J Syst Evol

• Research Articles •    

Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

Yves Bawin1,2,3,4*, Tom Ruttink1, Ariane Staelens1, Annelies Haegeman1, Piet Stoffelen3, Jean-Claude Ithe Mwanga Mwanga5, Isabel Roldán-Ruiz1,4, Olivier Honnay2, and Steven B. Janssens2,3   

  1. 1Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Caritasstraat 39, BE-9090, Melle, Belgium

    2Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 2435, BE‐3001, Leuven, Belgium

    3Crop wild relatives and useful plants, Meise Botanic Garden, Nieuwelaan 38, BE‐1860 Meise, Belgium

    4Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark Zwijnaarde 71, BE-9052, Zwijnaarde, Belgium

    5Centre de Recherche en Sciences Naturelles (CRSN), Lwiro, D.S.Bukavu, South-Kivu Province, D.R. Congo

  • Received:2020-03-25 Accepted:2020-09-28

Abstract: Interspecific hybridization events have played a major role in plant speciation, yet, the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. C. canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 thousand years ago, coinciding with periods of environmental upheaval which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.

Key words: Allopolyploidy, Coffea arabica (Arabica coffee), genotyping-by-sequencing, hybridization, molecular dating, self-compatibility