One approach is to allow for the possibility that the rapid expansion was not quite as geographically uniform as the simplest model suggests — that there were populations in different geographic areas at slightly different times, creating opportunities for localized admixture events that would show up in some regions and not others.

The complexity of the early archaeological record in South America — with sites from different time periods and different geographic locations showing different material culture assemblages — is consistent with a more complex early settlement history than a single undifferentiated wave would suggest.

Another approach is to focus on the deep ancestral structure model, in which the Population Y signal is not the product of a post-entry admixture event at all but rather reflects diversity that was present in the founding population itself.

Under this model, the geographic concentration of the signal in South America reflects not where mixing occurred after entry into the Americas but rather which specific lineages within the founding population settled in which geographic areas and then expanded locally.