Extraordinary new genetic evidence is revealing how Britain experienced a mysterious almost total change in its population in just a few centuries after the construction of Stonehenge.

It suggests that some sort of social, economic or epidemiological catastrophe unfolded.

The great 20-30 tonne stones of Stonehenge were erected by Neolithic farmers whose ancestors had lived in Britain for at least the previous 1,500 years – and new genetic research on 51 skeletons from all over Neolithic Britain has now revealed that during the whole of the Neolithic era, the country was inhabited mainly by olive-skinned, dark-haired Mediterranean-looking people.

But some 300 to 500 years after the main phase of Stonehenge was built, that mainly Mediterranean-looking British Neolithic-originating element of the population had declined from almost 100 percent to just 10 per cent of the population.

The new genetic research reveals that the other 90 per cent were a newly-arrived central-European- originating population (known to archaeologists as the Beaker People) who appear to have settled in Britain between 2500 BC and 2000 BC via the Netherlands.

But how this dramatic population change occurred is an almost complete mystery.

There’s absolutely no evidence for any large-scale conflict – so warfare or genocide is almost certainly not the explanation.

It’s much more likely that the incoming population, with more advanced technology (including metal-working), gained control of the best land and resources and succeeded in economically marginalising the Neolithic population.

There is also a distinct possibility that the native Neolithic population of Britain had no resistance to some continental European diseases. There is some evidence from Europe that bubonic plague may have been the culprit.

Stonehenge 'tunnel' explained

If lack of immunity did wipe out much of Neolithic Britain’s population, then demographers will regard it as a very early precursor of what we know actually happened to the American Indians as a result of European colonisation of the New World.

The genetic research reveals that the same sort of extreme population change did not occur on the continent. It’s likely therefore that while Britain’s island status no doubt protected or isolated it in some ways, it ultimately made the population much more vulnerable to eventual catastrophic change.

Having discovered the dramatic population replacement between 2500 and 2200 or 2000 BC (essentially the interface between the Neolithic and the Bronze Age), scholars will now, no doubt, be looking at the previous really major cultural interface (in around 4300 BC between Britain’s indigenous Mesolithic hunter-gatherer population and the incoming continental-originating early Neolithic culture) to see whether similar extreme population changes were occurring.

There’s always been a debate about how major cultural changes in Britain occurred in prehistory – through the movement of ideas and technologies or through the movement of people.

The new genetic discoveries show, for the first time, that at least in the Neolithic/Bronze Age transition it was people who arrived, not just ideas.

Today, in genetic terms, the Neolithic population of Europe substantially survives in only one place – Sardinia.

In Britain the genetic data was obtained from 51 Neolithic individuals (who died between 4000 and 2500 BC) and 104 Copper Age and Bronze Age people (who died between 2500 BC and 1000 BC).

Their skeletal material came from a range of prehistoric sites. Around 55 per cent of the Neolithic individuals’ remains came from large communal tombs, with a further 31 per cent coming from caves. Some 88 per cent of the Copper Age and Bronze Age individuals came from mainly individual graves and tombs, with just 9 per cent coming from caves.

The genetic analysis of the prehistoric British skeletal material formed part of the largest study of ancient human DNA ever conducted. The study is published this week in the journal Nature.

The research was carried out by an international team of 144 archaeologists and geneticists from institutions in Europe and the United States including the Natural History Museum, the University of Cambridge and Harvard Medical School.

The study was made possible by an unprecedented collaboration between most of the major ancient DNA laboratories in the world. “Different teams had different key samples and we decided to put together our resources to make possible a study that was more definitive than any of us could have achieved alone,” said co-senior author of the Nature paper Kristian Kristiansen, an archaeologist at the University of Gothenburg in Sweden.

Mark Thomas, Professor of evolutionary genetics at UCL and co-author on the study said: “The sheer scale of population replacement in Britain is going to surprise many, even though the more we learn from ancient DNA studies, the more we see large-scale migration as the norm in prehistory.”