"All the world's a stage we pass through." - R. Ayana

Wednesday, 15 June 2016

DNA Search for the First Americans Links Amazon Groups to Indigenous Australians

DNA Search for the First Americans Links Amazon Groups to Indigenous Australians
The new genetic analysis takes aim at the theory that just one founding group settled the Americas

Surui man

Brazil's Surui people, like the man pictured above, share ancestry with indigenous Australians, new evidence suggests. (PAULO WHITAKER/Reuters/Corbis)

More than 15,000 years ago, humans began crossing a land bridge called Beringia that connected their native home in Eurasia to modern-day Alaska. Who knows what the journey entailed or what motivated them to leave, but once they arrived, they spread southward across the Americas.

The prevailing theory is that the first Americans arrived in a single wave, and all Native American populations today descend from this one group of adventurous founders. But now there’s a kink in that theory. The latest genetic analyses back up skeletal studies suggesting that some groups in the Amazon share a common ancestor with indigenous Australians and New Guineans. The find hints at the possibility that not one but two groups migrated across these continents to give rise to the first Americans.

“Our results suggest this working model that we had is not correct. There’s another early population that founded modern Native American populations,” says study coauthor David Reich, a geneticist at Harvard University.  

The origin of the first Americans has been hotly debated for decades, and the questions of how many migratory groups crossed the land bridge, as well as how people dispersed after the crossing, continue to spark controversy. In 2008, a team studying DNA from 10,800-year-old poop concluded that a group of ancient humans in Oregon has ancestral ties to modern Native Americans. And in 2014, genetic analysis linked a 12,000-year-old skeleton found in an underwater cave in Mexico to modern Native Americans.

Genetic studies have since connected both these ancient and modern humans to ancestral populations in Eurasia, adding to the case that a single migratory surge produced the first human settlers in the Americas. Aleutian Islanders are a notable exception. They descend from a smaller second influx of Eurasians 6,000 years ago that bear a stronger resemblance to modern populations, and some Canadian tribes have been linked to a third wave.

Reich’s group had also previously found genetic evidence for a single founding migration. But while sifting through genomes from cultures in Central and South America, Pontus Skoglund, a researcher in Reich’s lab, noticed that the Suruí and Karitiana people of the Amazon had stronger ties to indigenous groups in Australasia—Australians, New Guineans and Andaman Islanders—than to Eurasians.

Other analyses haven’t looked at Amazonian populations in depth, and genetic samples are hard to come by. So the Harvard lab teamed up with researchers in Brazil to collect more samples from Amazonian groups to investigate the matter. Together they scrutinized the genomes of 30 Native American groups in Central and South America. Using four statistical strategies, they compared the genomes to each other and to those of 197 populations from around the world. The signal persisted. Three Amazonian groups—Suruí, Karitiana and Xavante—all had more in common with Australasians than any group in Siberia. 

Native American Ancestery Map

Researchers mapped similarities in genes, mutations and random pieces of DNA of Central and South American tribes with other groups. Warmer colors indicate the strongest affinities. (Pontus Skoglund, Harvard Medical School)

The DNA that links these groups had to come from somewhere. Because the groups have about as much in common with Australians as they do with New Guineans, the researchers think that they all share a common ancestor that lived tens of thousands of years ago in Asia but that doesn’t otherwise persist today. One branch of this family tree moved north to Siberia, while the other spread south to New Guinea and Australia. The northern branch likely migrated across the land bridge in a separate surge from the Eurasian founders. The researchers have dubbed this hypothetical second group “Population y” for ypykuéra, or “ancestor” in Tupi, a language spoken by the Suruí and Karitiana.

When exactly Population y arrived in the Americans remains unclear—before, after or simultaneously with the first wave of Eurasians are all possibilities. Reich and his colleagues suspect the line is fairly old, and at some point along the way, Population y probably mixed with the lineage of Eurasian settlers. Amazonian tribes remain isolated from many other South American groups, so that’s probably why the signal remains strong in their DNA.  

The results line up with studies of ancient skulls unearthed in Brazil and Colombia that bear stronger resemblance to those of Australasians than the skulls of other Native Americans. Based on the skeletal remains, some anthropologists had previously pointed to more than one founding group, but others had brushed off the similarities as a byproduct of these groups living and working in similar environments. Bones can only be measured and interpreted so many ways, while genes usually make a more concrete case.

