title: Towards a Phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences.
abstract: OBJECTIVE
  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.
  
  
  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.
authors.affiliation: Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
authors.forename: Olivier
authors.initials: O
authors.lastname: Maurin
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Davis
authors.forename: Michael
authors.initials: M
authors.lastname: Chester
authors.forename: Esther F
authors.initials: EF
authors.lastname: Mvungi
authors.forename: Yasmina
authors.initials: Y
authors.lastname: Jaufeerally-Fakim
authors.forename: Michael F
authors.initials: MF
authors.lastname: Fay
mesh_terms: D000349:Africa; D002467:Cell Nucleus / Q000235:genetics*; D040503:Coffea / Q000145:classification / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics*; D005843:Geography; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant