Light Skin Genetics! ❌

This entry will be dealing with all topics revolving around human skin colour and its evolution and adaptation throughout history. So specifically, the reason this type is being highlighted in the title, is because these mutations and their associated alleles and variants are found in many African population groups both North and South of the Sahara. It is also important because it is a clear phenotypic genetic marker, that is associated nowadays primarily with Western Eurasian populations and their ancestral components. Furthermore, it is significant to remember that the depigmentation alleles in other populations outside of Europe and the Middle-East like with East Asians, are not associated with the European SLC24A5 + SLC45A2 whatsoever. With that being said, presented here are all the relevant sources dealing with the origins and spread of these variants. It is also crucial to note that just because a population lacks the derived alleles, does not mean they would be as dark as for example equatorial Africans and other populations near the equator or deep tropics, but more intermediate to generally darker tones.
*credit: 🔗The Spread of the European Light Skin Mutation Alleles
The allele was dated to have coalesced around ~22-28 KYA. Lighter skin tones evolved independently in ancestral populations of north-west and north-east Eurasia, with the two populations diverging around 40,000 years ago. Studies have suggested that the two genes most associated with lighter skin colour in modern Europeans originated in the Near East and the Caucasus regions.
🔗The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent - PMC (nih.gov)
🔗The evolution of skin pigmentation-associated variation in West Eurasia - PMC (nih.gov)

