Pacific islanders got a double whammy of Stone Age DNA

Modern-day Melanesians carry a two-pronged genetic legacy of ancient interbreeding that still affects their health and well-being, researchers say.

Unlike people elsewhere in the world, these Pacific islanders possess nuclear DNA that they inherited from two Stone Age hominid populations, say population geneticist Benjamin Vernot, formerly of the University of Washington in Seattle, and his colleagues. At least some of that ancient DNA contains genes involved in important biological functions, the researchers find. Nuclear DNA is passed from both parents to their children.

The finding means that ancestors of people now living in the Bismarck Archipelago, a group of islands off Papua New Guinea’s northeastern coast, mated with Neandertals as well as with mysterious Neandertal relatives called Denisovans, the scientists conclude online March 17 in Science.

In support of previous research, the researchers find that non-Africans — including Melanesians — have inherited an average of between 1.5 and 4 percent of their DNA from Neandertals. But only Melanesians display substantial Denisovan ancestry, which makes up 1.9 to 3.4 percent of their DNA, the researchers say. (Present-day African populations possess little to no Neandertal or Denisovan DNA.)

The bits of Neandertal and Denisovan DNA carried by Melanesians encompass genes involved in metabolism and immunity, indicating that interbreeding influenced the evolutionary success of ancient humans, Vernot’s group reports.

The new study reconstructs the microscopic landscape of Neandertals’ and Denisovans’ contributions to Melanesians’ DNA “in impressive detail,” says Harvard University paleogeneticist Pontus Skoglund.

Vernot’s team studied DNA from 35 Melanesians at 11 locations in the Bismarck Archipelago. Analyses concentrated on DNA from 27 unrelated individuals. The researchers also looked for evidence of ancient interbreeding in previously acquired genomes of close to 1,500 modern-day individuals from different parts of the world. Denisovan DNA for comparisons came from fragmentary fossils found in a Siberian cave; comparative Neandertal DNA came from a genome previously extracted from a 50,000-year-old woman’s toe bone.

Among Melanesians, DNA sequences attributed to Neandertals and Denisovans encompassed several metabolism genes. One of those genes influences a hormone that increases blood glucose levels. Another affects the chemical breakdown of lipids. Other Melanesian genetic sequences acquired through ancient interbreeding either include or adjoin genes that help to marshal the body’s defenses against illness.

These findings follow evidence suggesting that once-useful genes that ancient humans inherited from Neandertals now raise the risk of contracting certain diseases (SN: 3/5/16, p. 18). Vernot’s group reaches no conclusions about good or bad effects of ancient hybrid genes in Melanesians.

No sign of Neandertal or Denisovan DNA appears in areas of Melanesians’ genomes involved in brain development, the scientists say. So brain genetics, for better or worse, apparently evolved along a purely human path.

Denisovans’ evolutionary history remains poorly understood. Previous DNA comparisons suggest that Denisovans must have reached Southeast Asia. Skoglund suspects that’s where the ancestors of Melanesians bred with Denisovans.

Substantial interbreeding of humans with Denisovans probably occurred only once, Vernot and his colleagues suspect. Genetic exchanges of humans with Neandertals took place at least three times, they add. These estimates are derived from comparisons of shared Denisovan and Neandertal DNA sequences among individuals in different parts of the world.