Coffea Diversity

picture ©Emmanuel couturon IRD

Wild coffea species db.

Phenotypic Diversity of African Coffea Fruits 

Pictures  © Emmanuel Couturon, IRD

Right: Internodes, fruits and seeds of C. richardii (A); Fruit of C. tsirananae (B); leaf of C. heimii (C) (Rimlinger et al., 2020)

The lush tropical rainforests of Africa and Madagascar are hotspots of biodiversity, showcasing an astonishing array of species richness and unique species found nowhere else on Earth. Within this vibrant ecological tapestry, certain genera have undergone radiative speciation, a process marked by significant phenotypic evolution even as genetic differences remain relatively minimal. This phenomenon leads to a striking mismatch between the genetic and phenotypic diversity observed, especially in the case of the Coffea species, excluding those formerly classified under the Psilanthus genus and the Baracoffea groups. Specifically, 58 species from Madagascar and 47 from Africa have been described, notwithstanding the fact that three species from Madagascar and seven from Africa have yet to receive formal recognition. These Coffea species exhibit wide-ranging phenotypic variations, including differences in phenological traits, fruit size and color, maturation timing, tree height, and the biochemical makeup of leaves and fruits, all alongside notable genetic diversity.

A breakthrough came with the development of a fully resolved molecular phylogenetic tree, constructed using 28,800 concatenated Single-Nucleotide Polymorphisms (SNPs) markers derived through Genotyping-By-Sequencing (GBS) techniques (Hamon et al., 2017). This advanced genomic approach was crucial for dissecting the nuanced genetic divergence between species, driven by two primary, not mutually exclusive factors: the presence of permeable genetic barriers allowing for continued, albeit limited, gene flow between species, and the phenomenon of recent speciation events followed swiftly by rapid morphological evolution. This dual dynamic underscores the complex interplay between genetic drift and natural selection in shaping the incredible diversity within the Coffea genus, emphasizing the intricate balance of evolutionary forces at work in the world's tropical rainforests

In this section, we present some recent studies describing the huge diversity of Coffea species at the phenotypic and genetic levels. Our current project include now the analysis of species not included into living collections. 

List of publications

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Salojärvi, J., Rambani, A., Yu, Z., Guyot, R. et al..Nat Genet 56, 721–731 (2024). 

The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes. Bezandry R, Dupeyron M, Gonzalez-Garcia LN, Anest A, Hamon P, Ranarijaona HLT, et al. (2024) PLoS ONE 19(1): e0296362. 

Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. Aurore Rimlinger, Nathalie Raharimalala, Véronique Letort, Jean-Jacques Rakotomalala, Dominique Crouzillat, Romain Guyot, Perla Hamon, Sylvie Sabatier. Annals of Botany, Volume 126, Issue 5, 9 October 2020, Pages 849–863,

WCSdb: a database of wild Coffea species. Database, Volume 2020, 2020, baaa069,

A photo bank of Coffea species: Guyot, Romain; Hamon, Perla; Couturon, Emmanuel; Raharimalala, Nathalie; Rakotomalala, Jean-Jacques, 2020, "Photo bank for: WCSdb: A database of Wild Coffea Species",, DataSuds, V1, UNF:6:D4jmlyKfcJyf9HHyxzxguQ== [fileUNF] 

Garavito A, Montagnon C, Guyot R, Bertrand B. Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol. 2016 Nov 4;16(1):242. doi: 10.1186/s12870-016-0933-y.

Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics. 2016 Feb;291(1):155-68. doi: 10.1007/s00438-015-1098-3. 

Couturon Emmanuel, Raharimalala N.E., Rakotomalala J.J., Hamon Serge, De Kochko Alexandre, Guyot Romain, Hamon Perla. (2016). Caféiers sauvages : un trésor en péril au coeur des forêts tropicales ! = Wild coffee-trees : a threatened treasure in the heart of tropical forests !. Montpellier : Association Biodiversité, Ecovalorisation et Caféiers, 117 p. ISBN 978-2-7466-9109-4

Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C, Poncet V, De Kochko A, Rakotomalala JJ, Hamon P. Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Ann Bot. 2013 Feb;111(2):229-48. doi: 10.1093/aob/mcs283.