The calculations are a way-station in efforts to decode the complete genome of Neanderthals, the extinct hominids whose existence was discovered 150 years ago with a fossil find in a German quarry.
This is the biggest scientific news in 2006, attempts to reconstruct the extinct hominids, Pavao Rudan of the Croatian Academy of Arts and Sciences said.
The scientists only have a few smudges of cell material from fossil finds to analyse.
Croatian scientist Paunovic was a member of a team, led by Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who compared human, Neanderthal and chimpanzee DNA to calculate that the divergence took place about 516,000 years ago.
The Paabo group said it hoped to complete the genome within two years. The research was published in the British journal Nature.
Experts said it was basically in harmony with a second, simultaneous report in the US journal Science from a group led by Edward Rubin of the Energy Joint Genome Institute in Walnut Creek, California.
The Rubin group said the last common ancestor had been 706,000 years ago. The two had been separate species by 370,000 years ago, although at least 99.5 per cent of their DNA was identical.
The Nature report suggested the two hominids may have interbred, but no evidence for that was found in the Science report.
Past DNA studies have been limited to mitochondrial DNA, inherited from mothers only. The Paabo group is using new techniques to detect complete DNA. They found sufficient traces on six out of 70 bones and teeth dug up in Europe and Asian to reconstruct 1 million DNA pairs.