Ancient Populations:
In 2015, scientists discovered that: "The modern humans who came out of Africa to originally settle Europe about 40,000 years are presumed to have had dark skin, which is advantageous in sunny latitudes. And the new data confirm that about 8500 years ago, early hunter-gatherers in Spain, Luxembourg, and Hungary also had darker skin: They lacked versions of two genes-SLC24A5 and SLC45A2-that lead to depigmentation and, therefore, pale skin in Europeans today. But in the far north-where low light levels would favor pale skin-the team found a different picture in hunter-gatherers: Seven people from the 7700-year-old Motala archaeological site in southern Sweden had both light skin gene variants, SLC24A5 and SLC45A2. They also had a third gene, HERC2/OCA2, which causes blue eyes and may also contribute to light skin and blond hair. Thus ancient hunter-gatherers of the far north were already pale and blue-eyed, but those of central and southern Europe had darker skin."
🔗How Europeans evolved white skin | Science | AAAS
In 2015, it was discovered that a 13,000 year old samples of Caucasus Hunter Gatherers (CHG) from Georgia carried the mutation and alleles for light skin, the individual was fair skinned, and is the oldest ancient sample carrying the derived alleles which corelated with the phenotypic results.
🔗Upper Palaeolithic genomes reveal deep roots of modern Eurasians | Nature Communications
🔗Pigmentation | Genetiker (wordpress.com)
A 2015 study found that: "The second strongest signal in our analysis is at the derived allele of rs16891982 in SLC45A2, which contributes to light skin pigmentation and is almost fixed in present-day Europeans but occurred at much lower frequency in ancient populations. In contrast, the derived allele of SLC24A5 that is the other major determinant of light skin pigmentation in modern Europe (and that is not significant in the genome-wide scan for selection) appears fixed in the Anatolian Neolithic, suggesting that its rapid increase in frequency to around 0.9 in Early Neolithic Europe was mostly due to migration."
🔗https://www.nature.com/articles/nature16152
Cheddar Man, a 10,000 year old Western Hunter Gatherer from Mesolithic Britain, based on DNA analysis, was much darker than Europeans today, but would have had blue eyes. Further genomic analysis revealed the individual belonged to Y-DNA Haplogroup I2-L38 (I2a2) and mtDNA Haplogroup U5a. The Western Hunter Gatherer DNA is highest in Modern Europeans, specifically those of the Baltic States. The 🔗WHG cluster with ancient and modern Europeans, including the lighter Eastern-Hunter Gatherers, and Scandinavian Hunter Gatherers. An issue discovered, is when it comes to the skin prediction program used, 🔗the HIrisPlex-S system does have problems. It does not take into account or include the MFSD12 gene that are strongly associated with darker skin pigmentation, which is a major drawback, meaning it cannot detect very deeply pigmented black skin alleles. Which is why the authors said: "That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci [...] therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is present. It is unlikely that this individual has the darkest possible pigmentation." In 2024, it was revealed in a study 🔗https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10927518/ that phenotypically, other WHG in France also had pale to intermediate skin tones.
🔗Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe’s First Farmers | Science
🔗Ancient genomes indicate population replacement in Early Neolithic Britain | Nature Ecology & Evolution
🔗Ancient genomes indicate population replacement in Early Neolithic Britain (whiterose.ac.uk)
🔗First modern Britons had 'dark to black' skin, Cheddar Man DNA analysis reveals | Genetics | The Guardian
🔗Was Cheddar man white after all? | Daily Mail Online
In 2018, a study was released showing many late Mesolithic Scandinavians (SHG) of 9,500 years ago in Northern Europe had blonde hair and light skin, which was in contrast to their contemporaries such as the darker Western Hunter Gatherers (WHG).
🔗Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation - PMC (nih.gov)
Another study in 2018, showed that the Eastern Hunter Gatherers (EHG), Scandinavian Hunter Gatherers, and the Baltic Hunter Gathers, all had the derived alleles for light skin pigmentation. 
🔗https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789860/
Two papers, one released in the year of 2018, and the other in 2023, showed that the KTG (Kaf Taht el-Ghar) and KEB (Khef El Baroud) populations, 7,000 and 5,000 years ago respectively in Morocco had light skin (SLC24A5 and OCA2) and lighter eye colours, the evidence strongly points to it being most likely derived from their Early European Farmer (EEF) ancestry, with the KTG being 100% Anatolian Farmer, and the KEB being 50% Anatolian Farmer related ancestries. In contrast, these genes were not found in the other population groups that existed in the region like the IAM (Ifri n'Amr Ou Moussa) communities that were dark skinned and dark eyed, who also completely lacked any EEF ancestry, being primarily derived from the prior paleolithic Iberomaurusians.
🔗pnas.org/doi/pdf/10.1073/pnas.1800851115
In 2019, a study on remains in the Calcolithic Southern Levant (4500 - 3900/3800 BCE), revealed that the cultural changes in the region, were influenced by the movements of people. The researchers sampled 22 genome-wide aDNA (Ancient DNA), and discovered that ~57% of their ancestry was local Levantine Neolithic, ~17% Iran Calcholithic and ~26% Anatolia Neolithic. The study also noted they carried genes for blue eyes and fair skin: "We highlight three findings of interest. First, an allele (G) at rs12913832 near the OCA2 gene, with a proven association to blue eye color in individuals of European descent, has an estimated alternative allele frequency of 49% in the Levant_ChL population, suggesting that the blue-eyed phenotype was common in the Levant_ChL. Second, an allele at rs1426654 in the SLC24A5 gene which is one of the most important determinants of light pigmentation in West Eurasians is fixed for the derived allele (A) in the Levant_ChL population suggesting that a light skinned phenotype may have been common in this population."
🔗https://www.sciencedaily.com/releases/2018/08/180820104204.htm
🔗https://www.nature.com/articles/s41467-018-05649-9
The Gibraltar National Museum in 2020, conducted a reconstruction of Calpeia, a 7,500 year old woman of Anatolian Farmer descent, who's ancestry showed that farmers from Anatolia during the Neolithic period had a high percentage of alleles for light skin, but dark straight hair and eyes. By contrast, hunter-gatherers from central and western Europe show genetic markers for dark skin and light eyes. The woman was between 25 and 40 years old upon her burial. She had 90% of her ancestry from Early European Farmers (EEF) and 10% from local Mesolithic Hunter Gatherers.
🔗How it was Made: The Facial Reconstruction of Calpeia (reachextra.com)
🔗Neolithic facial reconstruction reveals secrets of Gibraltar's earliest humans (nationalgeographic.com)
In 2021, Parabon Nanolabs using 1.24 million SNPs showed that Ancient Egyptian samples from the New Kingdom, Late Period, and Greco-Roman era, carried the SLC24A5 AA derived alleles, and had phenotypic traits for lighter skin which was shown to be in high frequency with the Neolithic Anatolians. These Egyptians were characterized as having a very light brown skin tone, but with other traits like darker hair and eye colours, with no freckles. The phenotypic results from the laboratory, were said to be consistent with the studies on Ancient Egyptians remains showing genomic ties to Near-Eastern populations.
🔗3 Egyptian mummy faces revealed in stunning reconstruction | Live Science
In 2022, the DNA of Otzi the Ice man from 5,500 years ago, he was 0.591405 while modern Sardinians are 0.589335 on the polygenic, which shows he was only slightly more pigmented than Southern Europeans today (basically no difference at all, ~1%), and not as dark as the Mesolithic Western Hunter Gatherers. He was given the Haplogroup K1, and was around 90% EEF ancestry, and 10% WHG or EHG, very similar to Calpeia in autosomal composition. For comparison modern West Africans scored around 0.76.
🔗https://dna-explained.com/category/otzi/
“The weighted genetic score of dark pigmentation in the Iceman is estimated to be 0.591, higher than the score of present-day southern European populations taking Sardinians as an example (Table S11), which the Iceman shares closest genetic affinity to (Figure S1) and which represent the highest level of pigmentation among modern-day European groups, although it is lower than the score of ancient LBK farmers and the Luxembourg_Loschbour.DG hunter-gatherer.”
Lazardis et al. (2022), noted that: "Blond hair was present in the Neolithic of Anatolia (Turkey) at Barcın, Chalcolithic Southeastern Europe (Romania at Bodrogkeresztur), Chalcolithic of the Levant (Israel) [14.3%], and a Minoan from Lasithi."
🔗https://www.science.org/action/downloadSupplement?doi=10.1126%2Fscience.abq0755&file=science.abq0755_sm.pdf

