If the Population Y signal is concentrated in the areas that show the most continuity with the early settlement — the areas where the descendants of the earliest South Americans are most clearly represented in later populations — then the signal’s geographic distribution might reflect the distribution of the earliest settlers rather than the distribution of any later admixture event.

This interpretation would be consistent with the deep ancestral structure model: the earliest South Americans carried the Population Y-related ancestry because it was part of the deep structure of the founding population, and those populations that maintained the most continuity with the earliest settlers — those that were replaced or admixed the least over the subsequent millennia — retained the signal most clearly.

Testing this interpretation requires detailed mapping of both the Population Y signal and the evidence for population continuity across South America at a resolution that the current dataset does not fully provide.

The expanding collection of ancient South American genomes is gradually providing that resolution, but the coverage is still uneven, with some regions much better represented than others.