Earlier ancient DNA analyses of Mesolithic individuals had been based on lower-coverage sequencing or targeted analysis of specific genome regions; the Cheddar Man whole-genome represented a more complete and powerful dataset.

Some scientists emphasized the importance of acknowledging the probabilistic nature of the pigmentation predictions.

While the dark-skin finding was reported with confidence in the media, researchers in the field noted that pigmentation prediction from ancient DNA involves statistical inference rather than direct observation, and that the specific intensity of pigmentation — precisely how dark the skin was — cannot be determined with high precision from genetic data alone.

The identification of Cheddar Man as belonging to the Western Hunter-Gatherer population was not controversial; the genetic markers for WHG ancestry are well-established in the literature, and Cheddar Man’s genome showed them clearly.