Ancient Human Kin’s DNA Code Illuminates Rise of Brains

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Photograph: IMAGEMORE Co, Ltd./Getty Images

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Photograph: IMAGEMORE Co, Ltd./Getty Images

DNA analysis of an extinct human ancestor that lived 80,000 years ago has pinpointed fundamental genes tied to the brain’s evolution, showing how genome testing is changing anthropology and archaeology along with medicine.

At least eight genes that rose to prominence in human DNA since the time of the ancient relatives, called Denisovans, affect nerve growth and language, an international team of researchers said today in the journal Science. The cognitive power conferred by these genes may have keyed the development of complex thinking skills, culture and civilization said Svante Paabo, a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

“This is perhaps in the long term, to me, the most fascinating part about this; what it will tell us in the future about what makes us special in the world,” he said yesterday on a conference call.

New DNA techniques are reshaping knowledge of human evolution just as quickly as they’re sparking the development of medical tests and treatments. Using a tiny amount of material from an ancient finger bone, scientists were able to analyze the ancient ancestor’s genes as closely as those of anyone who walked into a lab today, said David Reich, a Harvard Medical School genetics professor who contributed to the study.

Almost every cell in an organism holds a complete copy its genome, the chemical code for making proteins and tissues. The Denisovan genome analyzed in the study gives a broad visual picture of the individual it came from, holding genes that predict brown hair, brown eyes and dark skin in humans.

Young Denisovan

Denisovans, who lived in Asia, were closely related to Neanderthals, a group of human ancestors that existed at about the same time.

The structure of the bone the DNA came from suggests it was that of a young girl, about 7 or 8 years old, the scientists said. Paleontologists excavated the fragment, along with two teeth, at Denisova Cave in the Altai Mountains of southern Siberia in 2008.

“In some ways, this ancient genome is even higher quality than the modern-day genomes we’ve produced,” Reich said in a telephone interview. “This means that very degraded ancient DNA samples that weren’t possible to study before can now be studied.”

As part of the investigation, the researchers sequenced 11 new genomes from people in representative populations in Asia, Africa, Europe and the Americas. Among modern human populations, the Denisovan genome is most similar to the DNA of Papua New Guinea natives, the study said.

Conserved Genes

Certain portions of human genomes and their evolutionary relatives have changed very little over time. Nature preserves them over the ages because they’re so important to life and health. Scientists call these areas “highly conserved.” Differences in these highly conserved regions between the Denisovan and human genomes may help outline the most recent chapters in human brain evolution.

The study identified 23 highly conserved regions that differ significantly between humans and Denisovans. Eight are linked to genes involved in brain function, the study said. Four of these genes -- called SLITRK1, KATNA1, ARHGAP32 and HTR2B -- are known to be involved in nerve growth and function.

When compared with Denisovans and Neanderthals, the finding suggests that a primary change in the human brain is its enhanced capacity for making connections, Paabo said. Human intelligence relies on the brain’s ability to link ideas, memories and experiences through its networks of neurons.

“Neanderthals had just as large brains as modern humans had; relative to body size, they had even a bit larger brains,” he said. “It makes sense that what pops out is a sort of connectivity in the brain.”

Language Disorders

Three other highly conserved genes that have undergone changes from the Denisovans -- ADSL, CBTNAP2 and CNTNAP2 -- are linked to autism and other language disorders. These genes may provide some explanation for modern humans’ ability to see things from another person’s viewpoint, as well as to conceal things and lie, Paabo said.

The scientists used Illumina Inc. (ILMN)’s Genome Analyzer IIx to decode the Denisovan DNA. Illumina, based in San Diego, is developing machines that sequence an entire human genome in a day. Roche Holding AG dropped a $6.7 billion hostile bid for the company in April.

Matthias Meyer, also from the Max Planck Institute in Leipzig, said he developed ways to analyze genetic material that’s normally lost in the process of preparing it for sequencing.

New Technique

The technique is particularly useful for decoding short strands of DNA, and may be applied in forensic cases when samples have been damaged, Meyer said. The scientists have already tested the process on DNA samples of extinct cave bears, and will be used to get greater detail from Neanderthal genomes that have already been sequenced with conventional techniques, he said.

“This could also be helpful to researchers who are trying to sequence cancer DNA from tumor samples with limited material,” said Emily Hodges, a molecular biologist at Cold Spring Harbor Laboratory in New York. “It could be used in many applications in the field.”

The researchers were even able to split and analyze the two strands of the Denisovan’s DNA, and thus differentiate the contributions of each parent. The strands were alike enough to suggest that the Denisovan population had relatively little genetic diversity, yet different enough to show that the two parents were not closely related, the researchers said.

100,000 Differences

By counting all the differences between the genomes of Denisovan and modern human genomes, more than 100,000, the scientists estimated that they became separate groups about 170,000 years ago. That didn’t end the interaction between humans and Denisovans. The painstaking analysis shows that human DNA continues to contain some Denisovan genes.

Denisovans and humans probably “intermingled” in mainland Asia somewhere as they moved on to colonize southeast Asia and the Pacific Islands, the researchers said. More such discoveries are likely.

“I would not be surprised if in the future we find other groups of humans in addition to Neanderthals and Denisovans out there, particularly in Asia,” Paabo said.

To contact the reporters on this story: John Lauerman in Boston at jlauerman@bloomberg.net

To contact the editor responsible for this story: Lisa Wolfson at lwolfson@bloomberg.net

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