Coffee Phylogeny Project
A project aimed at understanding the relationships and evolution of coffee species using DNA technologies. Providing a framework for research, conservation and sustainability of this important crop.
The genus Coffea (Rubiaceae) comprises c. 100 species and contains the two main species used in the production of the beverage coffee: C. arabica and C. canephora. The objectives of the Coffee Phylogeny Project are to: (1) produce a family tree (phylogeny) for coffee and its relatives based primarily on DNA sequence data; (2) use the DNA data to conserve coffee genetic resources by investigating the circumscription of species and the relationships between them; (3) use the phylogeny to investigate the biogeography of coffee, and assess the historical relationships between Africa, Madagascar, the Mascarene Islands, Asia and Australasia; (4) integrate DNA phylogenetic data with other fundamental biodiversity information on coffee species and make it widely accessible.
So far c. 85% of all Coffea species have been sequenced for five DNA regions (plastid: trnL intron, the trnL-F IGS, rpl16 and the accD-psa1 IGS; nuclear: ITS), and for many species multiple samples have been sequenced. Other plastid and nuclear regions, which are likely to provide systematic data, are also being investigated. The results generated so far show that Coffea can be divided into geographical groupings, although it is evident that there has been significant gene exchange between species occurring in the various phytogeographical regions of Africa, and that the evolutionary history of coffee is complex. The work has helped to gain further understanding of the hybrid origin of C. arabica, and the circumscription of many species have been more completely understood. The data has also allowed us to formulate hypotheses regarding the evolutionary history of Coffea. Recently, it has been shown that the genus Psilanthus is part of the natural variation of Coffea, adding a further 20 species to Coffea.
In broader studies using sequence data using plastid DNA (trnL intron, the trnL-F IGS, rpl16 and the accD-psa1 IGS), it has been possible to identify the genera that have a close phylogenetic relationship with Coffea (tribe Coffeeae); ten other genera are proposed as close relatives (i.e. members of Coffeeae).
Ongoing work aims to resolve the remaining poorly undersood parts of Coffea phylogeny, particularly for species occurring in Madagascar and Asia, using new molecular markers and improved species sampling. Further work on species delimitation and the identification of in situ hybridization is also underway.
Project Partners and Collaborators
National Botanic Garden of Belgium, Meise: Dr Piet Stoffelen
Université de Yaoundé I: Prof. Bonaventure Sonké
University of Mauritius: Dr Yasmina Jaufeerally-Fakim
University of Johannesburg: Dr Olivier Maurin
University of Dar es Salaam: Dr Esther F. Mvung
National History Museum: Dr James Tosh
Royal Botanic Garden Edinburgh: Nicolas Ruch
Department of Biology, Duke University, Durham, Dr Michael D. Nowak, Dr Anne Yoder
Kraft Foods, London, England (2001 –2006)
Key papers published since 2006:
1. Davis, A.P., M. Chester, O. Maurin, & Fay, M.F. (2007) Searching for the relatives of Coffea (Rubiaceae, Ixoroideae): the circumscription and phylogeny of Coffeeae based on plastid sequence data and morphology. American Journal of Botany 94(3): 313–329.
2. Maurin, O, Davis, A.P., Chester, M., Mvungi, E.F., Jaufeerally-Fakim, Y & Fay, M.F. (2007). Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences. Annals of Botany 100: 1565–1583.
3. Davis, A.P., Maurin, O., Chester, M., Mvungi, E.F. & Fay, M.F. (2007). Phylogenetic relationships in Coffea (Rubiaceae) inferred from sequence data. Association Scientifique Internationale du Café, 21e Colloque: 868–875.
4. Tosh, J., Davis, A.P., Dessein, S., De Block, P., Huysmans, S., Fay, M.F., Smets, E. & Robbrecht, E. (2009). Phylogeny of Tricalysia (Rubiaceae) and its relationships with allied genera based on plastid DNA data: resurrection of the genus Empogona. Annals of Missouri Botanical Garden 96: 194–213.
5. Davis, A.P., Tosh, J., Ruch, N. & Fay, M.F. (2011). Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of plastid and nuclear DNA sequences; implications for the size, morphology, distribution and evolutionary history of Coffea. Botanical Journal of the Linnean Society 167 (part 4): in press.
Total number of papers published since 2006: 7