title: Phylogenetic analysis of Saccharum s.l. (Poaceae; Andropogoneae), with emphasis on the circumscription of the South American species.
abstract: OBJECTIVE
  Polyploidy and reticulate evolution are often a complication for discovering phylogenetic relationships between genera and species. Despite the huge economic importance of sugarcane (Saccharum officinarum-Poaceae, Andropogoneae), the limits of the genus Saccharum and its species are complex and largely unresolved, involving both polyploidy and reticulate evolution. This study aimed to assess the phylogenetic relationships of Saccharum s.l., including Erianthus and Tripidium, as well as investigate the taxonomic circumscription of the South American species of the genus.
  
  
  METHODS
  Molecular cloning and sequencing of five regions of four low-copy nuclear loci were performed, including Aberrant panicle organization1 (apo1), Dwarf8 (d8), two exons of Erect panicle2 (ep2-ex7 and ep2-ex8), and Retarded palea1 (rep1). Concatenated trees were reconstructed using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference analyses.
  
  
  RESULTS
  The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. The samples of Saccharum s.l. grouped in two distinct clades, with S. arundinaceum and S. ravennae (= Tripidium, or Erianthus sect. Ripidium) apart from all other species analyzed of the genus. Saccharum angustifolium, S. asperum, and S. villosum correspond to distinct clades (different species). The plants with intermediate morphology between S. angustifolium and S. villosum presented a pattern of paralogues consistent with a hybrid origin.
  
  
  CONCLUSIONS
  Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. However, no strong evidence was found to support the segregation of Erianthus. The taxonomic circumscription of the South American species of the genus was resolved and the occurrence of natural hybrids was documented. Better understanding of the phylogenetic relationships of Saccharum and relatives may be useful for sugarcane breeders to identify potential taxa for interspecific and intergeneric crosses in the genetic improvement of sugarcane.
authors: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil.
authors: Cassiano A D
authors: CA
authors: Welker
authors: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil.
authors: Tatiana T
authors: TT
authors: Souza-Chies
authors: Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil.
authors: Hilda M
authors: HM
authors: Longhi-Wagner
authors: Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias (UNNE), Sargento Cabral 2131, Corrientes, 3400, Argentina.
authors: Myriam Carolina
authors: MC
authors: Peichoto
authors: Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 USA.
authors: Michael R
authors: MR
authors: McKain
authors: Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 USA.
authors: Elizabeth A
authors: EA
authors: Kellogg
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D002965:Classification; D003001:Cloning, Molecular; D018744:DNA, Plant / Q000032:analysis*; D005091:Exons; D056426:Genetic Loci; D018745:Genome, Plant; D006824:Hybridization, Genetic; D010641:Phenotype; D010802:Phylogeny; D011123:Polyploidy; D031786:Saccharum / Q000033:anatomy & histology / Q000235:genetics*; D013020:South America; D013045:Species Specificity
chemical_list: D018744:DNA, Plant
keywords: Erianthus; Ripidium; Tripidium; hybridization; low-copy nuclear loci; polyploidy; species complex; species delimitation; sugarcane