A sequence of about a million base pairs ( about 0,03 % of the genome) has been achieved from a 45,000 years old male Neanderthal from Vindija Cave, in Northwestern Croatia. This sequence has allowed American and German scientists the first comparison of human and Neanderthal DNA.

The analysis showed that the two lineages diverged about 300,000 years ago and that Neanderthals may have had much DNA in common with chimps. Anyway, they share a common ancestor with us, but they are not more closely related than that.

Nucelar DNA analysis brought a new type of evidence to the longstanding debate over whether these hominids, which lived throughout Europe and western Asia from 300,000 years ago to 30,000 years ago, were a species separate, Homo neanderthaliensis, from our own, Homo sapiens, that did not contribute to the modern human gene pool, or whether they were a breed of our own species.

Previous researches were made only on mitochondrial DNA samples, which preserved better. Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, was the first to recover mitochondrial DNA (mtDNA) from a Neanderthal, back in 1997 and also the nuclear Neanderthal DNA. Several studies conducted on mitichondrial DNA pointed that it differed significantly from those of living humans.

Some critics argued that nuclear DNA might tell a totally different story. Nuclear DNA does not preserve so well as mt DNA in the fossils. In fact, very small fragments of nuclear DNA have been recoverable, which made the analysis even more difficult.

Human, chimpanzee and Neanderthal nuclear DNA samples have been compared. The team succeeded to manage such a small amount of DNA by using a novel sequencing technique. Neanderthal Y chromosome is very peculiar, differing substantially more from human and chimp Y chromosomes than are other chromosomes. This trait suggests that little interbreeding occurred, at least among the more recent Neanderthal populations and humans. "This is a hint of exciting things to come as more Neanderthal sequence is produced," says David Haussler at the University of California, Santa Cruz, US.

The traditional method of sequencing DNA indicates that Neanderthals split off from the lineage that led to modern humans around 315,000 years ago, sustaining previous estimates. This confirms the ideas that Neanderthals did not contribute substantially to the modern human genome. "Were there Neanderthals in our lineage? All of the genetics seems to be going in the direction that there weren't," says Richard Potts, head of the Smithsonian Institution's Human Origins Program in Washington DC, US.

Paabo's Neanderthal Genome Project is aiming to sequence 10 Neanderthal genomes in the next 10 years.