Ancient teen’s DNA may solve human migration mystery

"The Hoyo Negro girl was related to living Native Americans and has ancestry from the same Beringian population," says Deborah Bolnick. "This study therefore provides no support for the hypothesis that Paleoamericans migrated from Southeast Asia, Australia, or Europe." (Credit: "cave diver" via Shutterstock)

The ancient remains of a teenage girl found in an underwater Mexican cave establish a definitive link between the earliest Americans and modern Native Americans, report scientists.

The most ancient human remains in the Americas have baffled scientists because their skulls are narrower and have other measurably different features from those of Native Americans. Some researchers have hypothesized that these individuals came to the Americas from as far away as Australia, Southeast Asia, or Europe.

Cave diver Alexandro Alvarez inspects the newly-discovered skull of Naia, the 12,000-13,000 year-old human skeleton discovered in a submerged cave on the Yucatan peninsula of Mexico. (Credit: Daniel Riordan Araujo/Penn State)

“Individuals from 9,000 or more years ago have morphological attributes—physical form and structure—distinctive from later Native American peoples,” says Douglas Kennett, professor of environmental archaeology at Penn State.

“What we have here is the unique combination of an adolescent Paleoamerican skeleton with a Native American DNA haplotype.”

Science divers found the skeleton surrounded by a variety of extinct animals more than 130 feet below sea level in Hoyo Negro, a deep pit within the Sac Actun cave system in the Yucatán.

When did Naia enter the cave?

Kennett and Brendan J. Culleton, a postdoctoral fellow in anthropology at Penn State, were originally asked to directly date the skeleton.

Traditional and well-accepted direct-dating methods failed because the bones were mineralized from long emersion in warm salty water within this limestone cave system.


Instead, they worked closely with colleagues to build a geochronological framework for the ancient teen, dubbed “Naia” by scientists, using a unique combination of techniques to constrain the age of the skeleton to the end of the ice age.

To build the case for a late Pleistocene age they collaborated with researchers at the University of New Mexico and used global sea level rise data to determine when the cave system, which was dry at the time Naia and the extinct animals entered, filled with water.

The site where Naia lies is now 130 feet below sea level and sea level rise would have raised the groundwater level in the cave system and submerged everything between 9,700 and 10,200 years ago. So initial estimates of the latest that animals and humans could have walked into the cave system was 9,700 years ago.

Dripping in the cave

At the same time, the researchers experimented with uranium thorium dating the skeleton directly. The University of New Mexico team tried to directly date Naia’s teeth using this method, but that did not work well either.

The bones were found deep below today’s ground surface in a collapsed chamber connected to the surface via a web of now flooded tunnels that Naia once walked along to fall to her death. Because the caves are limestone, mineral deposits continued to form while the cave was largely dry.

Working with Patricia Beddows of Northwestern University, James Chatters, owner of Applied Paleoscience, noticed accumulations of calcium carbonate—tiny rosettes of calcite deposited by water dripping off the cave roof—which could be accurately dated using the uranium thorium method.

Because these drip water deposits formed on top of Naia’s bones, their date must occur after she fell in the cave. The oldest one dated so far is 12,000 years old.

Testing her tooth

Deborah Bolnick, assistant professor of anthropology at the University of Texas at Austin and her colleagues Brian Kemp of Washington State University and Ripan Malhi of the University of Illinois at Urbana-Champaign analyzed the DNA from the tooth of the adolescent girl who fell into a sinkhole in Mexico’s Yucatán Peninsula more than 12,000 years ago.

Naia’s tooth enamel was also radiocarbon dated to 12,900 years ago by Kennett’s lab.

“Unfortunately, we can’t rule out that the tooth enamel is contaminated with secondary carbonates from the cave system, but we removed potential contaminates using standard techniques and Tom Stafford of Stafford Research Laboratories, produced a comparable age,” says Kennett.

“We consider this a maximum age and when combined with the uranium thorium dates from the adhering speleothems, we argue that the skeleton dates between 12,000 and 13,000 years ago. Well placed as a Paleoamerican.”

Native American origins

Morphologically, Naia does not look like a contemporary Native American, but mitochondrial DNA testing—maternally inherited DNA—carried out by Brian Kemp at Washington State University and his collaborators—shows that she has a D1 haplotype.

This is consistent with the hypothesis that her ancestors’ origins were in Beringia, a now partially submerged landmass including parts of Siberia, Alaska, and the Yukon.

Early humans moved into this area from elsewhere in Asia and remained there for quite some time. During that time they developed a unique haplotype that persists today in Native Americans. Genetically, Paleoamericans have similar attributes as modern Native Americans even if their morphology appears different.

“The Hoyo Negro girl was related to living Native Americans and has ancestry from the same Beringian population,” Bolnick says. “This study therefore provides no support for the hypothesis that Paleoamericans migrated from Southeast Asia, Australia, or Europe.

“Instead, it shows that Paleoamericans could have come from Beringia, like contemporary Native Americans, even though they exhibit some distinctive skull and facial features.

“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.”

Mexico’s National Institute of Anthropology and History led the study, which Chatters coordinated. The findings appear in Science.

The National Geographic Society, Archaeological Institute of America, Waitt Institute, Instituto Nacional de Antropología e Historia, and the National Science Foundation supported this work. Penn State, the University of New Mexico, the University of Texas at Austin, and DirectAMS also supported the project.

The Hoyo Negro expedition will appear in National Geographic magazine and on a National Geographic Television program airing on the PBS series “Nova” in 2015.

Source: UT Austin, Penn State