Evolution of crop phenotypic spaces through domestication

Abstract

Summary We used domestication as an in vivo replicated experiment to investigate how divergent selection has shaped the evolution of multivariate phenotypic spaces. We measured 11 to 57 qualitative and quantitative traits in 13 species, either unique or shared between species, and established a framework for cross-species comparisons. Our results revealed significant convergence that translated into a cross-species domestication syndrome. Most species exhibited a reduction of the multivariate phenotypic space during domestication. We brought evidence that Near Infrared spectra measured on leaves reflect phenotypic evolution unrelated with domestication, enabling its use as a control for sampling effects across species. Building on this, we developed a multivariate Phenotypic Divergence Index (mPDI) to rank species by the extent of phenotypic divergence under domestication. We found a high disjunction of wild and domestic phenotypic spaces in all species. Neither the mPDI nor the relative size of wild versus domestic multivariate phenotypic spaces was influenced by the domestication timing or mating system. Lastly, we observed a progressive decoupling of trait correlations with increasing time since domestication. In addition to introducing a new index that can be applied for cross-species comparisons, our study uncovers recurring patterns shared among species, pointing to general principles underlying plant domestication.

Plant phenotyping relevance

多変量形質空間を比較する枠組みと新しいPhenotypic Divergence Index（mPDI）を開発しており、植物表現型の定量・比較手法が主要な貢献です。

Code and data availability

The paper's phenotypic data, NIR spectra, trait ontology, and R analysis scripts are explicitly deposited publicly: phenotype/NIRS data and MIAPPE trait ontology at doi 10.57745/QWEKVK, and R scripts on INRAE Forge. Both are paper-specific, public, and actionable.