The evolving pigment palette of European skin, eyes and hair as seen through ancient DNA
The evolving pigment palette of European skin, eyes and hair as seen through ancient DNA
Temporal and geographical distribution of skin pigmentation estimates in Eurasia from Paleolithic to Iron Age. Credit: bioRxiv (2025). DOI: 10.1101/2025.01.29.635495
University of Ferrara researchers in Italy have examined how European skin, eye and hair pigmentation evolved over the past 45,000 years. Findings indicate that lighter pigmentation traits emerged gradually and non-linearly, with dark skin persisting in many populations well into the Copper and Iron Ages. The study used a probabilistic genotype likelihood method to infer pigmentation traits from low-coverage ancient DNA.
Light pigmentation alleles became more common as Homo sapiens dispersed from Africa into regions with lower ultraviolet (UV) radiation. Evolutionary models suggest this was due to selective advantages related to vitamin D synthesis, as well as genetic drift and migration. However, the timing and pattern of pigmentation changes remain unclear.
In the study “Inference of Human Pigmentation from Ancient DNA by Genotype Likelihood,” available as a preprint on bioRxiv, researchers tested the accuracy of pigmentation inference methods using two ancient genomes with high coverage: the 45,000-year-old Ust’-Ishim individual from Russia and the 9,000-year-old SF12 individual from Sweden.
A downsampling experiment simulated low-coverage conditions to compare three genotype-calling methods: direct calling, imputation, and a probabilistic approach using genotype likelihoods. The probabilistic method was found to be the most reliable for samples with coverage below 8x. This approach was then used to analyze a dataset of 348 ancient genomes from Eurasia.
Dark pigmentation was inferred for nearly all Paleolithic individuals (~45,000 to 13,000 years ago), with only one exception showing an intermediate skin color.
During the Mesolithic period (~14,000 to 4,000 years ago), lighter eye colors became more frequent, with 11 out of 35 samples showing the light eye phenotype. These light-eye traits were primarily found in samples from Northern and Western Europe, with dark hair and skin remaining dominant. Light skin tones first appeared in Mesolithic Sweden but remained rare.
This spike in light eye pigmentation appears to be specific to the Mesolithic period. It suggests that, for a brief interval in human prehistory, there was a higher occurrence of the light eye trait compared to both earlier (Paleolithic) and later (Neolithic and Bronze Age) periods.
During the Neolithic period (~10,000 to 4,000 years ago), pigmentation diversity increased, coinciding with the migration of Anatolian farmers into Europe. Lighter skin tones became more frequent, but dark phenotypes persisted, particularly in Southern and Eastern Europe. Hair and eye color also showed variability, with instances of red hair appearing in Turkey.
Copper and Bronze Ages (~7,000 to 3,000 years ago) saw continued increases in light pigmentation, but dark phenotypes remained widespread. By the Iron Age (~3,000 to 1,700 years ago), light skin was nearly as frequent as dark skin, particularly in Northern and Central Europe. However, dark pigmentation remained common in regions such as Italy, Spain, and Russia.
Pigmentation changes appear to have been driven primarily by migration and gene flow rather than a linear pattern of selection. The spread of Neolithic farming populations played a key role in shifting pigmentation traits across Europe. Genetic analyses highlighted key variants, such as SLC24A5 and TYR, and others that contributed to these changes.
The findings suggest that light skin became common in Europe much later than previously thought and that pigmentation traits were shaped by a complex interplay of genetic and environmental factors over thousands of years.