@article{fdi:010079508,
  title = {{C}omplex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear {SNP} analyses, with particular emphasis on {C}offea canephora ({R}obusta coffee)},
  author = {{C}harr, {J}. {C}. and {G}aravito, {A}. and {G}uyeux, {C}. and {C}rouzillat, {D}. and {D}escombes, {P}. and {F}ournier, {C}. and {L}y, {S}. {N}. and {R}aharimalala, {E}. {N}. and {R}akotomalala, {J}. {J}. and {S}toffelen, {P}. and {J}anssens, {S}. and {H}amon, {P}erla and {G}uyot, {R}omain},
  editor = {},
  language = {{ENG}},
  abstract = {{F}or decades coffees were associated with the genus {C}offea. {I}n 2011, the closely related genus {P}silanthus was subsumed into {C}offea. {H}owever, results obtained in 2017-based on 28,800 nuclear {SNP}s-indicated that there is not substantial phylogenetic support for this incorporation. {I}n addition, a recent study of 16 plastid fullgenome sequences highlighted an incongruous placement of {C}offea canephora ({R}obusta coffee) between maternal and nuclear trees. {I}n this study, similar global features of the plastid genomes of {P}silanthus and {C}offea are observed. {I}n agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates {P}silanthus from {C}offea (with exception to {C}. rhamnifolia, closer to {P}silanthus than to {C}offea). {I}n contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both {P}silanthus and {C}offea species, and two with either {P}silanthus or {C}offea species. {I}nterestingly, {C}offea and {P}silanthus taxa sampled in {W}est and {C}entral {A}frica are members of the same group. {S}everal mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for {C}. arabica) are involved in the evolutionary history of the coffee species. {W}hile sharing similar morphological characteristics, the genetic relationships within {C}. canephora have shown that some populations are well differentiated and genetically isolated. {G}iven the position of its closely-related species, we may also consider {C}. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.},
  keywords = {{F}ull plastid genome sequencing ; {N}uclear {SNP}s ; {E}volutionary history ; {C}offee species - {C}offea canephora},
  booktitle = {},
  journal = {{M}olecular {P}hylogenetics and {E}volution},
  volume = {151},
  numero = {},
  pages = {106906 [13 p.]},
  ISSN = {1055-7903},
  year = {2020},
  DOI = {10.1016/j.ympev.2020.106906},
  URL = {https://www.documentation.ird.fr/hor/fdi:010079508},
}