Siberia as the Origin and Migration place of “Light Skin” genes SLC24A5 and SLC45A2, about 22,000 to 28,000 years ago?

Damien Marie AtHope’s Art

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Two genes, SLC24A5 and SLC45A2, are most associated with lighter skin colour in modern Europeans.

SLC24A5

“Sodium/potassium/calcium exchanger 5 (NCKX5), also known as solute carrier family 24 member 5 (SLC24A5), is a protein that in humans is encoded by the SLC24A5 gene that has a major influence on natural skin colour variation. The NCKX5 protein is a member of the potassium-dependent sodium/calcium exchanger family. Sequence variation in the SLC24A5 gene, particularly a non-synonymous SNP changing the amino acid at position 111 in NCKX5 from alanine to threonine, has been associated with differences in skin pigmentation. The SLC24A5 gene’s derived threonine or Ala111Thr allele (rs1426654) has been shown to be a major factor in the light skin tone of Europeans compared to Sub-Saharan Africans, and is believed to represent as much as 25–40% of the average skin tone difference between Europeans and West Africans. Possibly originating as long as 19,000 years ago, it has been the subject of selection in the ancestors of Europeans as recently as within the last 5,000 years, and is fixed in modern European populations. It was introduced into Khoisan people via “back-to-Africa” migration around 2,000 years ago, is partly responsible for their differing skin tone to most other African populations. One of the earliest known samples of the threonine allele is 13,000 years old from Satsurblia Cave in Georgia. The allele was widespread from Anatolia to Ukraine and Iran at the beginning of the Neolithic.” ref

“Membrane-associated transporter protein (MATP), also known as solute carrier family 45 member 2 (SLC45A2) or melanoma antigen AIM1, is a protein that in humans is encoded by the SLC45A2 gene. SLC45A2 has been found to play a role in pigmentation in several species. In humans, it has been identified as a factor in the light skin of Europeans and as an ancestry-informative marker (AIM) for distinguishing Sri Lankan from European ancestry. Mutations in the gene have also been identified as the cause of human Type IV oculocutaneous albinism. SLC45A2 is the so-called cream gene responsible in horses for buckskin, palomino, and cremello coloration, while a mutation in this gene underlies the white tiger variant. In dogs, a mutation to this gene causes white fur, pink skin, and blue eyes.” ref

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Earliest Colonization of Europe: Aurignacian and Gravettian cultures, both with different Migration routes, and different Subclades of C1 Y-DNA

“The earliest hominid ancestors of humans most likely had pale non-pigmented skin covered with dark black hair, like the chimpanzee and other great apes. As hominids gradually lost their fur between 1.2 and 4 million years ago, to allow for better cooling through sweating, their naked skin was exposed to sunlight. In the tropics, natural selection favoured dark-skinned human populations as high levels of skin pigmentation protected against the harmful effects of sunlight. Genetic evidence also supports this notion, demonstrating that around 1.2 million years ago there was a strong evolutionary pressure which acted on the development of dark skin pigmentation in early members of the genus Homo. All modern humans share a common ancestor who lived at least 200,000 years ago in Africa.” ref

“From the origin of hairlessness and exposure to UV-radiation to less than 100,000 years ago, archaic humans, including archaic Homo sapiens, were dark-skinned. As some Homo sapiens populations began to migrate, the evolutionary constraint keeping skin dark decreased proportionally to the distance north a population migrated, resulting in a range of skin tones within northern populations, although the bulk of humans remained dark-skinned. By the time modern Homo sapiens evolved, all humans were dark-skinned. Some researchers suggest that human populations over the past 50,000 years have changed from dark-skinned to light-skinned and that such major changes in pigmentation may have happened in as little as 100 generations (≈2,500 years) through selective sweeps.” ref

“After the ancestors of West Eurasians and East Eurasians diverged more than 40,000 years ago, lighter skin tones evolved independently in a subset of each of the two populations. In West Eurasians, the A111T allele of the rs1426654 polymorphism in the pigmentation gene SLC24A5 has the largest skin lightening effect and is widespread in Europe, South Asia, Central Asia, the Near East and North Africa. (Basu Mallick et al.) estimated the coalescent age (split date) for this allele to between ~28,000 and ~22,000 years ago. The second most important skin-lightening factor in West Eurasians is the depigmenting allele F374 of the rs16891982 polymorphism located in the melanin-synthesis gene SLC45A2. From its low haplotype diversity, Yuasa et al. (2006) likewise concluded that this mutation (L374F) “occurred only once in the ancestry of Caucasians.” ref

“Summarizing these studies, Hanel and Carlberg (2020) decided that the alleles of the two genes SLC24A5 and SLC45A2, which are most associated with lighter skin colour in modern Europeans originated in West Asia about 22,000 to 28,000 years ago, and these two mutations each arose in a single carrier. This is consistent with Jones et al. (2015), who reconstructed the relationship between Near Eastern Neolithic farmers and Caucasus Hunter-Gatherers: two populations which carried the light skin variant of SLC24A5. Analysing newly sequenced ancient genomes, Jones et al. estimated the split date at ~24,000 bp and localised the separation to somewhere south of the Caucasus. However, a coalescent analysis of this allele by Crawford et al. (2017) gave a more narrowly constrained, and earlier, split date of ~29,000 years ago (with a 95% confidence window from 28,000 to 31,000 years ago).” ref

