DNA offers sharp image of ancient humans

August 30, 2012

Scientists have produced a digital image of a genome tens of thousands of years old with the resolution of a typical living person’s, enabling them to describe the life and history of the ancient humans in great detail, they reported in Thursday’s issue of Science magazine.

Led by Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, the scientists have created the highest quality genome sequence of ancient humans yet.

Therefore, the Denisovans — as the group has been called, after the Siberian cave harboring its fossils: a finger bone and two teeth — are much better known genetically than Neanderthals, although there are hundreds of specimens from them.

“There is no difference in what we can learn genetically about a person that lived 50,000 years ago and from a person today,” Paabo said Wednesday in a conference call with reporters.

The international team of researchers used only genetic material from a tiny finger bone from a girl that lived in Siberia tens of thousands of years ago. The specimen was found in a cave in 2008 and, based on preliminary genetical analyses by the team in 2010, was attributed to a novel group of humans closely related to Neanderthals.

“The Denisovan genome is particularly close to my heart, because it was the first time that a new group of humans were discovered and defined just from DNA,” Paabo said.

The scientists owe their insights mainly to new technological advances in sequencing of prehistoric DNA. “All forensics on ancient DNA were originally developed for modern DNA,” said Matthias Meyer of the Max Planck Institute, lead author of the article. He was responsible for developing approaches that take into account challenges typical for ancient genetic material, such as its scarcity and degraded state.

The breakthrough came partly through starting the sequencing with single strands of DNA, as opposed to the usual approach of using double strands. Earlier this year, the researchers made the raw genome sequence available to the public by publishing it online.

Using the DNA alone, the scientists reconstructed the appearance of the Siberian girl: She had brown eyes and dark hair and skin. Also from genetic information, the scientists pieced together the girl’s pedigree and compared it with modern humans’ and Neanderthals’. The Denisovans contributed genetic material only to present Australian Aborigines and some people in Melanesia, whereas Neanderthals left their mark on everyone outside Africa, Paabo said.

The scientists analyzed the differences between the DNA of the Denisovan and that of modern humans around the world, allowing them to come up with an estimate of the specimen’s age. Based on the mutation rate in modern humans, the team approximated the age of the Siberian girl at about 80,000 years. That conflicts with archeological data that assign the geological layer of the fossil to an age of 30,000 to 50,000 years. Carbon dating, a standard procedure to determine the age of fossils, would provide a more definitive answer, but the specimen is too small for that.

“It is amazing that we can sequence the whole genome, but there is too little carbon to date it,” Paabo said.

The scientists estimated that the Denisovans split from modern humans between 700,000 and 200,000 years ago, a broad range attributed to uncertainties about the underlying mutation rates.

The researchers also inferred the population sizes of the ancient Denisovans based on the differences between genes from the father and the mother in the Siberian girl’s DNA. Because the genes are very similar to each other, the scientists estimated the genetic diversity and therefore the population size to have been low, although the Denisovans have occupied large parts of Asia.

Paabo shied away from calling the Denisovans a separate species, because they interbred with the ancestors of modern humans. “I wouldn’t call Neanderthals a different species from humans, either. I stay away from that debate,” he added.

The scientists speculated that a single population moving out of Africa gave rise to the Denisovans and Neanderthals. The new findings support the notion that the ancestors of modern humans mixed with groups of ancient humans, instead of quickly replacing them.

As a next step, the scientists plan to re-sequence the Neanderthal using the new methods and get it on par with the genome of the Siberian girl.

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