Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Domesticated crops have been disseminated by humans over vast geographic areas. After 1492, the common bean (Phaseolus vulgaris L.) was introduced in Europe. By combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we found that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro’s expedition to northern Peru in 1529. We found that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlighted the role of genes relevant to flowering and environmental adaptation, suggesting that introgression was crucial for the dissemination of this tropical crop to the temperate regions of Europe.