When scientists first sequenced the genome of a Neanderthal, our extinct, heavy-browed human cousin, we learned a surprising amount about our own species too: many modern humans carry Neanderthal genes, proving we interbred with them long ago.

Now, researchers have offered the first glimpse of the Neanderthal epigenome, and once again their results offer tantalizing new theories about the modern human brain and skeleton.

While the findings are surprising, the fact that the Neanderthal epigenome holds important secrets should not be. In the past decade, scientists have discovered that epigenetics, the chemical signals that regulate how genes are expressed, are almost as important as genetics in understanding how organisms look and act.

By exploiting a trick of how ancient DNA degrades, an Israeli-led team of researchers has created a map of the Neanderthal epigenetic landscape and that of another extinct human species, the Denisovans. Their work, hailed as a fantastically exciting technical achievement, was published Thursday in the journal Science.

The most intriguing findings of the study are the clues that emerged when the researchers compared those archaic epigenetic maps to those of present-day humans.

More than 99 per cent of the ancient and modern maps were the same, which is what one would expect to find in closely-related human species that shared a common ancestor approximately 600,000 years ago.

But the maps were almost twice as likely to differ in regions associated with disease and, in a third of those cases, in regions associated with psychological and neurological diseases.

Scientists are a long way from being able to understand what this means, stressed Liran Carmel, who led the study along with Eran Meshorer and David Gokhman, all of the Hebrew University of Jerusalem.

But this raises the hypothesis that perhaps many genes in our brain have changed recently, specifically in our lineage, the lineage leading to Homo sapiens. And perhaps things like autism, schizophrenia and Alzheimers are side-effects of these very recent changes, said Carmel.

This is an interesting suggestion, that (brain disease) is a side-effect of us being Homo sapiens and having our unique cognitive capabilities.

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Neanderthal genetic landscape reveals key differences with humans