title: Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities.
abstract: BACKGROUND
  Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone.
  
  
  RESULTS
  Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals.
  
  
  CONCLUSIONS
  Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.
authors.affiliation: UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier CEDEX 5, France. celine.gomez@ird.fr
authors.forename: Céline
authors.initials: C
authors.lastname: Gomez
authors.forename: Stéphane
authors.initials: S
authors.lastname: Dussert
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.forename: Alexandre de
authors.initials: Ad
authors.lastname: Kochko
authors.forename: Valérie
authors.initials: V
authors.lastname: Poncet
mesh_terms: D002980:Climate; D016000:Cluster Analysis; D040503:Coffea / Q000235:genetics*; D003223:Congo; D018744:DNA, Plant / Q000235:genetics; D017753:Ecosystem; D019143:Evolution, Molecular; D051456:Gene Flow; D005819:Genetic Markers; D005828:Genetics, Population; D018745:Genome, Plant; D005843:Geography; D016701:Guinea; D018895:Microsatellite Repeats; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers