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 lim-ited by low levels of sequence divergence, leading to insufficient topological resolution and statisticalsupport in phylogenetic trees, particularly for the major lineages and for the numerous species occurringin Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesisfor 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 additionalsamples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) asthe most likely ancestral locality for the origin of the coffee genus, with independent radiations acrossAfrica, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolutionof caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. Highand consistent caffeine content is found only in species from the equatorial, fully humid environmentsof 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 and4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already inplace during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subjectto convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate