"This changes our image of what humanity is," said anthropologist John Hawks of the University of Wisconsin, who was not involved in the work. "What they've done is sequenced the genome of an ancient group of people we'd left for dead."
The work, announced Friday in the journal Science, has stunned scientists by demonstrating what a wealth of information can be gleaned from bone fragments thousands of years old. It represents the first major result to come from what has been called the Neanderthal Genome Project - once considered a long shot initiated by Svante Paabo of the Max Planck Institute in Germany.
Using bone fragments from three Neanderthal women, the team was able to piece together a nearly complete genome - the three-billion-character code carried by DNA.
They compared that to the genetic codes of modern people of different ethnic backgrounds. That's beginning to reveal key genetic differences that separate us from our closest evolutionary cousins.
It also revealed that non-Africans have more genetic similarities to Neanderthals than do Africans. They conclude that people with European, Asian, or other non-African origins carry between 1 percent and 4 percent Neanderthal genes.
Scientists had long been divided over the nature of Neanderthal people and whether they had humanlike abilities to learn, communicate, and create art. Anthropologists have called the different factions the "smart Neanderthal camp" and the "dumb Neanderthal camp."
Hawks is in the smart Neanderthal camp. Neanderthal people had brains the same size or slightly bigger than those of modern humans, he said. They probably wore clothes and, apparently, used paints and jewelry. Most likely, he said, they had language.
The evidence for language comes from the anatomy of the Neanderthal larynx and from genetics. They carry a gene called FOXP2, said Hawks, which is not found in chimps or other animals. It has been associated with language because mutations in this gene lead to language disorders in people today.
Modern humans and Neanderthals are known to be closely related, sharing a common ancestor in Africa 400,000 years ago.
After that, according to the consensus view, the group that was to become Neanderthal man left Africa and moved into the Middle East and parts of Europe and Asia. The descendants who stayed behind evolved into anatomically modern humans around 100,000 years ago.
Over the time they were separated, the two branches evolved in slightly different directions. Neanderthals were heavier and stockier than modern humans, and in Europe they ate almost nothing but meat.
But in parallel, both groups evolved increasingly large brains.
Then, according to genetic and fossil evidence, our ancestors moved into the Middle East sometime after 100,000 years ago, and by 50,000 years ago, they had spread into Asia, China, Australia, and Europe. In the process, they were thought to have wiped out existing populations of Neanderthals, perhaps by competing for the same food sources.
But the Neanderthal DNA suggests the encounters with our ancestors weren't all hostile. "It wasn't that they came in like a Blitzkrieg and replaced everybody," said Wisconsin's Hawks.
Until recently, the question of mixing looked to be impossible to answer. Hawks said that, 10 years ago, he stood up at a conference and explained why reading the Neanderthal DNA would be difficult to impossible.
The problem is that most of the DNA in the bone fragments is not from Neanderthal people. Most comes from soil bacteria and other organisms that later lived on the bones. The researchers had to be extra careful to avoid contamination with their own DNA and that of other people handling the samples.
In the end, they were able to make a case that they had reduced the contamination to less than 1 percent.
The evidence for interbreeding comes from the way the Neanderthal DNA compares with that of people from different ethnic groups today, said geneticist Richard "Ed" Green of the University of California, Santa Cruz, the paper's lead author.
If there were no mixing, then all groups today should be equally distantly related to Neanderthals, since we all sprang from this common ancestor. But what they found instead was that people with European or Asian roots shared more DNA with Neanderthals than do Africans.
The simplest explanation, said Green, was that the mixing took place soon after the ancestors of today's non-Africans first left their continent of origin and went to the Middle East. Then, the modern humans fanned out over the globe taking a few Neanderthal genes with them.
"The evidence was clear and obvious that, yes, there was admixture," Green said.
Though humans and Neanderthals are 99.84 percent genetically identical, the scientists were able to find some specific genes that differ between the two groups. Some are associated with skin, hair, wound-healing, energy, metabolism, and brain function.
They also used a chimpanzee genetic code for comparison and found 78 genes that have changed only in our lineage, while Neanderthals share the chimpanzee version.
Over the coming months, they hope to understand more specifically what these genes do, how they make us different from Neanderthals, and what they tell us about our evolutionary history.
Does this mean Neanderthals are not a separate species? "We've avoided using taxonomy," said geneticist David Reich of Harvard Medical School, part of the team announcing the findings.
He said the word species may not help advance our understanding our past. "I think of them as another type of human," said Reich.
Neanderthals make up just one of a number of branches of humanity, sometimes called archaic humans. The same collaborators who did the Neanderthal genome announced earlier this year that genetic analysis of a 40,000-year-old finger bone in Siberia revealed a new group of humans, distinct from both modern humans and Neanderthals.
Anthropologist Christopher Stringer, who was not part of the collaboration, said he was surprised that there was such a significant amount of human-Neanderthal mixing. "As one of the architects of 'out of Africa,' I have regarded the Neanderthals as representing a separate lineage and, most likely, a separate species from Homo sapiens," he said. "Now, the Neanderthal genome strongly suggests those genes were not lost and that many of us outside of Africa have some Neanderthal inheritance."
Hawks said he's not too shocked by the interbreeding. "There were a number of us who argued it should be possible," he said.
If Homo sapiens and Neanderthals contacted each other, he said, "it seems likely that, from what we know about human behavior, they would have bred at some point."
Contact staff writer Faye Flam
at 215-854-4977 or firstname.lastname@example.org.