title: Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum.
abstract: OBJECTIVE
  Sorghum is an essential grain crop whose evolutionary placement within the Andropogoneae has been the subject of scrutiny for decades. Early studies using cytogenetic and morphological data point to a poly- or paraphyletic origin of the genus; however, acceptance of poly- or paraphyly has been met with resistance. This study aimed to address the species relationships within Sorghum, in addition to the placement of Sorghum within the tribe, using a phylogenetic approach and employing broad taxon sampling.
  
  
  METHODS
  From 16 diverse Sorghum species, eight low-copy nuclear loci were sequenced that are known to play a role in morphological diversity and have been previously used to study evolutionary relationships in grasses. Further, the data for four of these loci were combined with those from 57 members of the Andropogoneae in order to determine the placement of Sorghum within the tribe. Both maximum likelihood and Bayesian analyses were performed on multilocus concatenated data matrices.
  
  
  RESULTS
  The Sorghum-specific topology provides strong support for two major lineages, in alignment with earlier studies employing chloroplast and internal transcribed spacer (ITS) markers. Clade I is composed of the Eu-, Chaeto- and Heterosorghum, while clade II contains the Stipo- and Parasorghum. When combined with data from the Andropogoneae, Clade II resolves as sister to a clade containing Miscanthus and Saccharum with high posterior probability and bootstrap support, and to the exclusion of Clade I.
  
  
  CONCLUSIONS
  The results provide compelling evidence for a two-lineage polyphyletic ancestry of Sorghum within the larger Andropogoneae, i.e. the derivation of the two major Sorghum clades from a unique common ancestor. Rejection of monophyly in previous molecular studies is probably due to limited taxon sampling outside of the genus. The clade consisting of Para- and Stiposorghum resolves as sister to Miscanthus and Saccharum with strong node support.
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA Jennifer.hawkins@mail.wvu.edu.
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Hawkins
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Dhanushya
authors.initials: D
authors.lastname: Ramachandran
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Henderson
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Jasmine
authors.initials: J
authors.lastname: Freeman
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Carlise
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Harris
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Willison-Headley
mesh_terms: D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics*; D018628:Gene Dosage; D056426:Genetic Loci; D016013:Likelihood Functions; D010802:Phylogeny; D045868:Sorghum / Q000235:genetics*
keywords: Andropogoneae; Poaceae; Sorghum; low-copy nuclear loci; phylogeny; polyphyly