Extinct Genome From Fossil Finger Posted Online

Denisova Cave, Siberia

Ann Gibbons

Researchers in Germany today posted the first high-resolution version of an extinct human's genome on the Web site for the Max Planck Institute for Evolutionary Anthropology. The goal: to allow colleagues to download the most complete sequence data available for free.

A year ago, researchers published the first rough draft of the genome of an archaic girl who lived in Denisova Cave, Siberia, at least 30,000 years ago. In January, Max Planck paleogeneticist Svante Pääbo was at a meeting in Sweden when he realized that researchers in other labs were poring over year-old sequence data that was far less complete than what his colleagues had obtained in the lab in the past year using sensitive, new methods to sequence ancient DNA. "I felt bad knowing that we had this very much better version of the same genome and that it would be a few months before it became available," says Pääbo.

So, Pääbo and his colleagues decided to allow their colleagues to download the sequence data for the high-resolution genome today, even though they are still preparing a paper to publish their findings from studying the genome. The team has now sequenced every position in her genome an average of 30 times, using DNA extracted from less than 10 milligrams of the finger bone of the ancient girl. This "30x" coverage provides more detailed information than the 1.9-fold coverage the team published in Nature in late December 2010.

The higher resolution means Pääbo and his colleagues can now compare even small differences in copies of genes that this ancient girl inherited from her mother and father—and spot how her DNA differs precisely from that of living humans and Neandertals. The girl was more closely related to Neandertals than modern humans, but her genome was not within the range of variation found in Neandertals so far. Neandertals, Denisovans and modern humans all lived in Asia at about the same time and interbred at low levels; modern humans in Melanesia and other parts of Asia have inherited about 4% of their DNA from Denisovans.

Researchers are now examining the draft sequence obtained from the girl's ancient DNA to try to see exactly which genes modern humans have inherited from Denisovans. "We are cautious about talking about results as we intend to submit a paper with the analyses rather soon," says Pääbo. But he says the high coverage of the girl's genome makes it possible to see how much genetic variation there was within her population of Denisovans. He adds that it also makes it possible to make a "comprehensive and essentially complete catalog of all changes" that became fixed in modern humans' genomes since our ancestors parted company with Denisovans.