A tiny toebone from a Neanderthal woman who lived around 50,000 years ago has shown that several branches of early humans interbred before a single group, Homo sapiens, rose to dominate.
The bone has provided the final piece to a project, launched in 2006 by European evolutionary anthropologist Svante Paabo, to use ancient DNA to trace the human odyssey.
In a study published in the journal Nature on Wednesday, a team reports that the bone adds hugely to genetic knowledge of our cousins, the Neanderthals, who died out around 30,000 years ago.
The scientists compared the genome against those of two other human groups who shared the planet at the same time.
They were the Denisovans, another mysterious sub-group whose remains have been found in Siberia; and Homo sapiens, as anatomically modern man is called.
The comparison points to interbreeding -- "gene flow" in scientific parlance -- among the three groups, although the extent is rather limited.
Between 1.5 and 2.1 percent of the genomes of humans today can be attributed to Neanderthals, it found. The exceptions are Africans, who do not have a Neanderthal contribution.
"We don't know if interbreeding took place once, where a group of Neanderthals got mixed in with modern humans and it didn't happen again, or whether groups lived side by side, and there was interbreeding over a prolonged period," said Montgomery Slatkin, a professor at the University of California at Berkeley.
Denisovans, too, left their mark on modern man. Previous studies found that around six percent of the genomes of Australian aborigines, New Guineans and some Pacific Islanders came from this group.
The new analysis found that the genomes of ethnic Han Chinese and other mainland Asian populations, as well as of native Americans, contain about 0.2 percent Denisovan genes.
The Neanderthals, in turn, contributed at least 0.5 percent of their DNA to the Denisovans.
Both of these groups have an intriguing genetic past, the new study says.
Around five percent of the Denisovans' genome come from some ancient forerunner.
One bet is that it is Homo erectus, said Kay Pruefer, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the comparison.
Keeping it in the family
Incest -- to employ today's term for such behaviour -- appears to have been rampant among the Neanderthals, who like the Denisovans lived in small groups, and had a gene pool to match.
The scientists performed simulations of several inbreeding scenarios on the Neanderthal toebone.
They discovered that the parents of the female were either half siblings who had a mother in common; double first cousins; an uncle and a niece; an aunt and a nephew; a grandfather and a granddaughter; or a grandmother and a grandson.
Genetically, what makes Homo sapiens so different from these extinct branches of our family tree? Why did we survive, and why did they die out?
The answer may lie in at least 87 genes in our genome that appear to be "significantly different" from those found in Neanderthals and Denisovans, says the study, although further work is needed to define in what way.
"There is no gene we can point to and say, 'This accounts for language or some other unique feature of modern humans'," said Slatkin.
"But from this list of genes, we will learn something about the changes that occurred on the human lineage, though these changes will probably be very subtle."
The main source material for the comparison came from bones found in a cave in the Altai Mountains of southern Siberia.
In 2008, it yielded a bone from a little finger of a Denisovan woman in a layer of soil dated to 40,000 years ago.
The Neanderthal toebone was found in the same cave in 2010, but in a deeper layer of sediment dated to around 50,000 to 60,000 years ago.
The cave also has artifacts made by modern humans, which mean that at least three groups of early humans occupied the cave at different times.