“The genetic mutations leading to light skin, though partially different among East Asians and Western Europeans, suggest the two groups experienced a similar selective pressure after settlement in northern latitudes. The theory is partially supported by a study into the SLC24A5 gene which found that the allele associated with light skin in Europe “determined […] that 18,000 years had passed since the light-skin allele was fixed in Europeans” but may have originated as recently as 12,000–6,000 years ago “given the imprecision of method”, which is in line with the earliest evidence of farming. Paleolithic Cro-Magnon “European Early Modern Humans” groups, as well as Early Holocene Western and central European hunter-gatherers (Western Hunter Gatherers) have been suggested to have been dark skinned based on DNA analysis, with a number of the most prominent light-skin tone gene variants found in modern Europeans being introduced by Anatolian Neolithic Farmers that migrated into Europe beginning around 9,000 years ago, with selection pressure for lighter skin intensifying from the Neolithic period onwards.” ref 

“Research by Nina Jablonski suggests that an estimated time of about 10,000 to 20,000 years is enough for human populations to achieve optimal skin pigmentation in a particular geographic area, but that development of ideal skin coloration may happen faster if the evolutionary pressure is stronger, even in as little as 100 generations. The length of time is also affected by cultural practices such as food intake, clothing, body coverings, and shelter usag,e which can alter the ways in which the environment affects populations. 8,000-year-old hunter-gatherers in Spain, Luxembourg, and Hungary were dark skinned while similarly aged hunter gatherers in Sweden were light skinned (having predominately derived alleles of SLC24A5, SLC45A2 and also HERC2/OCA2). Neolithic farmers entering Europe at around the same time were intermediate, being nearly fixed for the derived SLC24A5 variant but only having the derived SLC45A2 allele in low frequencies. The SLC24A5 variant spread very rapidly throughout central and southern Europe from about 8,000 years ago, whereas the light skin variant of SLC45A2 spread throughout Europe after 5,800 years ago.” ref

“The light skin variants of SLC24A5 and SLC45A2 were present in Anatolia by 9,000 years ago, where they became associated with the Neolithic Revolution. From here, their carriers spread Neolithic farming across Europe. Lighter skin and blond hair also evolved in the Ancient North Eurasian population. A further wave of lighter-skinned populations across Europe (and elsewhere) is associated with the Yamnaya culture and the Indo-European migrations bearing Ancient North Eurasian ancestry and the KITLG allele for blond hair. Furthermore, the 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 and Cushitic speaking populations, compared with Omotic, Nilotic, or Niger-Congo speaking groups. It is 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. Meanwhile, in the case of East Asia and the Americas, a variation of the MFSD12 gene is responsible for lighter skin colour. The modern association between skin tone and latitude is thus a relatively recent development.” ref

“Huang et al. (2021) found the existence of “selective pressure on light pigmentation in the ancestral population of Europeans and East Asians”, prior to their divergence from each other. Skin pigmentation was also found to be affected by directional selection towards darker skin among Africans, as well as lighter skin among Eurasians. Crawford et al. (2017) similarly found evidence for selection towards light pigmentation prior to the divergence of West Eurasians and East Asians. The 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.” ref

Ancient Populations

“A study from 2015 found that genes contributing to fair skin were nearly fixed in the Anatolian Neolithic Farmers: “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 appears fixed in the Anatolian Neolithic, suggesting that its rapid increase in frequency to around 0.9 (90%) in Early Neolithic Europe was mostly due to migration.” In 2018, a study was released showing many late Mesolithic Scandinavians from 9,500 years ago in Northern Europe had blonde hair and light skin, which was in contrast to some of their contemporaries, the darker Western Hunter Gatherers (WHG).” ref

“However, a 2024 paper found that phenotypically most of their studied WHG individuals carried the dark skin and blue eyes characteristic of WHGs, but some other WHGs in France they sequenced also had pale to intermediate skin pigmentation. Another entry in 2018, showed that the Eastern Hunter Gatherers (EHG), Scandinavian Hunter Gatherers (SHG), and the Baltic foragers, all had the derived alleles for light skin pigmentation. The Western Steppe Herders, an early Bronze Age population are believed to have also contributed to the skin and hair pigmentation in Europe, having a dominant effect on the phenotypes of Northern Europeans in particular. Bagnasco, G et al. (2024), discovered that the phenotypic traits for a group of Etruscans from 3,000 to 2,700 years ago showed a population with blue-eyes, light to dark brown hair, and pale white to intermediate skin tones.” ref

“A research paper in 2017 indicated Egyptians at Abusir el-Meleq from 2,590 to 2,023 years ago, had a derived variant for the SLC24A5 locus, which contributes to lighter skin pigmentation, and was shown to be at high frequency in Neolithic Anatolia, accordant with the sample’s ancestral affinities. Parabon NanoLabs (2021) based on this data from Schuenemann et al. (2017) using whole genome sequencing and advanced bioinformatics, further discovered that these ancient Egyptian samples instead had a light brown complexion, but carried the main gene for light skin. They stated the results were highly consistent with Schueneman et al.’s findings. In the same year, according to phenotype SNP analysis, the precolonial Guanche inhabitants of the Canary Islands were showing consistent traits such as light and medium skin, with dark hair and brown eyes. A paper conducted by Fregel, Rosa et al. (2018) showed that in North Africa, Late Neolithic Moroccans had the European/Caucasus derived SLC24A5 mutation and other alleles and genes that predispose individuals to lighter skin and eye colours.” ref

