Summary Positive selection is the driving force underpinning local adaptation, and leaves footprints of selective sweeps at the underlying major genes. Quantifying the timing of selection and revealing the genetic bases of adaptation in plants species occurring in steep and varying environmental gradients is crucial to predict a species’ ability colonize new niches. We use whole genome sequence data from six populations across three different habitats of the wild tomato species Solanum chilense to infer the past demographic history and search for genes under strong positive selection. We then correlate current and past climatic projections with the demographic history, allele frequencies, the age of selection events, and distribution shifts. We find evidence for several selective sweeps targeting regulatory networks involved in root hair development in low altitude, and response to photoperiod and vernalization in high altitude populations. These sweeps occur in a concerted fashion in a given regulatory gene network at particular periods of substantial climatic change. We decipher the genetic bases and the timing of local adaptation during plant colonization of semi-arid habitats using a unique combination of genome scans for selection and modelling of past climatic data.

Local adaptation to novel habitats and climatic changes in a wild tomato species via selective sweeps