On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East

With more sequenced genomes, our understanding of the demographic history of Arabidopsis thaliana is rapidly expanding. However, no-one has yet compiled previous data to investigate patterns of genetic variation across Eurasia. While sub-Saharan accessions have been reported to be the most divergent group, in the nuclear genome we found accessions from Yunnan, China to be genetically closest to the sub-Saharan group. In chloroplast, several deeply diverged haplogroups exist only in Eurasia, and African populations have lower variation in many haplogroups that they share with the Eurasian populations. These patterns cannot be easily explained by a single out-of-Africa event suggested previously. For more recent demographic history, we dated the nonrelict expansion to 10 ka. In the Chinese Yangtze nonrelicts, we found clear traces of gene flow with local relicts, and genes under strong selection were enriched for traces of relict introgression, especially those related to biotic and immune responses. The results suggest the ability of nonrelicts to obtain locally adaptive alleles through admixture with relicts is important for the expansion across environmental gradients of Eurasia. Our re-analyses provide another model for the early history as well as elucidating factors contributing to the recent demographic turnover event of this species.