Scientists have found the first Native American

A large international team of scientists has retrieved the entire DNA from an 11,500-year-old skeleton of a child from Alaska. Their finding has just been published in Nature. This discovery pushes the date of the first migration to the American continent back by 10,000 years. It also shows that, at one point, the Native Americans split into two main, genetically divergent groups and tells us when the ancestors of the Native Americans first mixed their genes with those of Europeans. “The child’s skeleton represents the first Native American,” says the Danish DNA detective, Professor Eske Willerslev, who headed the analyses.

In a sense, acidic soil is excellent for burial purposes – the corpse decomposes pretty rapidly and the biological material returns to the great cycle of nature without unnecessary delay.

However, this can be problematic from a scientific perspective because only few really old human skeletal remains turn up in the parts of the world where the soil is relatively acidic. And this limits the potential for using modern DNA techniques to map very early migrations.

Large parts of Alaska have this type of acidic soil where old bones have difficulty surviving. But many scientists hoped that this absence of ancient human bones in Alaska was a thing of the past when a team of archaeologists, headed by stone-age expert Ben Potter from the University of Alaska, uncovered an 11,500-year-old burial ground at Upward Sun River in 2010. After the archaeologists had been digging for some time, they found bone fragments from a partially cremated child whose age at the time of its death was estimated to be about three.

The problem was that it was not possible to extract DNA from any of the charred skeletal parts.

Digging deeper

In 2013, Potter and his colleagues visited the burial site in central Alaska again, and when they dug into the ground just below the place where they had found the charred remains of the three-year-old child they were astonished to discover the skeletons of two infants, lying closely together. And they had been buried, not cremated.

One child was fully developed and may have lived for up to six months, whereas the other child had been aborted or had been born prematurely, in around the thirtieth week of pregnancy. There were burial gifts in the grave together with the two skeletons, including beautifully made double-edged arrow heads and decorated, arrow-like horn shafts – presumably cut from the antlers of a North American stag, also known as an elk or wapiti.

The scientists have now succeeded in retrieving a complete genome – the entire genetic material, the entire DNA code – from the first of these two children, the child referred to as Individual 1 in the scientific report.

This is the outcome of a major international research partnership, headed by Professor Eske Willerslev from the Centre for GeoGenetics at the University of Copenhagen, and the results have just been published in Nature, one of the world’s most prestigious scientific journals.

Funders of the project include the Danish National Research Foundation, the Lundbeck Foundation and the prestigious American National Institutes of Health (NIH). In addition to the University of Copenhagen, numerous other academic institutions participated in the extensive scientific work, including the Technical University of Denmark, DTU (Denmark), the University of Cambridge (UK), the University of Lausanne (Switzerland), the University of Alaska (USA) and the University of California, Berkeley (USA).

Sequenced 17 times

“The bones of Individual 1 – in all probability a girl – contained adequate amounts of usable DNA for our purposes,” says Eske Willerslev, who has performed numerous reconstructions of prehistoric, ancient DNA over the past 15 to 20 years.

It involves a good deal of detective work every time and it is impossible to avoid a substantial number of control measurements to make quite sure that the old material does not contain any ‘background noise’ that may distort the final picture.

“For example, we sequenced Individual 1, who died around 11,500 years ago, 17 times – the entire genome. Not until we’d done that did we dare to say: OK, we have it! And the results we now have – the actual genetic profile of this little stone-age person, who only lived for a few short months – tell an extremely important story. Of course, that’s why it got into Nature. Individual 1 quite literally represents the very first Native American. It’s a little crazy,” says the DNA detective.

Over the bridge

The story told by Individual 1 did not take on more detail until the DNA data were compared with similar data from a range of other prehistoric profiles of human genetic material, for example from Siberia, the origin of the first people to emigrate to the American continent. Today’s Native Americans are descendants of this group of immigrants.

These people came to Alaska via the Bering Bridge, the land bridge that connected Siberia and Alaska at that time. But Eske Willerslev explains that the actual date of this migration has long been a particularly hot point of debate in scientific circles:

“Until Individual 1 had been sequenced – and, fortunately, it became clear that it would actually be possible to recreate the small child’s entire genome – it was widely supposed that the migration took place around 15,000 years ago. We had no analysable – or datable – remains of biological material from human beings from the American continent from before this point. Some of this material consisted of fossilised faecal matter, so-called coprolites, which American archaeologist Dennis Jenkins had discovered in some natural caves in Oregon, the Paisley Caves. In 2008, the dating of the material and the site showed that the coprolites were 14,300 years old. At the Centre for GeoGenetics we helped sequence these fossilised droppings, which actually contained a certain amount of human DNA in the form of cells dislodged from the intestine, so-called epithelial cells. So, up to now, the findings in the Paisley Caves – supplemented by a few remains of human bones found on the American continent at pretty much the same time – have been our baseline for the date of migration over the Bering Bridge. But the analyses of Individual 1 have changed this dramatically,” Eske Willerslev emphasises.

“The DNA data from the small skeleton push back the date of the first migration by about 10,000 years – to a point about 25,000 years ago. And Individual 1 has also given us lots more – and, in many ways, at least as remarkable – data.”