“Variations in the KITL gene have been positively associated with about 20% of melanin concentration differences between African and non-African populations. One of the alleles of the gene has an 80% occurrence rate in Eurasian populations. The ASIP gene has a 75–80% variation rate among Eurasian populations compared to 20–25% in African populations. Variations in the SLC24A5 gene account for 20–25% of the variation between dark and light skinned populations of Africa, and appear to have arisen as recently as within the last 10,000 years. The Ala111Thr or rs1426654 polymorphism in the coding region of the SLC24A5 gene reaches fixation in Europe, but is found across the globe, particularly among populations in Northern Africa, the Horn of Africa, West Asia, Central Asia, and South Asia. The rs1426654-A allele in the SLC24A5 also plays a significant role in skin tone variation in North India.” ref

“The derived Ala111Thr allele in the SLC24A5 gene locus known to be associated with lighter skin pigmentation was in top selection signals in the Wolayta, and the select alleles of single-nucleotide polymorphisms rs1426654 and rs1834640 characteristic of fair complexions in Eurasian populations were of high frequency (47.9%) in this Omotic-speaking Ethiopian population. A higher proportion of these genes MYEF2-SLC24A5 were seen in high altitude (Amhara and Tigray) compared with the low-altitude (Afar) Ethiopians, with also elevated European admixture proportions observed in the high altitude tribes. The authors did not rule out the possibility that these European alleles were differentially selected in high-altitude populations due to unknown selective pressures. Africans carrying Eurasian ancestry like the Toubou were shown to have signals at HERC2 rs1129038, a major contributor to blue eye color in Europeans, as well as a signal at SLC24A5 rs1834640, a major contributor to pigmentation.” ref

“Solute carrier family 24 member 5 (SLC24A5) regulates calcium in melanocytes and is important in the process of melanogenesis. The SLC24A5 gene’s derived Ala111Thr allele (rs1426654) has been shown to be a major factor in light skin pigmentation and is common in Western Eurasia. Recent studies have found that the variant represents as much as 25–40% of the average skin tone difference between Europeans and West Africans. This derived allele is a reliable predictor of phenotype across a range of populations. It has been the subject of recent selection in Western Eurasia, and is fixed in European populations.” ref

“Solute carrier family 45 member 2 (SLC45A2 or MATP) aids in the transport and processing of tyrosine, a precursor to melanin. It has also been shown to be one of the significant components of the skin color of modern Europeans through its Phe374Leu (rs16891982) allele that has been directly correlated with skin color variation across a range of populations. This variation is ubiquitous in European populations but extremely rare elsewhere and shows strong signs of selection.” ref

“The TYR gene encodes the enzyme tyrosinase, which is involved in the production of melanin from tyrosine. It has an allele, Ser192Tyr (rs1042602), found solely in 40–50% of Europeans and linked to light-colored skin in studies of South Asian and African-American populations.” ref

“A number of genes known to affect skin color have alleles that show signs of positive selection in East Asian populations. Of these, only OCA2 has been directly related to skin color measurements, while DCT, MC1R, and ATRN are marked as candidate genes for future study.” ref

24,000 Years Old Proto-North Eurasian Language (Ancient North Eurasian) migrations? Became: Proto-Afroasiatic, Proto-Sino-Tibetan, Proto-Transeurasian, Proto-Indo-European, Proto-Yeniseian, Proto-Na-Dene, Proto-Caucasian, Sumerian, Proto-Austronesian, and the Basque language

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“Lighter skin and blond hair were in the Ancient North Eurasian population. The two genes SLC24A5 and SLC45A2, which are most associated with lighter skin colour in modern Europeans, originated about 22,000 to 28,000 years ago, and these two mutations each arose in a single carrier. 13,000-year-old samples of Caucasus Hunter Gatherers (CHG) from Georgia carried the mutation and derived alleles for very fair-skinned pigmentation similar to Early Farmers (EF).” ref

Eastern hunter-gatherer 14,000 to 9,000 years ago

“In archaeogenetics, eastern hunter-gatherer (EHG), sometimes east European hunter-gatherer or eastern European hunter-gatherer, is a distinct ancestral component that represents Mesolithic hunter-gatherers of Eastern Europe. The eastern hunter-gatherer genetic profile is mainly derived from Ancient North Eurasian (ANE) ancestry, which was introduced from Siberia, with a secondary and smaller admixture of European western hunter-gatherers (WHG). However, the relationship between the ANE and EHG ancestral components is not yet well understood due to lack of samples that could bridge the spatiotemporal gap.” ref

“During the Mesolithic, the EHGs inhabited an area stretching from the Baltic Sea to the Urals and downwards to the Pontic–Caspian steppe. Along with Scandinavian hunter-gatherers (SHG) and western hunter-gatherers (WHG), the EHGs constituted one of the three main genetic groups in the postglacial period of early Holocene Europe. The border between WHGs and EHGs ran roughly from the lower Danube, northward along the western forests of the Dnieper towards the western Baltic Sea. Schematic formation of the EHGs, through a main ancestry of Ancient North Eurasians (ANE), and a smaller admixture of WHGs.” ref

“During the Neolithic and early Eneolithic, likely during the 4th millennium BCE, EHGs on the Pontic–Caspian steppe mixed with Caucasus hunter-gatherers (CHGs) with the resulting population, almost half-EHG and half-CHG, forming the genetic cluster known as Western Steppe Herder (WSH). WSH populations closely related to the people of the Yamnaya culture are supposed to have embarked on a massive migration leading to the spread of Indo-European languages throughout large parts of Eurasia.” ref

“Haak et al. (2015) identified the EHG as a distinct genetic cluster in two males only. The EHG male of Samara (dated to ca. 5650–5550 BCE) carried Y-haplogroup R1b1a1a* and mt-haplogroup U5a1d. The other EHG male, buried in Karelia (dated to ca. 5500-5000 BC) carried Y-haplogroup R1a1 and mt-haplogoup C1g. The authors of the study also identified a WHG cluster and an SHG cluster, intermediate between WHG and EHG. They suggested that EHGs harbored mixed ancestry from Ancient North Eurasians (ANEs) and WHGs. Researchers have proposed various admixture proportion models for EHGs from WHGs and ANEs. Posth et al. (2023) found that most EHG individuals carried c. 70% ANE ancestry and c. 30% WHG ancestry The WHG-like ancestry was most likely not derived from the Oberkassel and Villabruna clusters directly, but from a related and yet unsampled Epigravettian population. The high contribution from Ancient North Eurasians is also visible in a subtle affinity of the EHG to the 40,000-year-old Tianyuan man from Northern China and other East/Southeast Asians, which can be explained by geneflow from a Tianyuan-related source into the ANE lineage (represented by Malta and Afontova Gora 3), which later substantially contributed to the formation of the EHG.” ref

“The formation of the EHG ancestral component is estimated to have happened 13,000–15,000 years BP. EHG associated remains belonged primarily to the human Y-chromosome haplogroups R1, with a lower frequency of haplogroup J and Q. Their mitochondrial chromosomes belonged primarily to haplogroup U2, U4, U5, as well as C1 and R1b. Geneflow from an East Asian-like source towards the EHG contributed around 9.4% (4.4%–14.7%). EHGs may have mixed with “an Armenian-like Near Eastern source”, which formed the Yamnaya culture, as early as the Eneolithic (5200-4000 BC). The people of the Yamnaya culture were found to be a mix of EHG and a “Near Eastern related population”. During the 3rd millennium BC, the Yamnaya people embarked on a massive expansion throughout Europe, which significantly altered the genetic landscape of the continent. The expansion gave rise to cultures such as Corded Ware, and was possibly the source of the distribution of Indo-European languages in Europe.” ref

“The people of the Mesolithic Kunda culture and the Narva culture of the eastern Baltic were a mix of WHG and EHG, showing the closest affinity with WHG. Samples from the Ukrainian Mesolithic and Neolithic were found to cluster tightly together between WHG and EHG, suggesting genetic continuity in the Dnieper rapids for a period of 4,000 years. The Ukrainian samples belonged exclusively to the maternal haplogroup U, which is found in around 80% of all European hunter-gatherer samples. The people of the Pit–Comb Ware culture (PCW/CCC) of the eastern Baltic bear 65% EHG ancestry. This is in contrast to earlier hunter-gatherers in the area, who were more closely related to WHG. This was demonstrated using a sample of Y-DNA extracted from a Pit–Comb Ware individual. This belonged to R1a15-YP172. The four samples of mtDNA extracted constituted two samples of U5b1d1, one sample of U5a2d, and one sample of U4a.” ref

“Günther et al. (2018) analyzed 13 SHGs and found all of them to be of EHG ancestry. Generally, SHGs from western and northern Scandinavia had more EHG ancestry (ca 49%) than individuals from eastern Scandinavia (ca. 38%). The authors suggested that the SHGs were a mix of WHGs who had migrated into Scandinavia from the south, and EHGs who had later migrated into Scandinavia from the northeast along the Norwegian coast. SHGs displayed higher frequences of genetic variants that cause light skin (SLC45A2 and SLC24A5), and light eyes (OCA/Herc2), than WHGs and EHGs.” ref

“Members of the Kunda culture and Narva culture were also found to be more closely related with WHG, while the Pit–Comb Ware culture was more closely related to EHG. Northern and eastern areas of the eastern Baltic were found to be more closely related to EHG than southern areas. The study noted that EHGs, like SHGs and Baltic hunter-gatherers, carried high frequencies of the derived alleles for SLC24A5 and SLC45A2, which are codings for light skin. Mathieson et al. (2018) analyzed the genetics of a large number of skeletons of prehistoric Eastern Europe. Thirty-seven samples were from Mesolithic and Neolithic Ukraine (9500-6000 BC). These were classified as intermediate between EHG and SHG. The males belonged exclusively to R haplotypes (particularly subclades of R1b1 and R1a) and I haplotypes (particularly subclades of I2). Mitochondrial DNA belonged almost exclusively to U (particularly subclades of U5 and U4).” ref

