The late Holocene — the last several thousand years — saw significant population movements across the Americas, driven by climate change, agricultural expansion, political and military competition, and other factors.

Some of these movements resulted in substantial genetic exchange between previously distinct populations; others resulted in the partial or complete replacement of one population by another.

Understanding the Population Y signal in this context requires distinguishing between ancestry components that reflect the original settlement history of the Americas — including whatever deep ancestral structure the founding population may have contained — and ancestry components that reflect subsequent population dynamics.

This is not always easy to do with the available data.