Arabidopsis thaliana, one of the most important model plants, has played an essential role in every biological field including evolutionary biology. Recent population genomic studies have gradually clarified the origin and evolution of this species. Nevertheless, incongruent patterns among gene trees based on cytogenetic data have highlighted the importance of understanding the life history evolution and landscape biogeography of extant A. thaliana populations. Here, we focus on the maternally inherited chloroplast genome in A. thaliana and carry out phylogeographic analyses and coalescent time estimations. The maternal lineage of A. thaliana originated in the European to West and Central Asian regions in the Early Pleistocene. Relicts, the ancient lineages suggested by population genomic data, are not ancestral maternal lineages, but are derived from the European population. Part of the European population then dispersed eastward and spread to the Indian region, and finally extended to the Yangtze River region. The branching patterns and evolutionary time scales of the maternal genealogy are significantly different from those estimated from analyses of autosomal genes, and these cannot be explained by incomplete lineage sorting of the ancestral polymorphisms during the coalescent process due to large differences in the evolutionary time scale involved.
Keywords: Arabidopsis thaliana; Bayesian timetree; ancestral state; chloroplast genome; evolutionary relationship.