“A large number of individuals from the Zvejnieki burial ground, which mostly belonged to the Kunda culture and Narva culture in the eastern Baltic, were analyzed. These individuals were mostly of WHG descent in the earlier phases, but over time EHG ancestry became predominant. The Y-DNA of this site belonged almost exclusively to haplotypes of haplogroup R1b1a1a and I2a1. The mtDNA belonged exclusively to haplogroup U (particularly subclades of U2, U4 and U5). Forty individuals from three sites of the Iron Gates Mesolithic in the Balkans were estimated to be of 85% WHG and 15% EHG descent. The males at these sites carried exclusively R1b1a and I (mostly subclades of I2a) haplotypes. mtDNA belonged mostly to U (particularly subclades of U5 and U4). People of the Cucuteni–Trypillia culture were found to harbor about 20% hunter-gatherer ancestry, which was intermediate between EHG and WHG. Narasimshan et al. (2019) coined a new ancestral component, West Siberian Hunter-Gatherer (WSHG). WSHGs contained about 20% EHG ancestry, 73% ANE ancestry, and 6% East Asian ancestry.” ref

“The EHGs are suggested to have had mostly brown eyes and light skin, with “intermediate frequencies of the blue-eye variants” and “high frequencies of the light-skin variants.” An EHG from Karelia was determined by Günther (2018) to have high probabilities of being brown-eyed and dark haired, with a predicted intermediate skin tone. Another EHG from Samara was predicted to be light skinned, and was determined to have a high probability of being blue-eyed with a light hair shade, with a 75% calculated probability of being blond-haired. The rs12821256 allele of the KITLG gene that controls melanocyte development and melanin synthesis, which is associated with blond hair and first found in an individual from Siberia dated to around 17,000 years ago, is found in three Eastern Hunter-Gatherers from Samara, Motala and Ukraine c. 10,000 years ago, suggesting that this allele originated in the Ancient North Eurasian population, before spreading to western Eurasia. Many remains of East Hunter-Gatherers dated to circa 8,100 years ago have also been excavated at Yuzhny Oleny island in Lake Onega. The Ancient North Eurasian (ANE) ancestry is by far the main component of the Yuzhny Oleny group, and is among the highest within the rest of the Eastern Hunter-Gatherers (EHG).” ref

“As hunter-gatherers, the EHGs initially relied on stone tools and artifacts derived from ivory, horns, or antlers. From circa 5,900 BCE, they started to adopt pottery in the area of the northern Caspian Sea, or possibly from beyond the Urals. In barely three or four centuries, pottery spread over a distance of about 3,000 kilometers, reaching as far as the Baltic Sea. This technological spread was much faster than the spread of agriculture itself, and mainly occurred through technology transfer between hunter-gatherer groups, rather than through the demic diffusion of agriculturalists.” ref

Anatolian hunter-gatherers 15,000–8,000 years ago

“Anatolian hunter-gatherer (AHG) is a distinct anatomically modern human archaeogenetic lineage, first identified in a 2019 study based on the remains of a single Epipaleolithic individual found in central Anatolia, radiocarbon dated to around 13,500 BCE or 15,500 years ago. A population related to this individual was the main source of the ancestry of later Anatolian Neolithic Farmers (also known as Early European Farmers), who along with Western Hunter Gatherers (WHG), Eastern Hunter Gatherers (EHG) and Western Steppe Herders (WSH) are one of the currently known ancestral genetic contributors to present-day Europeans.

“It has been discovered that populations of the Anatolian Neolithic (Anatolian Neolithic Farmers) derive most of their ancestry from the AHG, with minor gene flow from Iranian/Caucasus and Levantine sources, suggesting that agriculture was adopted in situ by these hunter-gatherers and not spread by demic diffusion into the region. The Anatolian hunter-gatherers began farming around 8300 BCE or around 10,300 years ago, at places such as Çayönü. Cows, sheep, and goats may have been domesticated first in southern Turkey. These farmers moved into Thrace (now European Turkey) around 7000 BCE, or around 9,000 years ago.” ref

“At the autosomal level, in the Principal component analysis (PCA) the analyzed AHG individual turns out to be close to two later Anatolian populations, the Anatolian Aceramic Farmers (AAF) dating from 8300-7800 BCE, and the Anatolian Ceramic Farmers (ACF) dating from 7000-6000 BCE or around 9,000 to 8,000 years ago. These early Anatolian farmers later replaced the European hunter-gatherer populations in Europe to a large extent, ultimately becoming one of the main genetic contributions to current European populations, especially those of the Mediterranean. In addition, their position in this analysis is intermediate between Natufian farmers and Western Hunter-Gatherers (WHG). This last point is confirmed by the ADMIXTURE and qp-Adm analysis and confirms the presence of hunter-gatherers of both European and Near-Eastern origins in Central Anatolia in the late Pleistocene.

