The legacy of the Neanderthals remains within many modern humans – particularly in their hair, skin and some very pernicious diseases like Crohn’s disease and type 2 diabetes. It’s a bit of a mixed genetic bag, it turns out.

Two new genetic analyses published in the journals Science and Nature on Wednesday examine the telltale signs of interbreeding between Neanderthals and early humans in Europe and Asia 40,000 to 80,000 years ago.

"Now that we can estimate the probability that a particular genetic variant arose from Neanderthals, we can begin to understand how that inherited DNA affects us," Harvard University geneticist David Reich, senior author of the Nature paper, said in a statement. "We may also learn more about what Neanderthals themselves were like."

To sift out what genetic variants in humans stem from Neanderthal ancestors, Reich and colleagues compared genes from 846 people of non-African heritage and 176 people of sub-Saharan African heritage to the gene sequence of a Neanderthal that lived 50,000 years ago. The team that published the Science study examined 665 genomes of modern humans.

Indigenous Africans are the only modern humans thought to be free of Neanderthal influence -- their ancestors never made it up north to have an opportunity to interbreed. So, the genomes of modern Africans can be a used as a litmus test. Where there's genetic overlap between a Neanderthal sequence and non-African sequences, but not with Africans, that suggests a genetic feature inherited directly from interbreeding of humans and Neanderthals (and not from an earlier primate past shared by all three groups).

Previous research has indicated that among non-Africans, an average of 2 percent of the genome can be traced back to Neanderthals. But this latest research suggests figure might be much higher: The Science study suggests that 20 percent of the Neanderthal genome survives in modern-day people of Europe and East Asian heritage.

Multiple Neanderthal-derived gene variants, or alleles, turn out to be associated with diseases in other studies. Two Neanderthal-introduced alleles are associated with Crohn’s disease, while another is associated with systemic lupus and another is connected to type 2 diabetes.

Other Neanderthal-derived gene variants seem to affect the keratin filaments that weave together in human hair, skin and nails. Perhaps some Neanderthal provided some genes for extra-strength keratin to help insulate their hybrid descendants?

“It's tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to humans,” Reich says.

What really interests the team is the regions of the human genome that are free from Neanderthal influence. Reich and colleagues found one of the most extensive “deserts” of Neanderthal DNA on the sex-linked X chromosome. This pattern suggests that some male human-Neanderthal hybrids were infertile, the team thinks.

“This [pattern] suggests that when ancient humans met and mixed with Neanderthals, the two species were at the edge of biological incompatibility,” Reich said in a statement.

Modern humans still share a pretty close evolutionary history, going back 100,000 years at most. But when humans and Neanderthals first encountered each other and interbred, they’d already been separated for 500,000 years – not especially long on a geological timeframe, but long enough for key genetic divergences to arise.

"It is fascinating that these types of problems could arise over that short a time scale," Reich says.

SOURCE: Sankararaman et al. “The genomic landscape of Neanderthal ancestry in present-day humans.” Nature 29 January 2014; Vernot, Benjamin and Joshua M. Akey, “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” Science 29 January 2014.

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