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

Abstract

Summary 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.

Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana

“…S15B). The wide Eurasian distribution of D-SY haplotypes suggests that their expanded germination niche may have facilitated postglacial expansion and spread of "nonrelict" genotypes out of central Asia into Europe and China (47,82). The recent expansion of the D-RY clade is consistent with invasion of new ruderal habitats made available by the spread of agriculture through Europe (43, 82,83).…”

“…Extensive sequence data are available for this annual species, facilitating genome-wide association (GWA) (42,43). A. thaliana inhabits a wide native climate range across Eurasia and Africa, and has shifted across the landscape with Pleistocene climate cycles, repeatedly contracting and expanding out of glacial refugia (44)(45)(46)(47). Across this range, the species exhibits substantial lifehistory variation (11,13,48).…”

Network-based hierarchical population structure analysis for large genomic data sets

“…split partitioning these three groups from the European group may reflect strong genetic similarity within the European branch, rather than genetic similarity between these three groups. Therefore, further study of the population in north Sweden, and increased geographic sampling in Africa and Asia, could help explain these patterns (e.g., Hsu et al 2019). The continuous differentiation, across hierarchical scales, in the European branch accords with past studies of this geographic region (Sharbel et al 2000;Nordborg et al 2005;François et al 2008; The 1001 Genomes Consortium 2016).…”

Transcriptional natural variation at FLM induces synergistic pleiotropy in Arabidopsis thaliana

“…The scenario of Arabidopsis migrations is regularly revisited as more data are available for population genetic studies Hsu et al, 2019). In many instances, Iberian Peninsula is consistently mentioned as a location where highly diverged Arabidopsis lines (called relicts) are found in preserved and ancestral habitats (Sharbel et al, 2000;Brennan et al, 2014;Alonso-Blanco et al, 2016).…”