“Mesolithic individuals from the Balkans, known as Iron Gates Hunter-Gatherers, are the most genetically similar group to the Anatolian Hunter-Gatherer lineage. Feldman et al. suggest that this affinity is not due to a genetic flow from the AHG to the ancestors of the Villabruna cluster, but on the contrary: there was a genetic flow from the ancestors of the Villabruna cluster to the ancestors of the AHG. Other genetic studies have shown that the relationship of AHG with WHG and Natufian hunter-gatherers is explained by the fact that these populations had a significant contribution from hunter-gatherers associated with the Upper Paleolithic of the Caucasus.” ref

“The AHG diverged from Caucasus hunter-gatherer around 25,000 years ago. The presence of Neolithic Anatolian ancestry among modern populations of the Levant and Iraq can be attributed to migrations during the Neolithic and Bronze Ages. The individual analyzed belongs to Y-chromosomal haplogroup C1a2 (C-V20), which has been found in some of the early WHGs, and mitochondrial haplogroup K2b. Both paternal and maternal lineages are rare in present-day Eurasian populations. As Early Neolithic groups expanded across Europe from Anatolia in the period from 10,000 to 5,000 years ago, they admixed with local Mesolithic hunter-gatherers, and by 6,000 years ago derived 20%–30% of their ancestry from these local groups.” ref, ref

“The greatest excess of Neolithic ancestry centered on SLC24A5 (Figures 2D and S3C), with a peak of +17.82% (|Z| = 3.46). The derived SLC24A5 allele, which is carried on the Neolithic ancestry background, is one of the two alleles which contributes most to light skin pigmentation in present-day West Eurasian-ancestry populations. It has previously been shown to have been at relatively high frequency in the Neolithic population and absent in the Mesolithic hunter-gatherers, and our results show that the selection removed hunter-gatherer ancestry at this locus in later admixed Neolithic groups.” ref

“The Neolithic transition brought about drastic changes in demography, culture, and diet, as well exposure to novel pathogens and increased potential of zoonotic disease. In admixed Neolithic individuals, we found excess Neolithic farmer ancestry at the pigmentation locus SLC24A5 and excess Mesolithic ancestry at the MHC immunity locus. Previous studies also found evidence of natural selection at SLC24A5 in European populations and showed that the allele was almost fixed in Anatolian farmers and was introduced into Western Europe during the Neolithic but our study now further demonstrates that subsequent selection during the Middle Neolithic was rapid enough to result in the removal of Mesolithic ancestry across the wider locus, covering an approximately 3 Mb region. In a similar but opposite process, the MHC locus has previously been demonstrated to have undergone selection in the ancestors of present-day Europeans and specifically in Neolithic Europe.¹¹ Here, we obtain further robust results for selection at the MHC locus corrected for multiple testing and demonstrate that this process specifically increased hunter-gatherer ancestry at the locus.” ref

“In contrast to SLC24A5, the second high-effect pigmentation variant in HERC displays an excess of Mesolithic ancestry (+10.79%, |Z| = 1.90). Together with the third high-effect pigmentation variant at SLC45A2, which arrived in Europe via later expansions from the steppe, selection on pigmentation in Europe thus targeted variants from each of the three major ancestral populations. This highlights the prominent role of admixture in the evolution of skin pigmentation in Western Eurasia. That this signal is not found in the allele frequency-based analysis with F_adm can likely be attributed to the small absolute change in allele frequency between our Neolithic populations, confirming recent demonstrations that local ancestry can in some cases be more powerful than allele frequency analysis for detecting selection in admixed populations.” ref

Anatolian Neolithic Farmers

“Early European Farmers (EEF) were a group of the Anatolian Neolithic Farmers (ANF) who brought agriculture to Europe and Northwest Africa. The Anatolian Neolithic Farmers were an ancestral component, first identified in farmers from Anatolia (also known as Asia Minor) in the Neolithic, and outside of Europe and Northwest Africa, they also existed in Iranian Plateau, South Caucasus, Mesopotamia and the Levant. Although the spread of agriculture from the Middle East to Europe has long been recognised through archaeology, it is only recent advances in archaeogenetics that have confirmed that this spread was strongly correlated with a migration of these farmers, and was not just a cultural exchange. The earliest farmers in Anatolia derived most (80–90%) of their ancestry from the region’s local hunter-gatherers, with minor Levantine and Caucasus-related ancestry.” ref

“The Early European Farmers moved into Europe from Anatolia through Southeast Europe from around 7,000 BCE, gradually spread north and westwards, and reached Northwest Africa via the Iberian Peninsula. Genetic studies have confirmed that the later Farmers of Europe generally have also a minor contribution from Western Hunter-Gatherers (WHGs), with significant regional variation. European farmer and hunter-gatherer populations coexisted and traded in some locales, although evidence suggests that the relationship was not always peaceful. Over the course of the next 4,000 years or so, Europe was transformed into agricultural communities, with WHGs being effectively replaced across Europe.” ref

“During the Chalcolithic and early Bronze Age, people who had Western Steppe Herder (WSH) ancestry moved into Europe and mingled with the EEF population; these WSH, originating from the Yamnaya culture of the Pontic steppe of Eastern Europe, probably spoke Indo-European languages. EEF ancestry is common in modern European and Northwest African populations, with EEF ancestry highest in Southern Europeans, especially Sardinians and Basque people. A distinct group of the Anatolian Neolithic Farmers spread into the east of Anatolia, and left a considerable genetic legacy in Iranian Plateau, South Caucasus, Levant (during the Pre-Pottery Neolithic B) and Mesopotamia. They also have a minor role in the ethnogenesis of WSHs of Yamnaya culture. The ANF ancestry is found in substantial levels in contemporary European, West Asian, and North African populations, and also found in Central and South Asian populations (through Bactria–Margiana Archaeological Complex and Corded Ware Culture) with lower levels.” ref

