Journal Article

Towards a Phylogeny for <i>Coffea</i> (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences

Olivier Maurin, Aaron P. Davis, Michael Chester, Esther F. Mvungi, Yasmina Jaufeerally-Fakim and Michael F. Fay

in Annals of Botany

Published on behalf of The Annals of Botany Company

Volume 100, issue 7, pages 1565-1583
Published in print December 2007 | ISSN: 0305-7364
Published online October 2007 | e-ISSN: 1095-8290 | DOI: http://dx.doi.org/10.1093/aob/mcm257
Towards a Phylogeny for Coffea (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences

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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.

Keywords: Africa; accD–psa1 IGS; Coffea; coffee; Indian Ocean Islands; ITS; Madagascar; molecular phylogeny; rpl16 intron; Rubiaceae; trnL–F intron; trnL–F IGS

Journal Article.  12222 words.  Illustrated.

Subjects: Ecology and Conservation ; Evolutionary Biology ; Plant Sciences and Forestry

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