-haired ones as well.

The Tarim Basin, with the Taklamakan Desert, and area of the Tarim mummies with main burial sites.

In a following article we will see when mutations for red hair could have first appeared.