If the founding population contained distinct genetic lineages that diverged before the dispersal into the Americas, then the differential distribution of those lineages across the Americas could produce patterns of allele sharing that might be interpreted as reflecting post-entry admixture events but actually reflect the structure of the founding population itself.

The more complex picture of founding population structure that is emerging from 2020s genomic work is broadly consistent with the deep ancestral structure explanation of Population Y, though it does not definitively resolve the question.

The 2020s work has also contributed important evidence on the population history of South America after the initial settlement.

The genetic record shows significant complexity in South American population history — patterns of local differentiation, evidence of contact and gene flow between different geographic groups, and in some areas evidence of more dramatic population replacement events in which earlier populations were replaced by later ones with substantially different ancestry.

This internal complexity of South American population history complicates the interpretation of any signal found in contemporary or ancient South American genomes, because it means that the ancestry of any given ancient or modern individual reflects not just the original settlement history but the subsequent population dynamics of the region.