Characterizing the extent and nature of reproductive isolation between wild and domesticated forms: a comparative approach in 14 plant systems

Characterizing the extent and nature of reproductive isolation between wild and domesticated forms: a comparative approach in 14 plant systems

Thesis defence
 12/03/2026
 14:00:00
 Arthur WOJCIK, GQE-Le Moulon
 IDEEV, salle Rosalind Franklin

Thesis directed by Maud Tenaillon (GQE-Le Moulon) and supervised by Catherine Dogimont (GAFL, Avignon).

Abstract

Domestication is a recent evolutionary process of divergent selection between wild forms, subject to natural selection in their original habitats, and domesticated forms, shaped by a combination of natural and human selection and adapted to anthropogenic environments. It provides a model for studying the adaptive mechanisms underlying the domestication syndrome, that is, the set of traits distinguishing domesticated forms from the wild forms from which they derive. One aspect that remains poorly studied is reproductive isolation between wild and domesticated forms, promoted by the counter-selection of hybrids in each environment.

This thesis aimed to use domestication in a comparative, multi-species framework to identify general principles of phenotypic evolution under domestication and to understand the emergence of reproductive isolation between forms. Fourteen diploid species were studied, covering a wide gradient of domestication timing and a diversity of life-history traits, using 20 wild populations and 20 traditional varieties per species.

In the first chapter, the domestication syndrome was characterized in 13 species using 11 to 57 phenotypic traits. Our results show interspecific convergence and, except in perennial species, a reduction of the multivariate phenotypic space during domestication. Leaf near-infrared spectra reflect phenotypic evolution independent of domestication, serving as a control for sampling effects. Based on this, we developed a multivariate phenotypic divergence index (mPDI) to rank species according to the extent of divergence between forms. A strong disjunction between wild and domesticated phenotypic spaces was observed, independent of the reproductive system or domestication date, with a progressive decoupling of trait correlations over time.

In the second chapter, RIDGE was used to estimate the proportion of the genome acting as a barrier to gene flow and to identify the underlying loci, based on sequencing of 40 individuals per species. The proportion of barrier loci ranged from 0 to 10% depending on the species and increased with time since domestication, indicating a progressive accumulation of reproductive isolation, with no effect of the reproductive system. One of the detected loci was previously known, allowing us to validate our approach, while others constitute new, interesting candidate genes. We also observed clustering of barrier loci in regions of low recombination, suggesting a potential role of chromosomal inversions in reproductive isolation.

In the third chapter, inter-form crosses were performed, with intra-form hybrids as controls, to identify mechanisms of reproductive isolation linked to hybrid depression. Survival and fertility were measured. While most inter-form hybrids were intermediate, we identified cases of transgression corresponding to hybrid vigor or depression. Notably common bean and einkorn wheat display abnormal development of storage tissues in inter-form F1 hybrids. The rate of transgression increases with time since domestication, consistent with Chapter 2.

By combining phenotypic divergence, genomic barriers, and performance of inter-form hybrids, this thesis demonstrates that domestication is a relevant model for studying the early stages of reproductive isolation induced by ecological divergence. Reproductive isolation between wild and domesticated forms increases over time and appears independent of the reproductive system.

Composition of the jury

  • Laurence Desprès (Professeure des universités, Université Grenoble Alpes, UMR LECA), reviewer
  • Joëlle Ronfort (Directrice de recherche, INRAE, UMR AGAP), reviewer
  • Jacqui Shykoff (Directrice de recherche, CNRS, UMR ESE), examiner
  • Marianne Elias (Directrice de recherche, CNRS, UMR ISYEB), examiner
  • Xavier Vekemans (Professeur des universités, Université de Lille, UMR EEP), examiner