The high-quality genome sequence was generated from this small Neanderthal toe bone.Bence Viola

Although tiny, this Neanderthal toe bone from a female who lived 50,000 years ago has yielded the most complete sequence of the Neanderthal genome. The analysis, published this week in Nature, reveals two interesting facts: First, Neanderthal family members often bred and had children -- the female whose toe was tested likely had half-sibling parents who shared the same mother. And second: Neanderthals and other human ancestral groups interbred...a lot.

Kay Prüfer of the Max Planck Institute for Evolutionary Anthropology and her colleagues compared the sequence to the genomes of modern humans and a recently recognized ancestral group called the Denisovans. Their analysis shows they all mated -- particularly Neanderthals and Homo sapiens. In fact, today, up to 2.1 percent of the genomes of modern non-Africans can be traced to Neanderthals, the researchers estimate.

"There was a lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered," co-author and University of California at Berkeley professor of integrative biology Montgomery Slatkin said.

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A French military band.Wikimedia Commons

Neanderthals and modern humans co-existed in Europe and Asia for at least 30,000 years, so it isn't surprising that interbreeding took place there. According to the study, people of French heritage today retain Neanderthal genes.

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Dancers from Sardinia. Cristiano Cani, Wikimedia Commons

Sardinians are also distantly related to Neanderthals, the study found. "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," Slatkin said.

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A man of Han Chinese ancestry.Jonathan Kos-Read, Flickr

The Han Chinese, native to East Asia, make up a large percentage of the people in China, Taiwan and Singapore today. The study found that their genomes contain both Neanderthal and Denisovan genes.

Human history was "a lot more complex and interesting" than previously thought, co-author Svante Paabo, director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology, told Discovery News.

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A Dai wedding party.Sophie Leblanc, Flickr

The Dai people of southern China are distantly related to both Neanderthals and Denisovans. "The ancestors of Neanderthals and Denisovans diverged from the main human lineage about 600,000 years ago, and then split from each other around 400,000 years ago," Ewan Birney and Jonathan Pritchard explained. "Thus, Neanderthals and Denisovans were quite distinct populations, having been separated for roughly three times longer than any modern human populations."

Birney is at the European Molecular Biology Laboratory, and Pritchard is in the Department of Genetics and Biology at Stanford University.

Indigenous people from Brazil.SeCom/Agencia de Noticias do Acre, Wikimedia Commons

Some indigenous people from Brazil, such as the Karitiana, are not only related to both Neanderthals and Denisovans, but they also show relatively high genetic contributions from the latter. About 1.5 to 2.1 percent of the genomes of all people with European ancestry can be traced to Neanderthals. The Karitiana possess substantially more Denisovan DNA in their genomes than do European people, but it only amounts to about 0.2 percent of their genes, the study found.

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Mixe hail from what is now the state of Oaxaca, Mexico.Wikimedia Commons

Indigenous people known as the Mixe, from what is now the state of Oaxaca, Mexico, retain genetic traces of both Neanderthals and Denisovans, the study concluded. Such DNA research in future might be able to trace the ancestry and migration patterns of the Mixe and other populations.

People of Papua New Guinea.Wikimedia Commons

Earlier studies found that the genomes of Papua New Guinea natives were a whopping 6 percent Denisovan. Natural blond hair is exceptionally rare outside of Europe, but many people from Papua New Guinea have blond hair yet very dark skin. The island used to be connected to the Australian continent thousands of years ago, so Denisovans may have made the trek.

Australian aborigines. Steve Evans, Wikimedia Commons

The genomes of Australian aborigines are also about 6 percent Denisovan, according to earlier studies. The new findings are consistent with that amount.

Native Americans at a Pow-Wow.Wisconsin Department of Natural Resources, Flickr

Denisovans only left genetic traces in some Oceanic and Asian populations. While scientists are still unraveling the ancestry of Native Americans, this study reveals that Native Americans did have ties to Asia and, as a result, Denisovans. About 0.2 percent of the genomes of Native Americans contain Denisovan genes.

An intriguing mystery is that the Denisovan genome contains genes from yet another archaic human ancestor. Prüfer said it might have been Homo erectus, aka Upright Man, or some yet-to-be discovered member of our family tree.