If the ancestral Native American population contained some individuals or lineages with more “Australasian-like” ancestry because they had more ancestry from the ancient southern-route populations of Asia, and if those individuals contributed differentially to some South American populations compared to North American populations, then the excess allele sharing between South American populations and Australasians could reflect this ancient, pre-American internal diversity.

This model is sometimes called the “Australasian ghost population” model or the “deep ancestral structure” model, and it is one of the most seriously discussed explanations in the current scientific literature.

It does not require Australasians to have reached South America.

It requires only that the population from which all Native Americans descend was itself structured in specific ways that left different genetic traces in different descendant groups.

The challenge with this model — and with all of the models proposed to explain Population Y — is that it requires ancient genetic data from the right times and places to test it directly.