African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Significance The principal plant model species, Arabidopsis thaliana , is central to our understanding of how molecular variants lead to phenotypic change. In this genome-sequencing effort focused on accessions from Africa, we show that African populations represent the most ancient lineages and provide new clues about the origin of selfing and the species itself. Population history in Africa contrasts sharply with the pattern in Eurasia, where the vast majority of samples result from the recent expansion of a single clade. This previously unexplored reservoir of variation is remarkable given the large number of genomic studies conducted previously in this well-studied species and implies that assaying variation in Africa may often be necessary for understanding population history in diverse species.