AOBPreview originally published online on October 22, 2007
Annals of Botany 2007 100(7):1565-1583; doi:10.1093/aob/mcm257
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Towards a Phylogeny for Coffea (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences
1 Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
2 Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
3 Department of Botany, University of Dar es Salaam, PO Box 35060, Dar es Salaam, Tanzania
4 Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, 2006, Gauteng, South Africa
5 School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
6 Faculty of Agriculture, University of Mauritius, Reduit, Mauritius
* For correspondence. E-mail a.davis{at}kew.org
Received: 28 June 2007 Returned for revision: 25 July 2007 Accepted: 30 August 2007 Published electronically: 22 October 2007
Background and Aims: The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling.
Methods: Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL–F intron, trnL–F intergenic spacer (IGS), rpl16 intron and accD–psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5·8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics.
Key Results: Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea.
Key words: Africa, accD–psa1 IGS, Coffea, coffee, Indian Ocean Islands, ITS, Madagascar, molecular phylogeny, rpl16 intron, Rubiaceae, trnL–F intron, trnL–F IGS
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