On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east
With the availability of more sequenced genomes, our understanding of the evolution and demographic history of the model plant Arabidopsis thaliana is rapidly expanding. Here we compile previously published data to investigate global patterns of genetic variation. While the Southeast African accessions were reported to be the most divergent among worldwide populations, we found accessions from Yunnan, China to be genetically close to the sub-Saharan accessions. Our further investigation of worldwide chloroplast genomes identified several deeply diverged haplogroups existing only in Eurasia, and the African populations have lower variation in many haplogroups they shared with the Eurasian populations. Bayesian inferences of chloroplast demography showed that representative haplogroups of Africa exhibited long-term stable population size, suggesting recent selective sweep or bottleneck is not able to explain the lower chloroplast variation in Africa. Taken together, these patterns cannot be easily explained by a single out-of-Africa event. Several Eurasian chloroplast haplogroups had rapid population growth since 10 kya, presumably reflecting the recent expansion of the weedy non-relicts across Eurasia. Our demographic analysis on a chromosomal region un-affected by relict introgression also suggested the European, Central Asian, and Chinese Yangtze populations diverged no earlier than 15 kya, in contrast to previous estimates of 45 kya inferred from whole genome that likely contains relict admixture. The most recent expansion is observed in the Yangtze population of China less than 2000 years ago. Similar to Iberia, the western end of non-relict expansion reported in our previous study, in this eastern end of Eurasia we find clear traces of gene flow between the Yangtze non-relicts and the Yunnan relicts. Genes under strong selection and previously suggested to contribute to adaptation in the Yangtze valley are enriched for traces of relict introgression, especially those related with biotic and immune responses. The results suggest the ability of non-relicts to obtain locally adaptive alleles through admixture with relicts is an important factor contributing to the rapid expansion across the environmental gradients spanning the eastern to the western coast of Eurasia.