DNA from Neanderthal leg shows distant split

An undated photograph shows the inside of the Vindija cave
in Croatia, where a leg bone from a male Neanderthal
was found and and used to sequence DNA by researchers who on
Wednesdauy said it shows that Neanderthals are truly distant
relatives of modern humans who interbred rarely, if at all,
with our own immediate ancestors. (Johannes Krause- Max-
Planck Institute of Evolutionary Anthropology/Handout/Reuters)

Researchers have sequenced DNA from the leg bone of a Neanderthal man who died 38,000 years ago and said on Wednesday it shows the Neanderthals are truly distant relatives of modern humans who interbred rarely, if at all, with our own immediate ancestors.

They estimate that modern humans and Neanderthals split from a common ancestor at least 370,000 years ago, and possibly 500,000 years ago, although we share 99.95 percent of our DNA.

"We see no evidence of mixing 40,000, 30,000 years ago in Europe. We don't exclude it, but see no evidence," Edward Rubin of the U.S. Department of Energy Joint Genome Institute in Walnut Creek, California, who led one study, told reporters.

This conflicts with some evidence from other researchers, including a team who said earlier this month that humans may have inherited a brain gene from Neanderthals.

The researchers reported their findings jointly in the journals Nature and Science.

Rubin's team used one method to isolate and sequence part of the Neanderthal's DNA, while another team, led by Svante Paabo of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, used a separate method to sequence a much larger amount.

Paabo was the first scientist to find and sequence Neanderthal DNA, in 1997, and first suggested that Neanderthals did not mix with modern humans.

"I think the sequence data will serve as a DNA time machine that will tell us about biology and aspects that we will never be able to get from their bones and a limited number of associated artifacts," Rubin said.

Neanderthals and modern humans are both descended from Homo erectus, which left Africa and spread around the world about 1.5 million years ago.

Neanderthals lived in Europe and the Middle East until about 30,000 years ago. Cro-Magnon people, the ancestors of modern humans, started a second wave of migration out of Africa about 10,000 years earlier.

One huge question is how closely they interacted. Paabo's and Rubin's genetic analysis both suggest there was little sexual contact, at least according to the genes from this one male found at the back of a cave in Croatia.

Paabo's team sorted through 70 Neanderthal specimens before they found a bone well-preserved enough to provide DNA. They took the tiniest samples they could to preserve the valuable bones.

They know it was a male because the DNA has a Y chromosome. Females have two X chromosomes.

Paabo's team used a gene sequencer made by 454 Life Sciences Corporation, a majority-owned subsidiary of CuraGen Corporation. He said they have refined their methods and hope to have a complete genetic sequence within two years.

They said the Neanderthal sequences are 99.95 percent identical to human DNA sequences. This compares to about a 98 percent similarity between humans and chimpanzees, who split from a common ancestor 6 million to 7 million years ago.

Three-way comparisons among the human, chimpanzee and Neanderthal genomes should shed light on what makes modern humans unique, experts agreed.

Rubin and other experts stressed that while full sequences of the human genome are available, very little is understood about what the code actually means.

They found, for instance, sequences linked with eye color but cannot read the code to tell what color Neanderthal eyes were.

Neanderthals have genome chunk sequenced

18:00 15 November 2006
NewScientist.com news service

Dan Jones

Outside the Vindija cave in Croatia (Image: Johannes Krause / Max-Planck-Institute of evolutionary Anthropology)

What are the genetic changes that set us apart from our Neanderthal cousins? Although the ancient race is long extinct, we may soon know the answers.

More than one million base pairs of fossilised Neanderthal DNA have now been sequenced – the most of any extinct organism – thanks to a new high-throughput sequencing technique well-suited to handling old, degraded DNA.

Two research teams collaborated closely on the project – the first steps towards sequencing the Neanderthal genome – in a marked difference to the competitive race to for the human genome.

Both teams used the same 38,000-year-old Neanderthal specimen, discovered in Croatia, from which to extract DNA and report their findings on Wednesday in the journals Nature and Science, respectively.

Common ancestor

The sequence suggests that humans and Neanderthals probably began to diverge about 600,000 years ago, and that our common ancestor lived in a small population comprising just 3000 individuals.

One group, led by palaeogeologist Svante Paabo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, used the rapid new "direct sequencing approach" on DNA culled from the ancient hominid’s thighbone. The technique was developed by research collaborators 45 Life Sciences, based in Branford, Connecticut, US.

The other team, led by geneticist Eddy Rubin at the Lawrence Berkeley National Laboratory, Walnut Creek, California, US, used a more traditional sequencing method involving cloning DNA using bacteria to generate 630,000 base pairs of the Neanderthal sequence.

Time difference

The studies only explored a tiny fraction of the full genome, and so the insights they provide are limited, so far. But both teams were able to use their results to estimate how long ago humans and Neanderthals shared a common ancestor.

Paabo’s group puts the date at around 516,000 years ago, while Rubin’s team reaches a slightly older date of 706,000 years ago. Both estimates have large errors of margin that in fact overlap, so the dates are broadly compatible.

One of the major problems confronting efforts to sequence such ancient DNA is contamination, both from microbial DNA and, more significantly, from modern human DNA, which could be confused with Neanderthal sequences. Researchers in both teams used a number of tests to ensure that they were working with genuine Neanderthal DNA, however.

“This is proof of principle that we can recover nuclear genome sequences from Neanderthals,” says Richard Green, one of Paabo’s team. We should have the full genome sequenced within two years," he says.

Journal reference: Nature (DOI: 10.1038/nature05336), and Science (vol 314, p 1113)

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