The key issue is that cranial morphology reflects both genetic influences and non-genetic influences, including developmental plasticity (the ability of the skull to change its shape in response to different developmental environments), dietary factors (certain diets produce different amounts of mechanical stress on the jaw and face, which can influence overall skull shape), and natural selection (different environments may favor different skull shapes, leading to convergent evolution of similar skull forms in unrelated populations).

The populations from sub-Saharan Africa, Australia, and Melanesia that the Lagoa Santa skulls resemble morphologically are populations that are understood, on genetic grounds, to have diverged from the ancestral human population that eventually gave rise to all modern humans and then to have experienced somewhat less subsequent genetic mixing with other populations than some other human groups.

This population history has left some populations with certain cranial characteristics that are, in a statistical sense, more similar to the characteristics of early modern humans than the characteristics of populations that have experienced more subsequent mixing and selection.

If the Lagoa Santa population shared this ancestry — if the founding Native American population contained lineages that were more closely related to these early-diverging populations, as the Population Y hypothesis suggests — then the morphological similarity between Lagoa Santa skulls and Australian and African skulls might reflect a genuine ancestral connection.