The skull shapes had changed, within a single lineage, over time.

Why skull shapes changed is a more complex question than whether they changed, and it is one that researchers are still working to answer.

Diet is one factor — the shift from the relatively tough, unprocessed foods of Ice Age hunter-gatherers to the agricultural diets that became common in many parts of the Americas over the past several thousand years would have changed the mechanical demands on the jaw and the skull, leading to developmental changes in skull shape.

Natural selection acting on traits related to climate, UV exposure, or other environmental factors could also have shaped skull morphology over thousands of years.