Light outside, dark inside
The strange evolution of eye pigmentation
Why did European eyes become lighter, while the inside of the eye may have gone in the opposite direction?
In the previous post, I discussed a recent study by Yuan et al. (2026) showing a strong within-Europe genetic gradient for retinal pigmentation, detected using AI-based phenotyping and population-structure–aware tests. The surprising result was that higher-latitude Europeans are genetically predisposed to darker retinal pigmentation, even though lighter eye color is more common in the north.
As I had promised, here I go further. Instead of looking only at present-day populations, I project the same retinal pigmentation polygenic score onto ancient European genomes and follow it through time. This allows us to ask a more informative question: how did the inside of the eye evolve as the outside was getting lighter?
This will also enable us to replicate the authors’ finding directly, without relying on indirect evidence provided by modern genomes only.
In the rest of this post, I project the retinal pigmentation genetic score onto thousands of ancient European genomes and follow it through time. I show how the signal changes across latitude, how it interacts with major cultural transitions, and why the turning point appears around the beginning of the Iron Age. The results suggest a coordinated but counterintuitive evolution of eye pigmentation, with the outside and the inside of the eye moving in opposite directions.
