A comparison of the high-quality genome sequence of a 50,000-year-old Neanderthal woman with those of modern humans and Denisovans reveals a long history of interbreeding among at least 4 species of early humans.

The comparison, conducted by a large group of genetic scientists, shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago.

Neanderthals and Denisovans split about 300,000 years ago.

Though Denisovans and Neanderthals eventually died out, they left behind bits of their genetic heritage because they occasionally interbred with modern humans.

The authors estimated that between 1.5 and 2.1 percent of the genomes of modern non-Africans can be traced to Neanderthals.

Denisovans also left genetic traces in modern humans, though only in some Oceanic and Asian populations.

The genomes of Australian aborigines, New Guineans and some Pacific Islanders are about 6 percent Denisovan genes, according to earlier studies.

The new analysis finds that the genomes of Han Chinese and other mainland Asian populations, as well as of Native Americans, contain about 0.2 percent Denisovan genes.

The genome comparisons also show that Denisovans interbred with a mysterious, fourth group of early humans also living in Eurasia at the time.

That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia a million or more years ago.

The study also indicates that the Neanderthal woman was highly inbred. She was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins.

Further analyses suggest that the population sizes of Neanderthals and Denisovans were small and that inbreeding may have been more common in Neanderthal groups than in modern populations.

The researchers were able to identify at least 87 specific genes in modern humans that are significantly different from related genes in Neanderthals and Denisovans, and that may hold clues to the behavioral differences distinguishing us from early human populations that died out.

They noted that no one is sure how long the various now-extinct groups lasted, but that there is evidence that Neanderthals and modern humans coexisted in Europe and Asia for at least 30,000 years.

Interbreeding was infrequent, though how infrequent is unclear given the genomic information available today.

“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 Dr Montgomery Slatkin from the University of California, Berkeley, who with co-authors reported their results in the journal Nature.

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Kay Prüfer et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, published online December 18, 2013; doi: 10.1038/nature12886