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A mystery surrounding human fossils found in a cave in China has been solved by DNA sequencing, according to a new study, and it sheds light on the ancestry of the very first Americans.

In 1989, a thigh bone and part of a skull were found in a cave in the Chinese province of Yunnan in the southwest area of the country.

Radiocarbon dating conducted in 2008 on the sediments where the fossils were found indicated they were around 14,000 years old – which would mean they were from a period of time when Homo sapiens (modern humans) had migrated to many parts of the world.

However, primitive features of the bones niggled scientists, who questioned what species of human the fossils belonged to.

The shape of the skull resembled that of Neanderthals – an archaic human population that disappeared about 40,000 years ago – and it seemed the brain would have been smaller than that of modern humans.

As a result, some experts in human evolution thought the skull probably belonged to a hybrid population of archaic and modern humans or perhaps a previously unknown human species that existed alongside our own. Researchers gave the group the name Red Deer People after the name of the cave in which the remains were found.

Now, Chinese scientists have extracted genetic material from the skull cap and sequenced the DNA. They found that the skull belonged to a female individual, who was most likely a direct human ancestor – a member of Homo sapiens – not a previously unknown type of human.

“Ancient DNA technique is a really powerful tool,” said Bing Su, a professor at the Kunming Institute of Zoology at the Chinese Academy of Sciences in Yunnan who was involved in the research, in a news release. “It tells us quite definitively that the Red Deer Cave people were modern humans instead of an archaic species, such as Neanderthals or Denisovans, despite their unusual morphological features.”

Su and his colleagues have shared their findings in a study that published Thursday in the journal Current Biology. Their analysis of the genome revealed the individual the bones belonged to had levels of Neanderthal and Denisovan ancestry that were similar to those found in modern humans – suggesting that they weren’t part of a hybrid population that interbred with one another.

DNA from Denisovans, a little understood group of archaic humans, and Neanderthals lives on in some humans today. That’s because long ago our Homo sapiens ancestors encountered these groups as they spread around the world and reproduced with them.

The researchers compared the genome extracted from the ancient DNA to the genomes of other people from around the world – both modern and ancient.

They found that the bones belonged to an individual who was linked deeply to the East Asian ancestry of Native Americans. The researchers believe that this group of people traveled north to Siberia and then crossed the Bering Strait to become some of the first Americans.

“Her genome fills in a really important missing piece of the overall story of how humans got to the Americas. A lot of work has been focused on the other branch of Native Americans’ ancestry – the Siberians – but not much was known until this paper about the East Asian ancestors of Native Americans. It’s really important to understand this branch, as it accounts for the majority of Native American ancestry!” said Jennifer Raff, a geneticist and anthropologist at the University of Kansas and the author of the book “Origin: A Genetic History of the Americas,” via email.

“I find their results plausible and very interesting. We’re still trying to figure out the geographic location of the population immediately ancestral to the First Peoples, but this paper gives us some additional clues,” added Raff, who wasn’t involved in the research.

This is an artist's impression of the Red Deer Cave People, who lived in Yunnan, China, about 14,000 years ago.

But what explained the unusual morphological features of the remains?

The researchers described the genome as “low coverage,” which means it doesn’t contain enough detail to offer an explanation as to why the bones looked different from modern human skeletons. Acidic soil and warm, humid conditions where the skull was found meant that scientists were only able to recover 11.3% of the genome. It was the first time DNA has been sequenced from a human fossil found in southern China.

The study noted that the individual the bones belonged to had a lot of genetic diversity, indicating that a number of different lineages of early modern humans must have coexisted in southern East Asia during the late Stone Age. Perhaps, the study suggested, the region had been a refuge during the height of the Ice Age.

Darren Curnoe, a research associate at the Australian Museum Research Institute in Sydney, said that in 2012 he published the first international scientific paper on the fossils, which he described as having a “very rugged anatomy.”

“I know these fossils better than anyone. They are anatomically very puzzling, even if they are modern humans, as the DNA suggests,” said Curnoe, who wasn’t involved in the latest study, via email.

“How do we reconcile that? Perhaps people’s anatomical form in the past – over long timescales – was very ‘plastic’ and responded to the environment and lifestyle of these early people. This could be something we have lost since we took up farming.”

Analysis of the Red Deer Cave genome could also help build up a more complete picture of ancient humans in east and southeast Asia – an exciting locale for paleoanthropologists.

It’s where some of the world’s oldest cave art has been found and the remains of puzzling archaic humans, such as the Hobbits of Flores in Indonesia and Dragon man in northern China, have been discovered. Other finds are shedding light on the enigmatic Denisovans.

Next, the Chinese team hopes to find additional support for its findings by sequencing more ancient human DNA using fossils from southern East Asia, especially ones that predated the Red Deer Cave people.

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