Ancient DNA From Teenage Girl Shows Link Between Ancient and Modern Americans

Deep in the flooded underground caves of Hoyo Negro in Mexico’s Yucatan peninsula a team of archaeologists recently unearthed a treasure trove of prehistoric remains that included the oldest human skeleton found to date in the Americas.  Falling to her death, the nearly intact skeleton is that of a teenage girl affectionately nicknamed Naia.

Divers make their way toward Hoyo Negro, an underwater cave on Mexico’s Yucatán Peninsula where the remains of “Naia,” a 12,000- to 13,000-year-old teenage girl, were found. Photo by Paul Nicklen/National Geographic
Divers make their way toward Hoyo Negro, an underwater cave on Mexico’s Yucatán Peninsula where the remains of “Naia,” a 12,000- to 13,000-year-old teenage girl, were found (Photo by Paul Nicklen/National Geographic)

She was found among dozens of fossilized saber tooth tiger and giant sloth remains from the late Pleistocene (13,000 to 10,000 years ago).  From DNA in her ancient teeth and bones geneticists discovered her mitochondrial (mtDNA) haplogroup , or branch of the human family tree.  She was haplogroup D1, one of the ancient founding Native American lineages. Could Naia be your long lost relative?

A diver carefully observes “Naia,” a 12,000- to 13,000-year-old teenage girl whose remains were found in the Hoyo Negro cave on Mexico’s Yucatán Peninsula (Photo by Paul Nicklen/National Geographic)

In a paper published Thursday in the acclaimed journal Science, scientists detail the context of the unusual Hoyo Negro site and its voluminous remains and explain how the shape of the girl’s skull and teeth, together with her mtDNA haplogroup, suggest evidence of a link between ancient Americans and modern indigenous people. In other words, modern Native Americans have a lot in common with America’s earliest settlers (Paleoamericans). And although she was found in a region of Mexico later occupied by Mayan populations who are approximately 90% haplogroup A2, the D1 lineage still exists among roughly 2% of Mayans today and among 15% of Otomi populations from central Mexico. For comparison, haplogroup D1 is found in only 0.2% of Genographic Project participants.

Map of Haplogroup D1 Frequencies
Map of Haplogroup D1 Frequencies (

To better understand similarities and differences among Native American populations, Genographic Project scientists are collaborating with indigenous groups from the United States, Canada, and Mexico, to learn about their genealogical stories and map their genetic lineages.  By working specifically with indigenous populations, scientists can infer where and often when mutations arose in distinct DNA lineages. They then use these mutational patterns in the DNA to estimate relatedness among populations and reconstruct the human family tree.

Native American groups carry in their DNA the key to understanding how people first came to populate and later disperse across North and South America. And as more Native American populations join the project, the more we will learn about human prehistory. Do you suspect you carry Native American DNA? Visit our website, learn more about The Genographic Project and join our citizen science effort to discover how unique each population is, yet how closely related we all really are.

Changing Planet

Dr. Miguel Vilar is the Science Manager for National Geographic's Genographic Project. Miguel is also a molecular anthropologist and a science writer. His fieldwork has taken him to remote places throughout the South Pacific, East Africa, Mesoamerica, and the Caribbean. In the laboratory he researches the modern genetic diversity of human populations from Melanesia, Micronesia, North and Central America, and the Caribbean. Miguel has published in several anthropology and genetics journals, as well as popular science magazines.