Their genomes indicate that they were part of the early South American radiation — the broader founding of South American populations from the migration out of Beringia and through North America.

They share this deep ancestry with all other Native Americans.

The distinctness is in their specific branch of that early radiation, not in being outside it entirely.

The study does not identify the mechanism by which the Checua genetic signature was replaced.

The paper documents the fact of replacement.

It does not establish whether replacement occurred through violent conflict, disease, absorption through intermarriage, outmigration of the Checua population, or some combination.

Saying that there was a “complete exchange of the population” describes a genetic outcome, not a historical cause.