DNA unveils enigmatic Denisovans

Genetic data of unprecedented completeness have been pulled from the fossil remains of a young Stone Age woman. The DNA helps illuminate the relationships among her group — ancient Siberians known as Denisovans — Neandertals, and humans.

The Denisovan’s genetic library suggest that she came from a small population that expanded rapidly as it moved south through Asia, says a team led by Matthias Meyer and Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Denisovans passed genes to Papua New Guineans but not to Asians, Europeans or South Americans, the researchers report online August 30 in Science. That’s in line with previous evidence that Denisovans contributed to the ancestry of present-day Australian aborigines and Melanesians.

The new investigation also finds that Asians and South Americans possess more Neandertal genes than Europeans do. Although Neandertals inhabited Europe and West Asia, they may have interbred most frequently with Homo sapiens in East Asia, or, possibly, had their genetic contributions to Europeans diluted as increasing numbers of Stone Age humans reached that continent.

“We can now start to catalog essential genetic changes that occurred after we separated from our closest extinct relatives,” Pääbo says. Preliminary DNA comparisons between people today and the young female Denisovan have identified eight human-specific genes involved in brain functions, including one linked to language and speech development.

Despite the new advance in retrieving ancient DNA, Denisovans’ evolutionary identity, and the full extent of Denisovan flings with human groups, is far from settled. Denisovan fossils, which date to at least 50,000 years old, consist of only a finger bone and two teeth unearthed at Siberia’s Denisova Cave.

Previous work partly reconstructed DNA from the finger fossil and unveiled a close genetic link between Neandertals and Denisovans (SN: 1/15/11, p. 10).

Think of the new achievement as Denisovan DNA 2.0. Meyer and Pääbo’s group devised a method that gets around the inevitable problems of missing data from DNA, which degrades over the millennia. The new method helps stitch together the remaining pieces, allowing the researchers to assemble a version of Denisovan DNA that’s about as complete and accurate as what can be obtained from a living person.

“Producing a full genome of such high quality from such an old specimen illustrates how far we have come in just a few years in the field of ancient DNA sequencing,” says evolutionary geneticist Rasmus Nielsen of the University of California, Berkeley.

Comparisons of premium-grade Denisovan DNA to large samples of DNA from people today should begin to clarify where and when ancient interbreeding took place, Nielsen says.

Meyer and Pääbo’s team compared its new-and-improved Denisovan material to genetic samples from 11 living people, including five Africans from different tribes or ethnic groups; two Europeans, one from France and one from Sardinia; two Chinese, one from a northern ethnic group and one from a southern ethnic group; a Papua New Guinean; and a villager from Brazil’s Amazon forest.

Relative to chimpanzee DNA, Denisovan DNA displayed fewer alterations than the genetic code of people today did. That disparity reflects the fact that Denisovans died out in the Stone Age and thus had less time than surviving humans to generate genetic changes relative to chimps. The scientists used that difference to calculate a provisional age of between 74,000 and 82,000 years for the Denisovan finger bone, tens of thousands of years older than previous data had suggested.

The Leipzig group’s method of analyzing the DNA also allowed them to spot a relatively small number of differences between Denisovan genes inherited from the mother and the father. That observation suggests the ancient Siberians had an extremely low genetic diversity, the researchers say. A small population of Denisovans likely expanded into new territories where interbreeding with H. sapiens occurred, with not enough time elapsing for many survival-enhancing genetic modifications to accumulate, the team proposes.

The same gene variants carried by the Denisovan individual are commonly found today in living people with dark skin, brown hair and brown eyes.

Papuans inherited 6 percent of their genes from Denisovans, the team estimates. They share more genes with Denisovans on chromosomes other than the sex-linked X chromosome. Females inherit two X chromosomes, whereas males inherit one X and one Y chromosome.

It’s possible that Denisovan males primarily mated with female Papuan ancestors, thus leaving a small genetic mark on present-day Papuan X chromosomes. Or, genetic incompatibility between Denisovans who interbred with modern humans may have resulted in the loss of Denisovan genes in later generations of Papuan ancestors, primarily on the X chromosome, the researchers suggest.

DNA found in living Chinese displays contributions from Neandertals but not Denisovans, although a tiny fraction of a percent of Chinese ancestry may have come from the ancient Siberian crowd, Pääbo says.

In contrast to the new findings, evolutionary geneticists Pontus Skoglund and Mattias Jakobsson, both of Uppsala University in Sweden, recently reported that southern Chinese possess roughly 1 percent Denisovan ancestry (SN: 8/25/12, p. 22). Skoglund and Jakobsson compared Neandertal and a less complete record of Denisovan DNA to genetic instruction books from more than 1,500 people living in different parts of the world.

Meyer and Pääbo’s team analyzed DNA from only two Chinese individuals, limiting the ability to statistically distinguish between Neandertal and Denisovan genetic contributions, Jakobsson says. “Until we have population data from East Asians and a high-quality Neandertal genome,” he says, “I think the jury is still out.”

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Back Story | Cave Treasures

The Denisova Cave in Russia has yielded at least 100,000 years’ worth of artifacts.
Courtesy of Max Planck Institute for Evolutionary Anthropology; Geoatlas/Graphi-Ogre, adapted by E. Feliciano

Before it became the namesake of a mysterious genetic ancestor of at least some present-day people, Siberia’s Denisova Cave was known as the home of numerous Stone Age archaeological finds excavated since 1977. Digs in the multi-chambered cave have revealed tens of thousands of years of inhabitants.

Stone tools dating to more than 100,000 years ago presumably were made by Neandertals. Researchers attribute stone and bone tools and personal decorations unearthed in 50,000- to 30,000-year-old soil layers inside the cave to modern humans. These finds include ornaments made of mammoth tusks, animal teeth, ostrich eggshells, seashells and semiprecious stones. Bone needles with drilled eyes and cylinder-shaped bone beads were found as well. Other artifacts found in the cave date to as recently as several hundred years ago.

Scientists can’t say whether Denisovans made any stone tools or ornaments that have been found in the cave. Fragmentary fossil remains make it impossible even to say what Denisovans looked like.