Cheddar Man and the Limits of Reading Skin From DNA

The hole was 2 millimetres wide. Scientists at London’s Natural History Museum drilled it into the skull of Cheddar Man to collect a few milligrams of bone powder from the dense inner-ear bone. From that dust came Britain’s oldest whole genome at the time, and a headline that spread around the world in February 2018: the first modern Britons had “dark to black” skin.

The genome holds up. The headline needs a closer look. This article separates what Cheddar Man’s DNA shows from what it can only suggest.

A skeleton found during drainage work

Workers uncovered the skeleton in 1903 while improving drainage at Gough’s Cave, a show cave in Cheddar Gorge, Somerset. Early claims made him the “earliest Englishman”, with inflated ages of 40,000 to 80,000 years. Radiocarbon dating from the 1970s onward brought that down to about 10,000 years. The museum says the bones have been dated twice, with consistent results.

His DNA survived because of where he lay. The museum credits the consistently cool conditions of Gough’s Cave and layers of natural mineral deposits. The team sampled the petrous bone, the densest bone in the human body, which shields DNA better than teeth or leg bones.

He was a young man, about 166 cm tall, who died in his twenties. He is the oldest almost complete skeleton of Homo sapiens found in Britain. He lived in the Mesolithic, the period after the last Ice Age when people in Britain lived by hunting, fishing and gathering, some four thousand years before farming reached Britain.

What the genome actually is

The full study appeared in Nature Ecology & Evolution in 2019, led by Selina Brace, Yoan Diekmann and Thomas Booth. It reported genome-wide data from six Mesolithic and 16 Neolithic Britons, combined with 51 previously published Neolithic individuals. Cheddar Man was the best-preserved of the six hunter-gatherers, sequenced to about 2.3-fold coverage. Coverage means the average number of times each position in the genome was read; 2.3-fold is modest, so some positions are missing or read only once.

His genome matches the population geneticists call western European hunter-gatherers, whose remains are known from Spain, Luxembourg and Hungary. Among them, the British Mesolithic genomes most closely resemble Loschbour, an 8,000-year-old man from Luxembourg.

The data behind our AADR Genome Atlas includes exactly six British Mesolithic individuals, matching the six in the Brace study. The only one from Gough’s Cave, catalogued I3016, has a mean date of about 10,280 years before present. Its maternal lineage is U5b1, which the museum reports for Cheddar Man, and its Y chromosome falls in haplogroup I2a. U5 and I2 are both typical of European hunter-gatherers of this period.

Five boxes, two of them dark

The skin prediction came from HIrisPlex-S, a forensic system developed partly by Susan Walsh of Indiana University–Purdue University Indianapolis. According to New Scientist, the version used reads 36 positions in 16 genes linked to pigmentation. It was trained and tested on genetic data from more than 1,400 people, mainly from Europe and the United States.

In those tests, the model sorted people with “light” skin from people with “dark-black” skin with a small margin of error. The middle of the range, where most of the world’s variation lies, is harder to call.

The tool does not output a colour. It assigns probabilities across five skin categories, from very pale to dark-to-black. The museum’s summary is precise: Cheddar Man’s skin was “most likely in one of the two most highly-pigmented of five categories”, and definitely not in the lightest ones. The paper adds blue or green eyes and dark brown, possibly black, hair.

Where the inference runs out

Within weeks, the scientists themselves were tempering the coverage. Walsh told New Scientist that the result is “his most probable profile, based on current research”, not “a simple statement of ‘this person was dark-skinned’”. Degraded ancient DNA means some of the 36 markers may be missing.

A deeper problem was raised by the geneticist Brenna Henn of Stony Brook University. Studies of southern and eastern African populations published in 2017 found that the known pigmentation genes, discovered mainly in Europeans and East Asians, fail to explain much of the variation in skin colour in Africa. If the model misses genes in living people, it may miss them in a man who lived 10,000 years ago, whose population has no exact modern match.

Henn gave a stark example. When her team tested an older prediction model on southern African populations, she told New Scientist, “it literally predicted that people with the darkest skins would have the lightest skin.” HIrisPlex-S is better validated than that model, but the warning stands: a tool is only as good as the populations it was trained on.

So the cautious reading is this. Cheddar Man lacked the gene variants that make most northern Europeans pale today, so his skin was very likely darker than theirs. How much darker is uncertain. The widely shared reconstruction is an informed portrait, not a photograph. The same caution applies to other trait predictions from ancient DNA, as our article on the evolution of human skin colour explains.

Pale skin arrived later, with migrants

The more important lesson is about timing. The museum notes that people carrying the main light-skin variants lived in parts of Scandinavia and western Asia around Cheddar Man’s time. In north-west Europe, those variants arrived thousands of years after his death with two migrations: early European farmers of Near Eastern origin, and later herders from the Pontic steppe. Ongoing natural selection then raised their frequency, probably because pale skin helps make vitamin D under weak sunlight.

The Brace study also found that farming reached Britain around 4000 BC with incoming continental farmers, mostly descended from Aegean populations that had travelled the Mediterranean route. Their genomes carry only small amounts of hunter-gatherer ancestry. Different skin tones, the authors conclude, coexisted in Europe by about 6000 BC.

Are British people descended from Cheddar Man?

Not in the direct way the 2018 coverage implied. The museum estimates that about 10% of the ancestry of British people without recent migration history comes from western hunter-gatherers. But it stresses that this ancestry does not relate specifically to Cheddar Man or to Mesolithic Britain. Most of it was picked up across mainland Europe by later migrants, who had mixed with hunter-gatherers on the way, and carried into Britain.

In other words, Cheddar Man is a window onto a population, not a founding father. To place him on the much longer story of our species, open the interactive family tree, or follow the farmers who replaced his people on the migration map.