The researchers modeled the Checua population as a deeply divergent branch of the initial South American radiation — a lineage that split early from the ancestors of other South American populations and then apparently went its own way, developing a distinct genetic character on the Colombian Altiplano.

This is what the paper meant when it called the Checua individuals “a previously unknown basal lineage.” Basal, in population genetics, means closer to the root of the population tree — an early branch that diverged before later differentiation produced the populations that are more familiar from other ancient South American genomes.

Basal is not a synonym for primitive or simpler; it is a structural description of where a group sits in the branching diagram of population relationships.

The Checua lineage was basal to the rest of the South American variation in the study’s comparison set.