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New technique clears up mysteries in extinct Denisovan human genome

MPIEA

Ancient DNA was extracted and analyzed using a novel sequencing approach.


Degraded DNA molecules from a group of human relatives who went extinct tens of thousands of years ago have been reassembled using a new technique, yielding a genetic code for the mysterious Denisovans that meets the standard for modern humans.

The findings are based on samples drawn from 40 milligrams of ground-up bone from a Siberian girl's finger. They confirm what scientists saw in a much less detailed genetic sequence they produced a couple of years ago, and address some of the deep questions surrounding the Denisovans. But they also raise a few new questions, including a basic one: Just how old was the sample they analyzed?

"The amazing thing is that we can sequence the whole genome to very high accuracy, but there is too little carbon in it to do a date," Svante Pääbo, a genetic researcher at the Max Planck Institute for Evolutionary Anthropology, told reporters during a teleconference this week. Pääbo is the leader of the research team behind a paper on the project, published online today by the journal Science.


The finger bone was found in southern Siberia's Denisova Cave during an excavation in 2008. That dig was aimed at untangling the genetic relationship between Neanderthals and modern humans, and bones representing both those species were indeed found in the cave. But the initial analysis of the finger-bone sample revealed a genome that was neither Neanderthal nor classically human. That tiny bone and two molars that were also found in the cave represent the only known specimens of the Denisovan race.

MPIEA

A replica of the Denisovan girl's finger bone sits on a pinky finger, providing a sense of scale.

Previous analyses of the Denisovan genome were considered merely a rough draft, doing no better than an average of 1.9 readings for every molecular base pair in the DNA, or 1.9X. In comparison, the latest analysis goes to a coverage depth of 30X, which is typical of whole-genome sequencing for present-day humans.

The accuracy was increased by taking short, degraded double-strands of DNA, which couldn't be analyzed  the usual tools for gene sequencing, and "unzipping" them into single strands. That made it easier to attach specially designed molecules known as adapters and read out the DNA code, piece by piece.

"There are many things you can do with such a high-coverage genome that you cannot do with the low-quality genome that we had before," said Matthias Meyer, a colleague of Pääbo's at the Max Planck Institute who developed with the new sequencing technique. Here are the main findings reported today:

  • A comparison of chromosomes that the girl inherited from her mother and father indicated that there was surprisingly low genetic diversity in the Denisovan population. That would suggest that the Denisovan population never was very large, and could explain why the group faded into extinction as populations of modern humans spread out. The analysis also confirms that the girl carried genes that have been associated with dark skin, brown hair and brown eyes. "It is very likely that they were dark-skinned, and that is really everything we can say about that," Pääbo said, "The truth is, of course, that one can say quite little about how people looked from just studying the DNA sequences." 
  • Detailed study of the "gene flow" over time suggests that the Denisovans interbred with Neanderthals as well as our own species, Homo sapiens. The analysis confirmed previous findings that Denisovans were more genetically similar to Neanderthals than to anatomically modern humans. So does that mean that Denisovans were a separate species? "I really stay away from species designation," Pääbo said. "I would not call it a different species, but clearly different groups with a different history. I would not call the Neanderthals a different species from humans either, actually."
  • A comparison of the genome with those of modern-day human populations confirmed that Melanesians, Australian Aborigines and other Southeast Asian islanders had the most in common genetically with the Denisovans. The Denisovan contribution to the genomes of present-day Papuans was estimated at 6 percent.
  • A deeper analysis of the Papuan-Denisovan connection showed that the Denisovan contribution was lower for the sex-linked X chromosome than it was for other chromosomes. That might suggest that the Denisovan males were more likely than the females to interbreed with modern humans. Or it could mean there was a genetic defect on the X chromosome that led to its elimination from modern-day genomes.
  • The researchers were able to triangulate, using the Denisovan genome as well as the genetic codes for Neanderthals and modern humans, to come up with an unexpected result: Present-day east Asians and Native Americans appear to have more in common genetically with the Neanderthals than present-day Europeans, even though Europe was thought to be the main hangout for Neanderthals hundreds of thousands of years ago.
  • The researchers also drew up a catalog of more than 100,000 genetic differences that apparently arose between modern humans and the now-extinct Denisovans and Neanderthals in the past 100,000 years or so. About 260 of the changes affect protein function, Pääbo said. "It's quite interesting to me to note that eight of them have to do with brain function and brain development — the connectivity in the brain, how synapses between nerve cells function. And some of them have to do with genes that, for example, can cause autism when these genes are mutated," he said. "I think this is perhaps in the long term, to me, the most fascinating thing about this: what it will tell us in the future about what makes us special in the world, relative to Denisovans and Neanderthals."

Genetic sequencing alone can't tell scientists how long ago the Denisovans lived, however. Pääbo and his colleagues factored in assumptions about the mutation rate of the human genome to estimate that the girl with the finger bone lived somewhere around 74,000 to 82,000 years ago. But a separate line of evidence, based on the rock layering in the cave, suggested that the bone was 30,000 to 50,000 years old.

"I'm very unsure about the archaeological dates, but I would say I'm equally unsure about our molecular dates," Pääbo told reporters.

Similarly, the researchers give a wide range of dates for their estimate of the time when the Denisovan population split off from the evolutionary line leading to modern humans: 172,000 to 700,000 years ago.

"Most of the uncertainty in that number ... comes from the uncertainty at present about the human mutation rate," said another co-author of the paper, David Reich, a geneticist at Harvard Medical School and the Broad Institute. "There is a lot of debate in the community about the rate at which mutations accumulate."

Future studies, involving DNA analysis as well as carbon-dating analysis of other specimens from the Denisova Cave, may help clear up that uncertainty. But for the team behind the research announced today, an even higher priority is to generate a gene sequence for the Neanderthals that's as good as the sequence they now have for the once-mysterious Denisovans.

John Hawks, an anthropologist at the University of Wisconsin at Madison, said the newly published paper was "solid work."

"It's really neat that they've organized a catalog of things that humans have that are not present in this ancient genome," Hawks, who studies human origins but was not part of Pääbo's research team, told me. He said the study of comparative brain genetics, for example, was becoming an increasingly important area, "and this study is part of it."

"We know that the human brain is a big target of evolution, but establishing the order of these changes is an important step now," he said. "This gives us a time stamp on some of those changes."

The technique developed for the Denisovan DNA could be applied much more widely in the future. Meyer said his method could be used on modern-day forensic samples that are too degraded to be analyzed using current techniques. And who knows? Anthropologists may find still more long-lost, extinct cousins in the fossil record whose genomes need to be done.

More about our human and near-human relatives:


In addition to Pääbo, Meyer and Reich, authors of the Science paper, "A High-Coverage Genome Sequence From an Archaic Denisovan Individual," include Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G. Schraiber, Flora Jay, Kay Prüfer, Cesare de Filippo, Peter H. Sudmant, Can Alkan, Qiaomei Fui, Ron Do, Nadin Rohland, Arti Tandon, Michael Siebauer, Richard E. Green, Katarzyna Bryc, Adrian W. Briggs, Udo Stenzel, Jesse Dabney, Jay Shendure, Jacob Kitzman, Michael F. Hammer, Michael V. Shunkov, Anatoli P. Derevianko, Nick Patterson, Aida M. Andrés, Evan E. Eichler, Montgomery Slatkin and Janet Kelso.

Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. To keep up with Cosmic Log as well as NBCNews.com's other stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.