If the Checua population became isolated on the plateau — separated from other South American populations by the geography of the Andes and the ecological barriers of the surrounding lowlands — they could have evolved a distinct genetic character over the thousands of years of their occupation.

Geographic isolation is one of the most powerful drivers of genetic differentiation, and the high-altitude environment of the Andes can create effective barriers even in the absence of long distances.

The Checua lineage’s deeply divergent position in the population tree is consistent with a history of geographic isolation on the plateau.

How long that isolation lasted before the 6,000-year-before-present individuals whose genomes were sequenced, and how the Checua population initially became established on the plateau, are questions that would require older ancient DNA from the same region to answer.

The Archaeology Behind The Genetics: More Than One Site