"The study allows us to conclusively reject an alternate theory that humans and Neanderthals evolved from the same sub-population," scientists said.
The new genome analysis also indicates that modern Europeans and Asians inherited more Neanderthal DNA than previously thought.
"Our approach can distinguish between two subtly different scenarios that could explain the genetic similarities shared by Neandertals and modern humans from Europe and Asia," explained Konrad Lohse, a population geneticist at the University of Edinburgh.
In the study, researchers used a different kind of genetic testing they had previously developed with rare species of European insects and Southeast Asian pigs.
They compared the genome of a Neanderthal, a European human, an African human, and a chimpanzee.
"The method makes maximum use of the information contained in individual genomes," Lohse added.
"Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neanderthal admixture in Eurasia at a higher rate (3.4 percent-7.3 percent) than suggested previously," said co-author Laurent AF Frantz of the Wageningen University in The Netherlands.
According to Mark Johnston, editor of the journal Genetics that published the study, "This work is important because it closes a hole in the argument about whether Neanderthals interbred with humans".
The method can be applied to understanding the evolutionary history of other organisms, including endangered species, he concluded.
In December last year, geneticists sequenced the most complete Neanderthal genome yet.
Neanderthals are genetically distinct enough from modern humans to earn them their own species designation, Homo neanderthalensis.
They lived among Homo sapiens in Europe, the Middle East, and central Asia as recently as 28,000 years ago before either going extinct or being incorporated into the modern human species.
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