The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes

Abstract

AbstractThe remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main genepools corresponding to three different ecogeographic areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios and the northern Peru/Ecuador population has been described as a new species calledP. debouckii,rekindling the debate about the origin ofP. vulgaris. Here we shed light on the origin ofP. vulgarisby analysing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms. We assembled 37 chloroplast genomesde novoand used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador genepools occurred ∼0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recentP. deboukiihypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account recombination events when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.