Scientists reconstruct genetic makeup of 50,000-year-old girl

Researchers built up portrait from finger-bone fragment of Denisovan who lived and died in a Siberian cave

Scientists have reconstructed the entire genetic makeup of a girl who lived and died in a Siberian cave more than 50,000 years ago. The young woman belonged to an ancient and long extinct group of humans called Denisovans, their existence known only from meagre fossil remains uncovered at the Denisova cave in the Altai mountains in 2008. These ancient relatives are thought to have occupied much of Asia tens of thousands of years ago. Previous tests on the remains found they were more closely related to Neanderthals than modern humans.

Writing in the journal Science, researchers in the US and Germany describe how they sequenced the girl's genome with an accuracy that was once considered impossible with such ancient specimens. The final sequence matched the quality of modern genetic tests on living people.

They achieved the feat through a procedure that sequenced single strands of DNA taken from a little finger bone found at the scene. The bone fragment, and two fossilised teeth, are the only remains of the Denisovans.

Studies on the girl's genes suggest she had dark skin, brown hair and brown eyes, but other genetic factors help shed light on the Denisovans more broadly. Comparison of genetic material inherited separately from the girl's mother and father points to a population with very low genetic diversity, probably a consequence of the Denisovans starting off as a small group of pioneers and expanding rapidly, with little time for genetic diversity to arise.

Svante Pääbo, at the Max Planck Institute for Evolutionary Anthropology in Leipzig, said there was now "no difference in what we can learn genetically about a person that lived 50,000 years ago and from a person today, provided that we have well-enough preserved bones".

The team from Leipzig and Harvard Medical School in Boston compared the Denisovan genome with similar sequences from Neanderthals and 11 modern humans from around the world. This revealed evidence for inbreeding, with Denisovan DNA living on in some populations alive today.

"It's clear that Denisovan material has contributed 3-5% of the genomes of people in Australia and New Guinea and aboriginal people from the Philippines, and some of the islands nearby," said David Reich, a Harvard geneticist who worked on the study. The research highlighted scores of intriguing gene variants that are found in modern humans but not in Denisovans. Eight mutations that have arisen since our ancestors split from Denisovans are involved in brain function and nerve connectivity, for example.

"I think that this is perhaps, in the long term for 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 the Denisovans and Neanderthals," said Pääbo.

Another 34 mutations found only in modern humans are associated with diseases, including four that affect the skin and eyes.

Chris Stringer, head of human origins at the Natural History Museum in London, said further genetic studies might shed light on the biological differences between Homo sapiens and the Neanderthal and Denisovan populations they replaced after they left Africa around 60,000 years ago. "Perhaps some of the skin and eye-related ones reflect resistance to diseases in the African homeland of modern humans, but the brain-related ones hint at possible enhancements in brain structure and function in our species," he said.

He said the low genetic diversity of the Denisovans may indicate that they only expanded into regions like the Altai mountains in southern Siberia in small numbers and during warm spells.


Ian Sample, science correspondent

The GuardianTramp

Related Content

Article image
Discovery of Higgs Boson rated year's top scientific achievement by Science
Other discoveries include sequencing DNA from extinct humans, turning stem cells into egg cells and landing Curiosity on Mars

Robert Booth

20, Dec, 2012 @7:34 PM

Article image
First modern Britons had 'dark to black' skin, Cheddar Man DNA analysis reveals
The genome of Cheddar Man, who lived 10,000 years ago, suggests that he had blue eyes, dark skin and dark curly hair

Hannah Devlin Science correspondent

07, Feb, 2018 @6:01 AM

Article image
New species of ancient human discovered in Philippines cave
Homo luzonensis fossils found in Luzon island cave, dating back up to 67,000 years

Hannah Devlin Science correspondent

10, Apr, 2019 @5:00 PM

Article image
DNA from fossilised eggshells could help reconstruct lives of extinct birds

Ancient DNA from fossilised eggshells will eventually yield clues about the birds' physiology, diet and how they went extinct

Ian Sample, science correspondent

10, Mar, 2010 @12:05 AM

Article image
Swarthy, blue-eyed caveman revealed using DNA from ancient tooth

Genome sequence of 7,000-year-old human remains overturns popular image of light-skinned European hunter-gatherers

Ian Sample, science correspondent

26, Jan, 2014 @6:00 PM

Article image
Neolithic chewing gum helps recreate image of ancient Dane
Analysis of birch tar describes a female hunter-gatherer with dark skin and blue eyes

Ian Sample Science editor

17, Dec, 2019 @4:00 PM

Article image
Shedding our penis spines helped us become human, DNA study hints

Genetic comparison with chimps suggests that losing chunks of DNA – including one associated with penis spines – played a crucial role in making us human

Ian Sample, science correspondent

09, Mar, 2011 @6:00 PM

Article image
Neanderthals live on in DNA of humans

The first comparison of the complete genomes of humans and Neanderthals reveals that up to 4% of our DNA is Neanderthal

Ian Sample, science correspondent

06, May, 2010 @6:00 PM

Article image
Did human women contribute to Neanderthal genomes over 200,000 years ago?
A recently published Neanderthal mitochondrial genome supports the hypothesis that there was an extremely early migration of a small group of African hominins, with whom they interbred.

Jennifer Raff

18, Jul, 2017 @2:34 PM

Article image
Scientists to grow 'mini-brains' using Neanderthal DNA
Geneticists hope comparing prehistoric and modern biology will help them understand what makes humans unique

Hannah Devlin in Leipzig

11, May, 2018 @1:42 PM