“The problem so far was that there has never been strong genetic evidence to support this notion,” says Mark Hubbe, an anthropologist at Ohio State University who was not affiliated with the latest study.

But even genetic evidence is subject to skepticism and scrutiny. Cecil Lewis Jr., an anthropological geneticist at the University of Oklahoma, cautions that Amazonian groups are low on genetic diversity and are more susceptible to genetic drift. “This raises very serious questions about the role of chance … in creating this Australasian affinity,” he says.

Another group led by Eske Willerslev and Maanasa Raghavan at the University if Copenhagen reports in Science today that Native Americans descend from just one line that crossed the land bridge no earlier than 23,000 years ago. While they didn’t look at Amazonian groups in-depth, the team did find a weak link between Australasians and some South American populations, which they chalk up to gene flow from Eskimos. 

There’s just one problem: Evidence of Population y doesn’t persist in modern Eurasian groups, nor does it seem to show up in other Native Americans. If Aleutian Islanders or their ancestors had somehow mixed with an Australasian group up north or made their way south to the Amazon, they'd leave genetic clues along the way. “It’s not a clear alternative,” argues Reich. 

Both studies therefore suggest that the ancestry of the first Americans is a lot more complicated than scientists had envisioned. “There is a greater diversity of Native American founding populations than previously thought,” says Skoglund. “And these founding populations connect indigenous groups in far apart places of the world.”

DNA From 12,000-Year-Old Skeleton Helps Answer the Question: Who Were the First Americans?

In 2007, cave divers discovered remains that form the oldest, most complete and genetically intact human skeleton in the New World


Diver Susan Bird

Diver Susan Bird works at the bottom of Hoyo Negro, a large dome-shaped underwater cave on Mexico’s Yucatán Peninsula. She carefully brushes the human skull found at the site while her team members take detailed photographs. (Image courtesy of Paul Nicklen/National Geographic)

Some 12,000 years ago, a teenage girl took a walk in what’s now the Yucatan Peninsula and fell 190 feet into a deep pit, breaking her pelvis and likely killing her instantly. Over time, the pit—part of an elaborate limestone cave system—became a watery grave as the most recent ice age ended, glaciers melted and sea levels rose.

In 2007, cave divers happened upon her remarkably preserved remains, which form the oldest, most complete and genetically intact human skeleton in the New World. Her bones, according to new research published in Science, hold the key to a question that has long plagued scientists: Who were the first Americans?

Prevailing ideas point to all Native Americans descending from ancient Siberians who moved across the Beringia land bridge between Asia and North America between 26,000 and 18,000 years ago. As time wore on, the thinking goes, these people spread southward and gave rise to the Native American populations encountered by European settlers centuries ago.

skull of Naia

The skull of Naia on the floor of Hoyo Negro, as it appeared in December 2011, having rolled into a near-upright position. (Photo by Roberto Chavez Arce)

But therein lies a puzzle: "Modern Native Americans closely resemble people of China, Korea, and Japan… but the oldest American skeletons do not," says archaeologist and paleontologist James Chatters, lead author on the study and the owner of Applied Paleoscience, a research consulting service based in Bothell, Washington.

The small number of early American specimens discovered so far have smaller and shorter faces and longer and narrower skulls than later Native Americans, more closely resembling the modern people of Africa, Australia, and the South Pacific. "This has led to speculation that perhaps the first Americans and Native Americans came from different homelands," Chatters continues, "or migrated from Asia at different stages in their evolution."

The newly discovered skeleton—named Naia by the divers who discovered her, after the Greek for water—should help to settle this speculation. Though her skull is shaped like those of other early Americans, she shares a DNA sequence with some modern Native Americans. In other words, she’s likely a genetic great-aunt to indigenous people currently found in the Americas.


New genetic evidence supports the hypothesis that the first people in the Americas all came from northeast Asia by crossing a land bridge known as Beringia. When sea levels rose after the last ice age the land bridge disappeared. (Julie McMahon)

To reach these findings, scientists had to first conclusively determine Naia’s age.

It helped that the cave she was found in—a submerged chamber called “Hoyo Negro” (Spanish for “black hole”) of the Sac Atun cave system, accessible only by divers climbing down a 30-foot ladder in a nearby sinkhole, swimming along a 200-foot tunnel, then making a final 100-foot drop—was littered with fossils of saber-toothed tigers, giant ground sloths, cave bears and even an elephant-like creature called a gomphothere. These creatures last walked on Earth thousands of years ago during the last ice age.

