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## The Phenotype Analysis: What the DNA Suggested About Appearance
The ancestry analysis placed Cheddar Man within a well-characterized ancient population. The phenotype analysis — the attempt to predict what he actually looked like — required a different set of tools and came with a different set of caveats.
Physical traits like skin color, eye color, and hair texture are polygenic: they are influenced by many genetic variants scattered across the genome, often interacting in complex ways. The relationship between genetic variants and the traits they influence is not perfectly understood, and our understanding of skin pigmentation genetics in particular is incomplete. The genes and variants we know about explain a large proportion of the variation in pigmentation among modern people from populations similar to those in which the research was conducted — but not all of it, and the predictive models are calibrated on modern reference populations that do not include ancient people.
The tool the Natural History Museum’s team used to predict pigmentation from genetic data was a forensic phenotyping model based on genetic variants known to influence skin, hair, and eye color. Specifically, the researchers applied a tool derived from work by Susan Walsh and colleagues — the same Walsh who would later be quoted expressing caution about the certainty of the skin color prediction — which assigns individuals to pigmentation categories based on which variants they carry at relevant positions in the genome.
The skin pigmentation result placed Cheddar Man in categories described as “dark” and “dark to black” — specifically, the two most darkly pigmented of five categories in the prediction framework. The lightest skin categories were ruled out. The midrange categories were less probable. The result was expressed as a probability estimate rather than a certainty: one widely cited figure was a 76 percent probability of dark skin.