The study appears to refute the picture of Europeans as a simple mixture of indigenous hunters and Near Eastern farmers who arrived 7,000 years ago.
The findings by an international team have been published in Science journal.
DNA was analysed from 364 skeletons unearthed in Germany - an important crossroads for prehistoric cultures.
"This is the largest and most detailed genetic time series of Europe yet created, allowing us to establish a complete genetic chronology," said co-author Dr Wolfgang Haak of the Australian Centre for DNA (ACAD) in Adelaide.
"Focusing on this small but highly important geographic region meant we could generate a gapless record, and directly observe genetic changes in 'real-time' from 7,500 to 3,500 years ago, from the earliest farmers to the early Bronze Age."