Ancient DNA Sequenced from "Sky Cave" Burials in Nepal

The cold and dry conditions of the Himalayan sites have resulted in extraordinary ancient DNA preservation. In some cases, more than 50 percent of the DNA recovered from prehistoric skeletal remains is endogenous, or of local origin. Image credit: Christina Warinner

In the Upper Mustang region of Nepal, thousands of rock-cut tombs are scattered across towering Himalayan cliff faces. It’s only in the last few decades that archaeologists—led by expert climbers—have been able to explore these remote “sky caves.” They’ve discovered a wealth of artifacts, including intact silk fabric, bronze jewelry, and bamboo baskets still full of rice among skeletons of people laid to rest hundreds of years ago.

Scientists recently sequenced the whole genomes of eight individuals found in these ancient chambers, revealing the secrets of the first inhabitants of the Himalayas. It turns out their descendants still live in the region. The researchers published their findings yesterday in the Proceedings of the National Academy of Sciences.

“The big question we had was, ‘Who were these people?’ We didn't really have any idea where they came from,” Christina Warinner, a senior author of the new study and an anthropologist at the University of Oklahoma, told mental­_floss.

Thousands of human-made caves dot the Himalayan landscape. Since prehistory, these caves have been used as tombs, dwellings, and apartments. Image credit: Christina Warinner

Though strategically located between the Indian subcontinent and the Tibetan plateau, the Himalayan high mountain valleys were among the last places on Earth to be colonized by humans—and it’s easy to see why. Little rain, meager vegetation, and low levels of oxygen make it difficult to live there. The first known settlers only arrived a little more than 3000 years ago. But where those first intrepid people arrived from has been a matter of debate.

Some archaeological similarities had suggested that the first Himalayan settlers came from the south. But by looking at the ancient DNA, Warinner and her colleagues found that the first inhabitants of the Himalayas came down from the north, from East Asian populations of the Tibetan plateau. Their genetic profile most closely resembles modern-day Sherpa and Tibetan populations.

This 3000-year-old tooth from the site of Chokhopani has yielded the highest coverage (7x) ancient East Asian human genome to date. Image credit: Andrew Ozga and Christina Warinner

It's logical, Warinner said, that people who already had genetic adaptations to make them suited to life at high altitudes would have been able to colonize this region. What was more surprising to her is that over thousands of years, the population seems to have remained quite genetically homogenous, despite cultural upheavals and contact with outside civilizations.

Warinner and her colleagues took DNA samples from remains from three distinct cultural phases of the Annapurna Conservation Area: Chokhopani (3150–2400 years ago), Mebrak (2400–1850 years ago), and Samdzong (1750–1250 years ago).

Each one of these cultures is associated with significant changes in artifacts as well as changes in mortuary practices, which archaeologists typically see as a reflection of religious beliefs.

The earliest Chokhopani tombs date back to about 3150 years ago and contain artifacts like jewelry made from faience, bronze, and copper, as well as ceramic, wooden, and stone objects among the dead, who were buried in groups. The Mebrak tombs of the next cultural phase often contained a more elaborate set of grave goods, including the mummified heads of sheep and goats, and disarticulated horse remains. The dead were also placed on decorated wooden platforms.

A gruesome new death ritual—defleshing—was introduced during the Samdzong culture (1750–1250 years ago), according to recent excavations led by Mark Aldenderfer, of the University of California, Merced (who is also an author on the new study). Cut marks on the bones suggest that the bodies were stripped of their flesh before being laid out on wooden platforms—a practice that may have been adopted from Zoroastrians of West Asia and that may have in turn influenced the Tibetan “sky burials” of later periods. Perhaps this influence was made possible by the Samdzongs’ connection to the Silk Road, which the archaeologists recently discovered thanks to well-preserved cloth artifacts. 

“If it was the same population through all these cultural phases, that's pretty amazing, because other places around the world that experience that much cultural change are typically associated with a turnover in population or a conquest event,” Warinner said.

Local villagers assist with the identification of 1500-year-old artifacts recovered from prehistoric cliff tombs at the site of Samdzong, Nepal. Image credit: Christina Warinner

The study also marks the first five whole genomes to be published for ancient people from East Asia (excluding Siberia). “There’s been very little work done on whole ancient genomes anywhere outside of Europe,” Warinner said. That's because the first labs to do this type of analysis were in Europe, where there also is a wealth of well-preserved ancient European human remains.

Warinner is hopeful that with improvements in the study of ancient DNA, scientists can start to study samples from overlooked places, like archaeological sites closer to the equator, where preservation of human remains isn’t as stellar.

“The field of ancient DNA has matured dramatically in the last five years,” Warinner said. “We’ve entered the golden age of paleogenomics, where we can actually do full genomic studies of ancient people.”