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.”

Meanwhile, dive into Hoyo Negro with the project’s cave explorers, courtesy of Mexican government’s National Institute of Anthropology and History and supported by the National Geographic Society:

Get the latest Science stories in your inbox.