“Populations of the Anatolian Neolithic derived most of their ancestry from the Anatolian hunter-gatherers (AHG), with a minor geneflow from Iranian/Caucasus and Levantine related sources, suggesting that maybe agriculture was adopted in situ by these hunter-gatherers and not spread by demic diffusion into the region. Ancestors of AHGs and EEFs are believed to have split off from Western Hunter-Gatherers (WHGs) between 45,000 to 26,000 years ago during the Last Glacial Maximum, and to have split from Caucasus Hunter-Gatherers (CHGs) between 25,00 to 14,000 years ago. Genetic studies demonstrate that the introduction of farming to Europe in the 7th millennium BCE or around 9,000 years ago, was associated with a mass migration of people from Northwest Anatolia to Southeast Europe, which resulted in the replacement of almost all (c. 98%) of the local Balkan hunter-gatherer gene pool with ancestry from Anatolian farmers.” ref

“In the Balkans, the EEFs appear to have divided into two wings, who expanded further west into Europe along the Danube (Linear Pottery culture) or the western Mediterranean (Cardial Ware). Large parts of Northern Europe and Eastern Europe nevertheless remained unsettled by EEFs. During the Middle Neolithic there was a largely male-driven resurgence of WHG ancestry among many EEF-derived communities, leading to increasing frequencies of the hunter-gatherer paternal haplogroups among them. Around 7,500 years ago, EEFs originating from the Iberian Peninsula migrated into Northwest Africa, bringing farming to the region. They were a key component in the neolithization process of the Maghreb, and intermixed with the local forager communities.” ref

“The farmers of the Neolithic British Isles had entered the region through a mass migration c. 4,000 BCE. They carried about 80% EEF and 20% WHG ancestry and were found to be closely related to Neolithic peoples of Iberia, which implies that they were descended from agriculturalists who had moved westwards from the Balkans along the Mediterranean coast. The arrival of farming populations led to the almost complete replacement of the native WHGs of the British Isles, who did not experience a genetic resurgence in the succeeding centuries. More than 90% of Britain’s Neolithic gene pool was replaced with the arrival of the Bell Beaker people around 2,500 BCE, who had approximately 50% WSH ancestry.” ref

“The individuals buried in Neolithic Ireland were found to be largely of EEF ancestry (with WHG admixture), and were closely related to peoples of Neolithic Britain and Iberia. It was found that the Neolithic peoples of Ireland had almost entirely replaced the native Irish Hunter-Gatherers through a rapid maritime colonization. The people of the Funnelbeaker culture of southern Scandinavia were largely of EEF descent, with slight hunter-gatherer admixture, suggesting that the emergence of the Neolithic in Scandinavia was a result of human migration from the south. The Funnelbeakers were found to be genetically highly different from people of the neighboring hunter-gatherer Pitted Ware culture; the latter carried no EEF admixture and were instead genetically similar to other European hunter-gatherers.” ref

“The most common paternal haplogroup among EEFs was haplogroup G2a, while haplogroups E1b1 and R1b have also been found. Their maternal haplogroups consisted mainly of West Eurasian lineages including haplogroups H2, I, and T2, however significant numbers of central European farmers belonged to East Asian maternal lineage N9a, which is almost non-existent in modern Europeans, but common in East Asia. However, the high frequency of the East Asian mitochondrial haplogroup N9a in Neolithic cultures of the Carpathian Basin was disputed by another study.” ref

“During the Chalcolithic and early Bronze Age, the EEF-derived cultures of Europe were overwhelmed by successive migrations of Western Steppe Herders (WSHs) from the Pontic–Caspian steppe, who carried roughly equal amounts of Eastern Hunter-Gatherer (EHG) and Caucasus Hunter-Gatherer (CHG) ancestries. These migrations led to EEF paternal DNA lineages in Europe being almost entirely replaced with WSH-derived paternal DNA (mainly subclades of EHG-derived R1b and R1a). EEF maternal DNA (mainly haplogroup N) was also substantially replaced, being supplanted by steppe lineages, suggesting the migrations involved both males and females from the steppe.” ref

“A 2017 study found that Bronze Age European with steppe ancestry had elevated EEF ancestry on the X chromosome, suggesting a sex bias, in which Steppe ancestry was inherited by more male than female ancestors. However, this study’s results could not be replicated in a follow-up study by Iosif Lazaridis and David Reich, suggesting that the authors had mis-measured the admixture proportions of their sample. EEF ancestry remains widespread throughout Europe, ranging from about 60% near the Mediterranean Sea (with a peak of 65% in the island of Sardinia) and diminishing northwards to about 10% in northern Scandinavia. According to more recent studies however, the highest EEF ancestry found in modern Europeans ranges from 67% to over 80% in modern Sardinians, Italians, and Iberians, with the lowest EEF ancestry found in modern Europeans ranging around 35-40% in modern Finns, Lithuanians and Latvians. EEF ancestry is also prominent in living Northwest Africans like Moroccans and Algerians.” ref

