The Evolution of Pigmentation in Europe Through Ancient DNA

Researchers from the University of Ferrara in Italy have traced how European skin, eye, and hair pigmentation evolved over the past 45,000 years. Their findings show that lighter pigmentation traits emerged gradually and non-linearly, with dark skin persisting in many populations well into the Copper and Iron Ages. Using a probabilistic genotype likelihood method, they inferred pigmentation traits from low-coverage ancient DNA.

Gradual Lightening of Pigmentation

As Homo sapiens dispersed from Africa into regions with lower ultraviolet (UV) radiation, lighter pigmentation alleles became more common. Evolutionary models suggest that selective advantages related to vitamin D synthesis, genetic drift, and migration played key roles. However, the exact timing and pattern of these changes remained unclear until now.

The study, titled "Inference of Human Pigmentation from Ancient DNA by Genotype Likelihood," available as a preprint on bioRxiv, tested pigmentation inference methods on two ancient high-coverage genomes: 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 the most reliable for samples with coverage below 8x, and it was used to analyze a dataset of 348 ancient genomes from Eurasia, including regions that are now modern Greece.

Dark Pigmentation Dominated for Millennia

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 traits were mostly found in Northern and Western Europe, while dark hair and skin remained dominant. Light skin tones first appeared in Mesolithic Sweden but were still rare in Southern Europe, including Greece.

This spike in light eye pigmentation appears to be specific to the Mesolithic period, suggesting a temporary increase before a return to darker pigmentation dominance in later periods.

The Neolithic and Beyond: Greece’s Role in Pigmentation Evolution

During the Neolithic period (~10,000 to 4,000 years ago), pigmentation diversity increased, coinciding with the migration of Anatolian farmers into Europe, including Greece. While lighter skin tones became more frequent, darker phenotypes persisted, particularly in Southern and Eastern Europe. Genetic evidence suggests that some Neolithic Greeks had darker pigmentation, though lighter traits began appearing due to increased interactions with farming populations from Anatolia and Central Europe.

The 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, darker pigmentation remained common in regions such as Italy, Spain, and Greece.

Migration and Gene Flow as Key Drivers

Pigmentation changes were driven primarily by migration and gene flow rather than a straightforward pattern of selection. The spread of Neolithic farming populations, including those in Greece, played a major role in shifting pigmentation traits across Europe. Genetic analyses highlighted key variants, such as SLC24A5 and TYR, that contributed to these changes.

A Complex Evolution of Skin, Hair, and Eye Color

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. Greece, situated at the crossroads of Europe, Anatolia, and the Near East, played a significant role in this evolutionary process, absorbing and influencing genetic traits that defined European pigmentation diversity.