Researchers used DNA evidence from the ancient bones and teeth of people who lived in Europe from the Late Pleistocene to the early Holocene - spanning almost 30,000 years of European prehistory.
They pieced the missing history together by reconstructing the mitochondrial genomes of 35 hunter-gatherer individuals who lived in Italy, Germany, Belgium, France, the Czech Republic, and Romania from 35,000 to 7,000 years ago.
"We uncovered a completely unknown chapter of human history - a major population turnover in Europe at the end of the last Ice Age," said lead author Johannes Krause of the Max Planck Institute for the Science of Human History in Germany.
"There has been a real lack of genetic data from this time period, so consequently we knew very little about the population structure or dynamics of the first modern humans in Europe," Krause said.
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The new data show that the mitochondrial DNA of three individuals who lived in present-day Belgium and France before the coldest period in the last Ice Age - the Last Glacial Maximum - belonged to haplogroup M.
The absence of the M haplogroup and its presence in other parts of the world had previously led to the argument that non-African people dispersed on multiple occasions to spread across Eurasia and Australasia.
The researchers said the discovery of this maternal lineage in Europe in the ancient past now suggests instead that all non-Africans dispersed rapidly from a single population, at a time they place around 50,000 years ago.
Then, at some later stage, the M haplogroup was apparently lost from Europe.
The researchers say their biggest surprise, however, was evidence of a major turnover of the population in Europe around 14,500 years ago, as the climate began to warm.
"Our model suggests that during this period of climatic upheaval, the descendants of the hunter-gatherers who survived through the Last Glacial Maximum were largely replaced by a population from another source," said senior author Adam Powell, of the Max Planck Institute.