Woolf pointed out that ancient texts such as the laws of Inewritten 200 years after the Anglo-Saxons arriveddemonstrate that the Anglo-Saxons had the upper hand.
The laws reveal that the life of an Anglo-Saxon was worth far more than that of a native Briton, who was known as a "Welshman" by the Anglo-Saxons at the time.
If an Anglo-Saxon was killed, for example, the "blood money" payable to the victim's family was two to five times more than that of a "Welshman."
To test Woolf's theory, Thomas devised a computer population model to study how such an apartheid-like structure would affect genetics.
By testing different combinations of ethnic intermarriage rates and levels of Anglo-Saxon social dominance, Thomas and his colleagues found that a small immigrant population could easily gain genetic supremacy.
When intermarriage rates were kept to less than 15 percent and Anglo-Saxons had a reasonably high social standing, then Germanic genes flourished.
"The surprising thing was that it didn't take much at all," Thomas said.
Servant and Master
The scientists say native Britons and Anglo-Saxons may have lived in a segregated, servant-and-master relationship.
Such a system would give the Anglo-Saxons a strong reproductive advantage, the researchers say.
"People with German ancestry had a higher social and legal status, and they tended to have more children," said Michael Stumpf, a genomics professor at Imperial College London and a co-author of the study.
But not everyone agrees with the team's theory. Alex Burghart, an Anglo-Saxon historian at Kings College London, thinks that "apartheid" is far too strong a word.
"It is nonsense. There would be no need to legislate against interbreeding. All you need is a society with huge economic and social divides," he said.
Sarah Foot, a medieval historian at England's University of Sheffield, also thinks the word "apartheid" is unwarranted. But she believes the research has merit.
"What is interesting is that there was seemingly no intermarriage between Britons and Anglo-Saxon settlers," she said.
"That isn't what one might have anticipated, and [it] also of course reinforces the fact that this was a migration of a people, not an invasion of a male military force," she said.
Chris Tyler-Smith, a geneticist at the Wellcome Trust Sanger Institute in Cambridge, England, also thinks Thomas' team has arrived at an interesting idea, but he has some reservations.
"I think they have come up with a reasonable deduction, but it rests on a complex series of pieces of evidence," he said.
"It is not necessarily the only possible interpretation," Tyler-Smith added.
Another question posed by the new study is why the native Britons ended up accommodating the Anglo-Saxons and their culture instead of rebelling.
"The natives realized they were the underdogs and realized that the only way to assimilate upwards was to adopt the new culture," said Heinrich Härke, study co-author and archaeologist at England's University of Reading.
"They tried to improve their status by learning English, which is why English was adopted," he added.
He notes that Anglo-Saxon cemeteries provide further evidence of a segregated society.
Archaeological surveys have shown that 47 percent of adult males were buried with their weapons, while the rest were buried without them, he says.
"We looked at [physical] stature and found that the men who were buried with their weapons were taller," Härke said.
Anglo-Saxon men are believed that have been one or two inches (about two and a half to five centimeters) taller than native British men.
This suggests that the men buried with their weapons were of Germanic origin and had a higher social status, while the men buried without their weapons were native Britons with lower social status.
Historical evidence shows that these kinds of differences continued until the early seventh century, after which the apartheid-like structure appears to have broken down, Härke adds.
Just 300 years of Anglo-Saxon dominance was enough to almost obliterate native Britons' gene pool and culture, he concludes.
"In England today there is no ancient British identity left except for a few place- and river names," Härke said.
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