The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature journal reports.
Blue-eyed, swarthy hunters mingled with brown-eyed, pale skinned farmers as the latter swept into Europe from the Near East.
But another, mysterious population with Siberian affinities also contributed to the genetic landscape of the continent.
The findings are based on analysis of genomes from nine ancient Europeans.
Agriculture originated in the Near East - in modern Syria, Iraq and Israel - before expanding into Europe around 7,500 years ago.
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