Ancient DNA Analysis Reveals Hundreds of Human Genes Shaped by Recent Natural Selection

Analysis of 16,000 ancient genomes from West Eurasia, covering the last 10,000 years, identified 479 genetic variants with strong selection signatures—far more than the ~21 regions previously reported for Europeans. The variants affect hair color, skin pigmentation, disease risk, and psychiatric traits; MC1R alleles linked to red hair and pale skin are among the strongest signals. The authors suggest lighter skin may have been favored for enhanced vitamin D synthesis as diets shifted toward plant foods.

ScienceAlert

Researchers combined the ancient dataset with DNA from over 6,000 modern individuals and applied a pipeline that models relationships among samples to isolate selection signals while controlling for migration and drift.

ScienceAlert

David Reich noted that the study doubles the size of the ancient human DNA literature and fills gaps left by earlier analyses, adding that detecting frequency changes beyond random expectation requires thousands of genomes across millennia. Ali Akbari described the techniques as enabling real-time observation of selection, allowing researchers to let the data speak rather than rely on simplified models.

ScienceAlert

The authors caution that the functional impact of the identified variants may have changed over time and that modern environments differ from ancient ones, so direct links to present-day traits should be interpreted conservatively. They also note that the vitamin D hypothesis for MC1R alleles lacks direct experimental support.

ScienceAlert

• "This single paper doubles the size of the ancient human DNA literature," — David Reich, Geneticist, Harvard University

ScienceAlert

• "It reflects a focused effort to fill in holes that limited the power of previous studies to detect selection." — David Reich, Geneticist, Harvard University

ScienceAlert

• "If the goal is to uncover changes in the frequency of genetic variants in the last ten millennia that are greater than can be expected by chance, then we need to detect subtle effects, which requires having thousands of genomes spanning that time period." — David Reich, Geneticist, Harvard University

ScienceAlert

• "With these new techniques and large amounts of ancient genomic data, we can now watch how selection shaped biology in real time." — Ali Akbari, Geneticist, Harvard University

ScienceAlert

• "Instead of searching for the scars natural selection leaves in present-day genomes using simple models and assumptions, we can let the data speak for itself." — Ali Akbari, Geneticist, Harvard University

ScienceAlert

The team plans to apply the analytical framework to genomic data from other continents to map recent selection events globally and to refine disease-risk predictions based on ancient adaptations.

ScienceAlert