First of all, your premise is wrong. Human history is a long sequence of populations interbreeding with each other, forming new populations, and on and on. For example, people in modern India are a mix of three major population groups who met about four thousand years ago - before then, there likely wouldn’t have been that many people who look like they do now. Incidentally, this fact makes notions of racial purity even more ridiculous than they already are. (If you’re interested in this kind of thing, I recommend David Reich’s book - his lab at Harvard has been at the forefront of this research).

And secondly, even outside of genetics, there is a lot of literature about how the different diets of pre-modern humans led to them having different facial structures (the introduction of sugar and soft foods have led to degeneration in our jaw and facial shape today). These reconstructions can bring those epigenetic changes to life as well.