But the researchers needed to get more specific than that. So they took a close look at regional sea-level data to get a minimum age at which the cave filled with seawater. Their analysis showed that the site, which is now 130 feet below sea-level, would have been become submerged between 9,700 and 10,200 years ago. Thus, Naia had to have fallen into the cave before then.

Unlike previous skeletons of early Americans, Naia’s included her teeth. Led by co-author Douglas Kennett, a professor of environmental archaeology at the Pennsylvania State University, researchers radiocarbon-dated her tooth enamel to 12,900 years ago.

But Naia’s exposure to seawater within the limestone caves, however, had mineralized her bones. "Unfortunately, we can't rule out that the tooth enamel is contaminated with secondary carbonates from the cave system,” Kennett explains.

Tooth enamel also contains trace amounts of uranium and thorium, radioactive minerals that decay at known rates. But results from those analyses, while they indicated that the remains were at least 12,000 years old, were also inconclusive.

However the scientists noticed something interesting about the bones themselves: they were spotted with rosette-looking mineral deposits. Before the cave was submerged, water dripping from the cave’s roof created a mineral mist that dried on the bones in floret patterns.

"Because the florets grew on the human bones, we knew that dating them would give us a minimum age for the bones," explains Victor Polyak, a research scientist at the University of New Mexico’s Department of Earth and Planetary Sciences. "And again, given that Hoyo Negro pit was dry when Naia made her way to the bottom, the florets had to have grown between the time of her death and 10,000 years ago when the bottom of the pit became submerged by brackish water because of rising sea level. Therefore, the oldest pieces of florets provided the oldest minimum age."

Analysis of these florets agreed with other readings—Naia fell into cave no earlier than 12,000 years ago.

upper right third molar of Naia

The upper right third molar of Naia, which was used for both radiocarbon dating and DNA extraction. The tooth is held by ancient genetics expert Brian Kemp of Washington State University, who led the genetic research on the skeleton. (Photo by James Chatters)

Naia’s teeth had another role to play: With her age established, scientists then sought to extract her DNA from her molars.  "We tried a DNA extraction on the outside chance some fragments might remain," says Chatters. "I was shocked when we actually got intact DNA."

The researchers focused on mitochondrial DNA (mtDNA), which is used by geneticists to examine how populations are related. mtDNA is more abundant than DNA found in a cell’s nucleus, so it’s easier to study. Researchers focused especially on haplotypes, which are sequences of genes that mutate more slowly than the rest of the mtDNA.

Their analysis showed that Naia’s mtDNA contains a haplotype that occurs in modern Native Americans and only is found in the Americas; scientists believe it evolved in Beringia.

“We were able to identify her genetic lineage with high certainty," says Ripan Malhi, a professor of anthropology at the University of Illinois. Malhi’s lab was one of three that analyzed Naia’s mtDNA; all three analyses yielded the same results. "This shows that living Native Americans and these ancient remains of the girl we analyzed all came from the same source population during the initial peopling of the Americas."

Naia proves that migrations from Beringia made it to southern Mexico. As for why Naia’s skull is so different from modern Native Americans, co- author Deborah Bolnick, assistant professor of anthropology at the University of Texas at Austin has an explanation: “The physical differences between Paleoamericans and Native Americans today are more likely due to changes that occurred in Beringia and the Americas over the last 9,000 years.” Bolnick’s lab was one of the three to confirm the mtDNA findings.

Studies of Naia—namely the fact that she’s a genetic forerunner to modern Native Americans—ironically raises some interesting questions about whether scientists will be able to get access and extract the remains of early Americans yet to be uncovered.

For example, Chatters—who discovered the scientific importance of the ~9000-year-old Kennewick Man in 1996—could not further analyze those remains due to local tribes claiming the body as an ancestor under the Native American Graves Protection and Repatriation Act (NAGPRA), passed in 1990. However, in 2004, the 9th Circuit Court of Appeals upheld a previous decision that ruled that the remains could not be defined as “Native American” under NAGPRA law, and studies of the body resumed.

Naia’s discovery may open the door to more legal struggles in the future. But Chatters dismisses this idea, noting that in the current study, “We’re not looking at an ancestor-descendent relationship here necessarily. We’re simply looking at a common heritage.”

For more information about Native Americans see http://nexusilluminati.blogspot.com/search/label/native%20americans
For more information about human origins see http://nexusilluminati.blogspot.com/search/label/human%20origins  
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