title: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.
abstract: A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
authors.affiliation: UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address: perla.hamon@ird.fr.
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA. Electronic address: corrinne@iastate.edu.
authors.forename: Corrinne E
authors.initials: CE
authors.lastname: Grover
authors.affiliation: Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. Electronic address: A.Davis@kew.org.
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Davis
authors.affiliation: FOFIFA, BP 1444, Ambatobe, Antananarivo 101, Madagascar. Electronic address: rakotomalala.jjr@moov.mg.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Rakotomalala
authors.affiliation: FOFIFA, BP 1444, Ambatobe, Antananarivo 101, Madagascar. Electronic address: evanathie.rha@gmail.com.
authors.forename: Nathalie E
authors.initials: NE
authors.lastname: Raharimalala
authors.affiliation: Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA. Electronic address: vaalbert@buffalo.edu.
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
authors.affiliation: Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India. Electronic address: Sreenath.lakkanna@gmail.com.
authors.forename: Hosahalli L
authors.initials: HL
authors.lastname: Sreenath
authors.affiliation: Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium. Electronic address: piet.stoffelen@plantentuinmeise.be.
authors.forename: Piet
authors.initials: P
authors.lastname: Stoffelen
authors.affiliation: Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA. Electronic address: sem30@cornell.edu.
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Mitchell
authors.affiliation: UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address: emmanuel.couturon@ird.fr.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Couturon
authors.affiliation: UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address: serge.hamon@ird.fr.
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.affiliation: UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address: alexandre.dekochko@ird.fr.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.affiliation: Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France. Electronic address: dominique.crouzillat@rdto.nestle.com.
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
authors.affiliation: Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France. Electronic address: michel.rigoreau@rdto.nestle.com.
authors.forename: Michel
authors.initials: M
authors.lastname: Rigoreau
authors.affiliation: Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia. Electronic address: ucu_sumirat@yahoo.com.
authors.forename: Ucu
authors.initials: U
authors.lastname: Sumirat
authors.affiliation: University Jean Lorougnon Guédé, Daloa, Cote d'Ivoire. Electronic address: selastique.akaffou@ujlg.edu.ci.
authors.forename: Sélastique
authors.initials: S
authors.lastname: Akaffou
authors.affiliation: UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address: romain.guyot@ird.fr.
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
mesh_terms: D000349:Africa; D001208:Asia; D005075:Biological Evolution; D002110:Caffeine / Q000032:analysis*; D040503:Coffea / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D018744:DNA, Plant; D005838:Genotype; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D002110:Caffeine
keywords: Biogeography; Coffee; Evolution of caffeine content; Genotyping-by-sequencing; Molecular phylogeny