Sex with Europeans

Once Eske Willerslev and his colleagues from the 18 research institutions participating in the work had plotted the entire genome from Individual 1 into the extensive network of both prehistoric and contemporary DNA profiles on which they based their analysis, the following picture of the first migration to the American continent began to take form:

“We need to go back about 36,000 years. We’re in Siberia, where a group of people splits into two – let’s call them A and B – and Group B, for reasons unknown, slowly begins to migrate.

They set course for Alaska, but progress is sedate and, over the next 11,000 years, there’s still contact – also sexual contact – between the members of the two groups, which originally were one,” says Eske Willerslev.

“But contact stops around 25,000 years ago, and Group B is now on the Siberian side of the Bering Bridge – ready to move on, ready to cross over. And then something happens – they meet a group of very, very early Europeans. Who they are, and why they happen to be on the Siberian side of the Bering Bridge, we don’t know. But our DNA analyses don’t lie when they tell us that the Siberian migrants and these early Europeans – who, by the way, we have not seen in any other contexts – interact sexually. The Siberian migrants, descendants of the original B Group, trudged on towards Alaska.”

“And here comes the key point,” says the DNA professor, who has now quite warmed up to his subject.

“The very first Native Americans were the outcome of this gene flow between Group B and the early Europeans. And our Individual 1 was a child of this group,” says Eske Willerslev.

“The genetic lineage to which she belonged no longer exists, and we were completely unaware of it until, in an impressive piece of work, Ben Potter and his colleagues from the University of Alaska discovered and secured Individual 1 for science. But the European component we were able to identify in Individual 1’s DNA profile is precisely the same as the genetic component that can be found in all of today’s Native Americans.”

Therefore, science now knows when this European gene component was introduced into the DNA of the Native American.

“And, due to the knowledge we now have, we can say that Individual 1 represents the first Native American. Because we can’t go any further back – or rather any higher up – in the Native American’s genealogical tree right now.” Eske Willerslev explains.

The Asian component

The mapping of Individual 1’s genome has also answered another question that has long puzzled science: the reason for a previously inexplicable genetic difference between the two main groups – the two lineages – of today’s Native Americans, the northern and the southern.

And Eske Willerslev is very pleased that this question has now been answered.

“The northern group includes the Apache Indians, and many will have heard of the great Apache chief, Geronimo. The southern group includes the Lakota tribe, and the most famous chief of the southern tribes is undoubtedly Sitting Bull.”

Scientists were interested in the difference between the two main groups even before DNA analysis was possible, and northern Native Americans often have a more Asian appearance than those in the south. Once DNA analysis became possible, this was naturally something scientists pounced on – and they certainly hit the jackpot.

“Although the northern and southern Native Americans mostly have the same genetic makeup – including the same European components in their genetic material – the northern group has an Asian component that the southern group doesn’t possess. And now we know why,” says Eske Willerslev.

In certain respects, it is a rather complex story – one of the many elements of Individual 1’s general narrative – but, in essence, the DNA analyses of the child’s skeleton show that the group of immigrants from Siberia, who walked to Alaska over the Bering Bridge 25,000 years ago – NB: not before having sex with some very early Europeans – chose to split into two groups after about 5,000 years on the American continent.

“One group stayed in Alaska, the other travelled down into what is now the USA. At that time, the northern states were covered by a gigantic block of ice, stretching from the Atlantic to the Pacific Ocean. It covered the entire breadth of the country, apart from a small ice-free strip along the coast of the Pacific, and the southern group walked along this strip,” Eske Willerslev explains.

Once they had safely reached the ice-free part of North America – the prairies, among other places – they settled down, and their descendants are today’s Native Americans, both the northern and the southern lineage.

“But,” says Eske Willerslev, “about 13,000 years ago, when the climate gradually became warmer and there was an ice-free north-south corridor in the gigantic block of ice, a large group returned to Alaska. This was later to become the northern lineage of Native Americans. Why? We have no idea, but they did. And once they arrived in Alaska, they drove out the group to which Individual 1 belonged – the descendants of the half of the original immigrants who’d remained in Alaska. You could say that they ousted their own ancestors.”

And then it was time for sex again.

“That’s just the way it is. It’s what drives genetics. And the returning Native Americans, who were now alone in Alaska, didn’t waste their time when a group of Asians turned up to try their luck in Alaska about 11,000 years ago,” says Eske Willerslev.

“We know that these Asians were closely related to the Koryak, who live on the Russian Kamchatka peninsula to this day. And it was here, when they met these Asians, that the northern Native Americans picked up the unique Asian strain in their DNA.”

Individual 1’s DNA was studied with the permission of the Native American tribes in Alaska who currently live in the area where the findings were discovered. “And this is very important,” says Eske Willerslev. “Apart from the fact that this is just and fair, I feel it also adds a cultural dimension to the scientific work.”

Moreover, the studies show that the ancestors of today’s Greenlanders were the outcome of a meeting between stone-age Eskimos and northern Native Americans. “There’ve been theories claiming that the stone-age Eskimos mixed their genes with the southern Native Americans and this resulted in today’s Greenlanders. But these theories don’t hold, and we can thank Individual 1 for this knowledge,” explains the professor.

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