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Phylogeographic analysis of the Coffea subgenus Coffea was performed using data on plastid DNA sequences and interpreted in relation to biogeographic data on African rain forest flora. Parsimony and Bayesian analyses of trnL-F, trnT-L and atpB-rbcL intergenic spacers from 24 African species revealed two main clades in the Coffea subgenus Coffea whose distribution overlaps in west equatorial Africa. Comparison of trnL-F sequences obtained from GenBank for 45 Coffea species from Cameroon, Madagascar, Grande Comore and the Mascarenes revealed low divergence between African and Madagascan species, suggesting a rapid and radial mode of speciation. A chronological history of the dispersal of the Coffea subgenus Coffea from its centre of origin in Lower Guinea is proposed. No relation was found between phylogenetic topology and the age of emergence of the volcanic islands that Coffea species have colonised in the Indian Ocean, suggesting dispersal from mainland Africa after the emergence of the youngest island, Grande Comore, 500,000 years ago. Additional sequences were obtained from GenBank for 24 species of other Rubiaceae genera, including the Rubia genus whose origin has been dated from the Upper Miocene. Estimates of substitution rates suggested that diversification in Coffea subgenus Coffea occurred about 460,000 years ago or as recently as the last 100,000 years, depending on the cpDNA region considered and calibration. The phylogenetic relationships based on plastid sequences confirmed biogeographic differentiation of coffee species, but they were not congruent with morphological and biochemical classifications, or with the capacity to grow in specific environments. Examples of convergent evolution in the main clades are given using characters of leaf size, caffeine content and reproductive mode.

Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar