Ancient DNA provides a snapshot of the domestication history of Sorghum bicolor within a temporal series from a single archaeological site. We find a combination of diverse selection pressures and local adaptation result in decreasing diversity and increasing mutation load.

The evolution of domesticated cereals was a protracted, complex process with shifting selection pressures and repeated introgressions as plants and society co-evolved. We show a temporal series of archaeogenomes from a single archaeological site that reveals the evolutionary trajectory of sorghum under domestication. Contrary to expectations we find no evidence for a domestication bottleneck but a steady decline in diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially on architectural and nutritional domestication traits, and local adaptation including in phytochrome A metabolism. Durra type sorghum adaptively introgressed into the local population assuming environmental and donating domestication traits. These results reveal a model of domestication in which genomic adaptation and deterioration is a uniformitarian process unrestricted to the distant past.