Modern Populations:
A study in 2013, estimated  that "the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000–19,000 years, well after the first migrations of modern humans into Europe."An older study from 2014, showed that this variant has been selected in Europeans, over the last thousands of years, including the light hair, eye colour traits.
🔗https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525146/
🔗https://www.pnas.org/doi/full/10.1073/pnas.1316513111

🔗https://www.psu.edu/news/research/story/studies-skin-color-gene-across-global-populations-reveal-shared-origins/
Multiple studies have shown that the common SLC24A5 gene linked with light pigmentation in Europeans was introduced into East Africa from Europe over five thousand years ago. These alleles can now be found in the San, Ethiopians, and Tanzanian populations with Afro-Asiatic ancestry. The SLC24A5 in Ethiopia maintains a substantial frequency with Semitic-Cushitic populations, compared with Omotic, Nilotic or Nigerian-Congolese groups whom lack its presence. It's inferred that it may have arrived into the region via migration from the Levant, which is also supported by linguistic evidence. In the San people, it was acquired from interactions with Eastern African pastoralists.
🔗Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool (core.ac.uk)
🔗Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection - PMC (nih.gov)
In 2017, the genes were said to have been introduced into South East Africa some 5,000 years ago, where it has now risen to high frequency. The origin of this allele in the region according to the evidence is undoubtable attributed to the geneflow from non-Africans into these populations. The variant in Africans, is the exact same as the haplotype background as that of Europeans, reflecting geneflow from Western Eurasia. It would initially move from Ethiopia to Tanzania and elsewhere further south of the continent and undergo extreme selective adaptation in the Khoisan.
🔗Loci associated with skin pigmentation identified in African populations - PMC (nih.gov)
A study from 2021, similarly revealed that the mutation, after being introduced from a non-African population whom migrated into the Horn of Africa, would experience a substantial positive selection in the Khoesan speaking tribes. Continuing, it was shown that the rs1426654 which plays a key role in pigmentation is so common within East African populations of higher Afro-Asiatic ancestry, and was said to be confirmed by multiple studies to have been spread via introgression by West Asian sources. 
🔗Evolutionary genetics of skin pigmentation in African populations - PMC (nih.gov)
🔗Rapid evolution of a skin-lightening allele in southern African KhoeSan - PMC (nih.gov)
🔗https://www.pnas.org/doi/full/10.1073/pnas.1801948115
According to Meng Lin (2018): "Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. […] The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. […] We show that the allele was introduced into the KhoeSan only 2,000 years ago via a back-to-Africa migration and then experienced a selective sweep. The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans." In this context, and population genetics, the 15% association is considered to be substantial, as well as its relation to phenotype, according to the researchers. 
Overall, globally this A111T mutation in the SLC24A5 gene, predominates in populations with Western Eurasian ancestry. The geographical distribution shows that it is nearly fixed in all of Europe and most of the Middle East, extending east to some populations in present-day Pakistan and Northern India. It shows a latitudinal decline toward the Equator, with high frequencies in North Africa (80%), and intermediate (40-60%) in Ethiopia and 🔗Somalia, and in select Tanzanian populations (35%).
🔗Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection (silverchair.com)
🔗Anthromadness: Some Horn African phenotypes: The Supposed Controversy

Origins of Light Skin in East Asian Populations:
Research shows that Europeans and East Asians were shown to have quite distinct polymorphism genes and evolution/adaptation for their light skin mutations.
🔗Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians | Molecular Biology and Evolution | Oxford Academic (oup.com)
In the case of north-east Asia and the Americas, a variation and loss of the MFSD12 gene is responsible for their lighter skin colour.


Other Findings and Research!
Ancient Hominids hundreds of thousands of years ago had light skin under the hair, before living and adapting in the tropical savannah, which caused a need for darker skin with the loss of excessive body hair.
🔗New gene variants reveal the evolution of human skin color | Science | AAAS
🔗Scientist Suggests Cancer Drove Skin Color Evolution (nbcnews.com)
Dark skin may have also been a later adaptation.
🔗https://www.science.org/content/article/new-gene-variants-reveal-evolution-human-skin-color#:~:text=Two%20mutations%20that%20decrease%20expression,created%20today%20by%20these%20mutations.
Some studies have also noted limitation with the lack of more representative samples when it comes to skin colour. They also suggest utilizing more sophisticated phenotyping methods, larger sample sizes, and additional diverse population samples from Africa and other understudied areas of the world to fully capture the evolutionary history of light skin, as well as human variability.

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