Archaic lineages broaden our view on the history of Arabidopsis thaliana

Abstract

Contents Summary 1194 I. Introduction 1194 II. Origin of the A. thaliana species 1194 III. The classic model of the history of A. thaliana 1195 IV. New genomic data from outside Eurasia challenge our view of A. thaliana history 1195 V. Conclusions 1197 Acknowledgements 1197 References 1197 SUMMARY: Natural variation in Arabidopsis thaliana has contributed to discoveries in diverse areas of plant biology. While A. thaliana has typically been considered a weed associated primarily with human-mediated environments, including agricultural and urban sites and railways, it has recently been shown that it is also native in remote natural areas, including high altitude sites in Eurasia and Africa, from the Atlas mountains in Morocco to the afro-alpine regions in Eastern and South Africa to Yunnan in China, the Himalayas and the Tibetan Plateau. This finding suggests that while A. thaliana has been extensively studied in Europe and Western Asia there are still many open questions about its population history, genotype-phenotype relationships and mechanisms of adaptation.

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

“…A phylogenetic tree using Arabidopsis lyrata as the outgroup confirmed the previous observation that the Tanzanian (TZ) and South African (SA) accessions (hereafter the ‘TZSA’ clade) were most divergent to all others (Figs a, S1). Interestingly, two accessions from Yunnan (YU), China were also genetically close to the TZSA clade, inconsistent with the single out‐of‐Africa event suggested previously (Durvasula et al ., ; Fulgione & Hancock, ). These two accessions were also highly divergent from most accessions except TZSA (Fig.…”

“…Our results from the nuclear genome suggest a more complex demography than a single out‐of‐Africa event (Durvasula et al ., ; Fulgione & Hancock, ). To better understand this situation, we investigated the chloroplast genomes which were dated with 11 outgroup species (Hohmann et al ., ; Novikova et al ., ).…”

“…227 ka (95% highest posterior density 121–340 ka; Figs S9, S10). This considerably predates the inferred divergence time between African and Eurasian nuclear genomes (90–120 ka) (Durvasula et al ., ; Fulgione & Hancock, ).…”

“…Assuming the current population size of Morocco is N 0 , the ancestral population size was set to 1.6 N 0 . Based on previous studies, the Moroccan and Levantine population separated at 90 ka with population size N 0 and 0.6 N 0 respectively (Durvasula et al ., ; Fulgione & Hancock, ). As suggested by our chloroplast demography (below), the population size of Morocco remained stable after the split.…”

“…Migration of the Moroccan population northwards to Iberia was illustrated as well as the Levantine migration wave westward into Europe and eastward to Central Asia at c . 45 ka (Fulgione & Hancock, ). Conversely, it remains unclear how A. thaliana first arrived Africa given all other Arabidopsis species were found in the temperate Northern Hemisphere (Novikova et al ., ), and the pattern in which Africa contains most variation can be equally likely explained by a non‐African origin of A. thaliana followed by nonrelict expansion wiping out most Eurasian variation (Lee et al ., ).…”