Ancient genomes reveal early farmers selected common beans while preserving diversity

All crops are the product of a domestication process started less than 13,000 years ago from one or more wild populations. Farmers selected desirable phenotypic traits, such as improved energy accumulation, palatability of seeds or reduced natural shattering, while leading domesticated populations through several demographicbottlenecks. As a consequence, erosion of wild genetic variation is typical of modern cultivars making them highly susceptible to pathogens, pests and environmental change. The loss of genetic diversity hampers further crop improvement programs to increase food production in a changing world, posing serious threats to food security. Analyzing the temporal dynamic of genetic variation and selection during domestication of common bean (Phaseolus vulgaris) in the Southern Andes in ancient and modern seeds, here we show that most of the genetic changes probably occurred before 2,500 years ago, but genetic erosion is, on the contrary, a more recent process, not detectable in 600 years old seeds. Considering that most desirable phenotypic traits are likely controlled by multiple polymorphic genes, a likely explanation of this decoupling is that early farmers used many phenotypically similar but genomically diverse individuals as breeders. Selection strategies in the last centuries were probably less sustainable and produced further improvements focusing on few seeds with extreme values of the traits of interest, at the cost of marked genetic erosion.