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

Natural variation in model organisms is a vital tool for answering fundamental biological questions. DNA sequence variation across Eurasia and North America has been extensively surveyed and has provided insights into the recent expansion of Arabidopsis thaliana throughout these continents. However, even with thousands of genotyped and sequenced strains, the early history of the species has remained elusive. We sequenced the genomes of a set of modern and herbarium samples from Africa and analyzed these together with previously sequenced Eurasian samples. Contrary to expectations, we find that all African individuals sampled appear native to this continent, including those from sub-Saharan Africa. We show, further, that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Moreover, our results reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral population began to split by ~120-90 kya, during the last interglacial and Abbassia pluvial, and that Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for humans and other species and implies that climatic events during interglacial and pluvial periods shaped the current distributions of a wide range of species. Note: samples from fresh material are paired end and samples from herbarium material are single-end reads.