Neanderthals, such as the one to whom this skull once belonged, died out 30,000 years ago. But many of their immune genes are common among humans outside Africa. (Nikola Solic/Reuters)

Some immune system genes carried by modern humans came from interbreeding with Neanderthals and other ancient hominins called Denisovans, a new study suggests.

"The cross breeding wasn't just a random event that happened," said Peter Parham, who co-authored the study published online in Science Express, in a statement. "It gave something useful to the gene pool of the modern human."

Parham, a professor of microbiology and immunology at California's Stanford University, and his collaborators analyzed a family of immune system genes called human leukocyte antigen (HLA) genes, which are extremely varied and help the body recognize and destroy disease-causing pathogens.

They sequenced and compared HLA genes from humans with those from:

  • Neanderthals, who lived in West Asia and Europe and died out 30,000 years ago.
  • Denisovans, a group of hominins who lived in East Asia 30,000 to 50,000 years ago and were discovered in 2008 from a finger bone and a tooth in a cave in Siberia. Those are still the only known Denisovan remains.

Hominins and hominids

Humans are part of a larger group of closely related human-like species, such as Neanderthals, called hominins. All hominins are themselves part of a larger group known as hominids that includes all the great apes such as chimpanzees and gorillas.

What the researchers found was that humans outside Africa share certain HLA genes with Denisovans and certain HLA genes with Neanderthals. This suggests that these genes entered the human genome through interbreeding with those other hominin groups after humans spread out of Africa 65,000 years ago.

A Denisovan gene variant called HLA-B*73 was most common in West Asia, leading scientists to believe that was "the most likely site for the fortuitous mating to have taken place," said a Stanford University news release.

While Neanderthal genes typically make up one to six per cent of the genome of humans from outside Africa, Parham said, Neanderthal and Denisovan HLA genes account for a much higher percentage of HLA gene variants.

For one class of HLA genes, over half the variants in Europeans, 80 per cent in Asians and 95 per cent of variants in Papua New Guineans originally came from Neanderthals and Denisovans.

That suggests that these variants gave a survival advantage to humans who carried them, the researchers concluded.