Résumé
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 4 Mya) 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.