Researchers analyzing ancient DNA extracted from the skeletons and mummies of nearly 100 people who lived in South America 500 to 8,600 years ago reveal that European colonization led to the extinction of many indigenous genetic lineages. The findings were published in Science Advances last week.

Because of their geographic isolation, the Americas weren’t settled until the end of the Pleistocene some 10,000 to 20,000 years ago. Archaeological evidence indicates the presence of humans as far south as Monte Verde in Chile by 14,600 years ago. That was shortly after the retreat of ice sheets that blocked access from Beringia – the region that includes the ancient land bridge that connected Asia to Alaska. However, we still don’t know exactly when, where, and how early people entered the Americas. 

To investigate, University of Adelaide’s Bastien Llamas and colleagues sequenced 92 whole mitochondrial genomes of pre-Columbian South American individuals: 70 archaeological samples from Peru, nine from Bolivia, six from northern Chile, five from Mexico, and two from the Argentinian Pampas. Mitochondrial DNA is maternally inherited, and by combining this genetic analysis with demographic reconstructions and population modeling, the team managed to narrow the window of arrival into the Americas.

^{A burial associated with the Lima culture. The Huaca Pucllana archaeological site in Lima, Peru, housed three successive pre-Inca cultures: the Lima (500-700 AD), the Wari (800-1000 AD), and the Ychsma (1000-1450 AD). DNA from individuals buried at Huaca Pucllana were used in this study. Proyecto de Investigación, Conservación y Puesta en Valor Huaca Pucllana}

Their findings reveal that a small population – one that was previously isolated in eastern Beringia – entered the Americas around 16,000 years ago using a route along the Pacific. This small group was isolated on the Beringian land bridge – and separated from eastern Siberian populations – for 2,400 to 9,000 years. But using this coastal route, they were able to skirt around the ice sheets that blocked movement inland. Then they spread southward rapidly, with some populations reaching southern Chile just 1,000 years or so later. 

Surprisingly, all of the mitochondrial lineages detected were absent from modern datasets – which suggests a high extinction rate of ancient lineages. "None of the genetic lineages we found in almost 100 ancient humans were present, or showed evidence of descendants, in today's indigenous populations," Llamas says in a statement. 

European contact, among other factors, may have played a role in reducing the overall genetic diversity of Native Americans to the low levels observed today. "The only scenario that fit our observations was that shortly after the initial colonization, populations were established that subsequently stayed geographically isolated from one another, and that a major portion of these populations later became extinct following European contact," Llamas adds. "This closely matches the historical reports of a major demographic collapse immediately after the Spaniards arrived in the late 1400s."