“European hunter-gatherers were much taller than EEFs, and the replacement of European hunter-gatherers by EEFs resulted in a dramatic decrease in genetic height throughout Europe. During the later phases of the Neolithic, height increased among European farmers, probably due to increasing admixture with hunter-gatherers. During the Late Neolithic and Bronze Age, further reductions of EEF ancestry in Europe due to migrations of peoples with steppe-related ancestry is associated with further increases in height. High frequencies of EEF ancestry in Southern Europe might partly explain the shortness of Southern Europeans as compared to Northern Europeans, who carry increased levels of steppe-related ancestry.” ref

“The Early European Farmers are believed to have been mostly dark haired and dark eyed, and light skinned, with the derived SLC24A5 being fixed in the Anatolia Neolithic, although a genetic study of Ötzi the Iceman, a Chalcolithic mummy of EEF ancestry, found that he had a darker skin tone than contemporary southern Europeans. A study on different EEF remains throughout Europe concluded that they most likely had an “intermediate to light skin complexion”. A 2024 paper found that risk alleles for mood-related phenotypes are enriched in the ancestry of Neolithic farmers. EEFs and their Anatolian forebears kept taurine cattle, pigs, sheep, and goats as livestock, and planted cereal crops like wheat.” ref

“Genetic analysis of individuals found in Neolithic tombs suggests that least some EEF peoples were patrilineal (tracing descent through the male line), with the tombs’ occupants mostly consisting of the male descendants of a single male common ancestor and their children, as well as their wives, who were genetically unrelated to their husbands, suggesting female exogamy. A Neolithic royal buried at Newgrange was found to be highly inbred and possibly the product of an incestual relationship, suggesting that this community was highly socially stratified and dominated by a line of powerful “god-kings.” ref

“In terms of overall size, some settlements of the Cucuteni–Trypillia culture, such as Talianki (with a population of around 15,000) in western Ukraine, were as large as the city-states of Sumer in the Fertile Crescent, and these Eastern European settlements predate the Sumerian cities by more than half of a millennium. Research indicates that the settlements had a three-level settlement hierarchy, with the possibility of state-level societies. An excavated mega-structures suggests the presence of public buildings for meetings or ceremonies.” ref

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“Satsurblia 13,300 years ago, belongs to mtDNA K3 and Y-DNA J1-Y6313*, and was found to carry the derived SLC24A5 allele for light skin. Genetically closest to 9,700 years old Kotias Klde in Georgia. Together referred to as Caucasus Hunter-Gatherers.” ref

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“According to one model, the Mesolithic/Neolithic Iranian lineage basal to the Caucasus hunter-gatherers are inferred to derive significant amounts of their ancestry from Basal Eurasian (c. 38–48%), with the remainder ancestry being closer to Ancient North Eurasians or Eastern European Hunter-Gatherer (ANE/EHG; c. 52–62%). The CHG displayed an additional ANE-like component (c. 10%) than the Neolithic Iranians do, suggesting they may have stood in continuous contact with Eastern Hunter-Gatherers to their North. The CHG also carry around 20% additional Paleolithic Caucasus/Anatolian ancestry. In addition, CHG cluster with early Iranian farmers, who significantly do not share alleles with early Levantine farmers. Caucasus hunter gatherer/Iranian-like ancestry, was first reported as maximized in hunter-gatherers from the South Caucasus and early herders/farmers in northwestern Iran, particularly the Zagros, hence the label “CHG/Iranian.” ref

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“GD13a has similar runs of homozygosity (ROH) lengths to Neolithic individuals, while Caucasus Hunter Gatherers (Kotias and Satsurblia), like European Hunter Gatherers (Loschbour and Bichon), underwent recent large population bottlenecks potentially associated withthe LGM. Anatolian Neolithic samples, Caucasus Hunter Gatherers, and GD13a. The SLC24A5 variant for light skin has been found in both Neolithic farmer and Caucasus Hunter-Gatherer groups and all tests where a difference could be detected, Caucasus Hunter Gatherer and GD13a were equally likely sources.” ref

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Tarim mummies with 72% Afontova Gora 3 mt-DNA and gene SLC24A5 (Light skin colour variation)

“A 2021 genetic study on the Tarim mummies (13 mummies, including 11 from Xiaohe Cemetery, ranging from 2,135 to 1,623 BCE or around 4,135 to 3,623 years ago) found that they were most closely related to an earlier identified group called the Ancient North Eurasians, particularly the population represented by the Afontova Gora 3 specimen (AG3), genetically displaying “high affinity” with it. The genetic profile of the Afontova Gora 3 individual represented about 72% of the ancestry of the Tarim mummies from Xiaohe, while the remaining 28% of their ancestry was derived from Ancient Northeast Asians (ANA, Early Bronze Age Baikal populations).” ref, ref, ref

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Pottery moves from China to Siberia, then to the Middle East, and Europe

R2a from Siberia spreading to Iran, influenced the creation of Proto-Indo-European languages, transferring to R1b, emerging south of the Caucasus, and then spreading north into Russia/Europe