How ancient civilizations socially distanced neighborhoods to evade diseases

Whether the people of Nebelivka knew it or not, this lower-density, clustered layout could have helped prevent any disease outbreaks from consuming the entire settlement.

In my research focused on early farmers of Europe, I have often wondered about a curious pattern through time: Farmers lived in large dense villages, then dispersed for centuries, then later formed cities again, only to abandon those as well. Why?