Booth said Cheddar Man's dark hair and blue eyes "subverts people's expectations" about the pairing of certain genetic traits.
No prehistoric Briton of this age had previously had their genome analysed. Each genome contains all of the information needed to build and maintain that organism.
With that, the group posited that lighter complexion associated with northern European population was more of a recent genetic change and skin colour had no connection to the geographical location at that time.
They cross-referenced the genomes of modern inhabitants of Cheddar, near Gough's Cave in the Cheddar Gorge, where the remains were discovered in 1903, as well as other fossils from across Europe.
"Cheddar Man" - the oldest skeleton found in the United Kingdom - had black skin, curly hair and blue eyes. "It is very exciting to think that we will be able to share these results and enable the rest of the United Kingdom to see what the first 'Brit" really looked like'.
The museum's research leader in human origins, Professor Chris Stringer, first excavated at Gough's Cave 30 years ago and has been involved in the project ever since.
"Modern Europeans are a mixture of people like this, who are older hunter-gatherer inhabitants of western Europe, and people who came in with the advent of agriculture, and people who came from the east in the Bronze Age and who also brought new genetics into the region".
It was only about 6,000 years ago that pale skin genes arrived in Britain with the migration of Middle Eastern farmers.
"Pale skin is better at absorbing UV light and helps humans avoid vitamin D deficiency in climates with less sunlight", said researcher Tom Booth.
Then, a pair of Dutch artists who are experts in palaeontological model-making, Mr Alfons Kennis and his brother, Mr Adrie Kennis, used a high-tech scanner to make a three-dimensional model of Cheddar Man's head.
And as it happens, details about Cheddar Man's skin and eye color were not the only intriguing finds to result from the DNA analysis.
"I think we all know we live in times where we are unusually preoccupied with skin pigmentation", said Steven Clarke, director of the documentary, which will be aired on the UK's Channel 4 on February 18. The avowed white nationalist told Younge that due to his race "you'll never be an Englishman", on a Channel 4 documentary on Whiteness.
"We love our labels don't we, we love putting ourselves in little pots - but you have still got what is essentially quite a small genetic pool to start with in Homo sapiens", added Dr Undertown.
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