A new study uses epigenetics to explain the differences between modern humans and Neanderthals.

Epigenetics refers to external modification of DNA. Research has shown that these changes are important in shaping key biological functions.

The study, conducted by a team of Israeli, Spanish and German researchers, was based on maps of gene expression of humans and our ancient cousins, the Neanderthals and the Denisovans.

The research explains why despite being 99.84 percent identical genetically, the Neanderthals looked quite different from humans, nbcnews.com reports.

According to the researchers, the answer lies in a process that controls gene expression called DNA methylation. In this process, a methyl group attaches to a gene and prevents normal genetic activity.

"We wanted to know if we could say anything about how genes were active or regulated in our closest evolutionary relatives," computational biologist Liran Carmel and stem cell biologist Eran Meshorer, at the Hebrew University of Jerusalem, told Nature. "This may be very relevant to explaining some of the known phenotypic differences between us."

Researchers created methylation maps that revealed several regions with different genetic activity, especially in those associated with body shape and neurological diseases such as autism and schizophrenia. However, the maps aren't complete as the research was based on DNA obtained from a few bones.

In the study, researchers created methylation maps by measuring the levels of decayed products of unmethylated cytosines and cyctones. Researchers then compared these methylation maps with similar maps of modern humans, according to a news report by Physorg

Carmel and colleagues found some 2000 different regions where gene expression was on in humans, but off in Neanderthals or Denisovans or vice versa, nbc.news reported.

The team found significant changes in methylation in some regions such as HoxD cluster, which has earlier been linked with changes in physical appearance. The alterations in HoxD cluster might explain why Neanderthals were short and stout.

Also, researchers found that methylated regions linked with neurological disorders such as autism and schizophrenia were present in modern humans, but not our primitive cousins.

The study is published in the journal Science.