Skin color, eye color, and hair color are polygenic traits — influenced by multiple genes, each of which contributes a small effect.

The genetics of human pigmentation has been studied intensively, and several genes with major effects on pigmentation are well characterized.

By looking at which variants an ancient individual carried at these genes, researchers can make probabilistic inferences about their likely pigmentation — not with certainty, since environmental factors and gene interactions also matter, but with enough confidence to provide useful information for facial reconstruction.

The genes involved include SLC45A2 and SLC24A5, which have large effects on skin pigmentation, and HERC2 and OCA2, which are major determinants of eye color.