A signal that looks like a contribution from Population Y might, in some cases, reflect later population mixing events within South America that brought together individuals with different proportions of the original founding lineages.

South American Population Turnover and What It Reveals

One of the most striking findings of ancient South American DNA research is evidence for significant population turnover in various regions — episodes in which the people living in a particular area in one period are genetically quite different from the people living in the same area in a later period.

The evidence for such turnover comes from comparing the ancient genomes of individuals from the same geographic area but different time periods.

In some cases, the comparison shows clear continuity — the later population descends primarily from the earlier population, with gradual change over time.