Humans and chimpanzees may have split away from a common ancestor far more recently than was previously thought.
The new finding raises questions about the Toumai fossil from Chad
A detailed analysis of human and chimp DNA suggests the lines finally diverged less than 5.4 million years ago.
The finding, published in the journal Nature, is about 1-2 million years later than the fossils have indicated.
A US team says its results hint at the possibility that interbreeding occurred between the two lines for thousands, even millions, of years.
This hybridisation would have been important in swapping genes for traits that allowed the emerging species to survive in their environments, explain the scientists affiliated to the Broad Institute of MIT and Harvard and the Harvard Medical School.
And it underlines, they believe, just how complex human evolution has been.
"This is a hypothesis; we haven't proved it but it would explain multiple features of our data," said David Reich, assistant professor of genetics at the Harvard Medical School and an author on the Nature paper.
"The hypothesis is that there was gene flow between the ancestors of humans and chimpanzees after their original divergence.
"So, there might have been an original divergence and a separation for long enough that the species became differentiated - for example, we might have adapted features such as upright walking - and then there was a re-mixture event quite a while after; a hybridisation event," he told the Science in Action programme on the BBC World Service.
Humans and chimps contain DNA sequences that are very similar to each other; the differences are due to mutations, or errors, in the genetic code that have occurred since these animals diverged on to separate evolutionary paths.
By analysing where these differences occur in the animals' genomes, it is possible to get an insight into the two species' histories - the timing of key events in their evolution.
Scientists have been able to do this for some time but the recent projects to fully decode the two primates' genomes have provided details that have taken this type of study to a more advanced level.
The US investigation indicates the human and chimp lines split no more than 6.3 million years ago and probably less than 5.4 million years ago.
It is a problematic finding because of our current understanding of early fossils, such as the famous Toumai specimen uncovered in Chad.
Toumai (Sahelanthropus tchadensis) was thought to be right at the foot of the human family tree. It dates to between 6.5 and 7.4 million years ago. In other words, it is older than the point of human-chimp divergence seen in the genetic data.
"It is possible that the Toumai fossil is more recent than previously thought," said Nick Patterson, a senior research scientist and statistician at the Broad Institute of MIT and Harvard, and lead author on the Nature paper.
"But if the dating is correct, the Toumai fossil would precede the human-chimp split. The fact that it has human-like features suggests that human-chimp speciation may have occurred over a long period with episodes of hybridisation between the emerging species."
Commenting on the research, Daniel Lieberman, a professor of biological anthropology at Harvard, told the Associated Press: "It's a totally cool and extremely clever analysis.
"My problem is imagining what it would be like to have a bipedal hominid and a chimpanzee viewing each other as appropriate mates, not to put it too crudely."