title: Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?
abstract: OBJECTIVE
  Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life.
  
  
  METHODS
  Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support.
  
  
  RESULTS
  Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies.
  
  
  CONCLUSIONS
  Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.
authors.affiliation: Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA.
authors.forename: Craig F
authors.initials: CF
authors.lastname: Barrett
authors.forename: Chelsea D
authors.initials: CD
authors.lastname: Specht
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: Dennis Wm
authors.initials: DW
authors.lastname: Stevenson
authors.forename: Wendy B
authors.initials: WB
authors.lastname: Zomlefer
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
mesh_terms: D005075:Biological Evolution; D003062:Codon; D020939:Zingiber officinale / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics*; D019862:Zingiberales / Q000145:classification / Q000235:genetics*
chemical_list: D003062:Codon; D010940:Plant Proteins
keywords: Illumina; Tropical gingers; Zingiberales; ancient radiation; evolution; monocots; next-generation sequencing; phylogenomics; phylogeny; plastid gene set; plastome; support