title: Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods.
abstract: OBJECTIVE
  Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera.
  
  
  METHODS
  DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree-species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted.
  
  
  RESULTS
  Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia-Lepidozamia-Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia.
  
  
  CONCLUSIONS
  A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.
authors.affiliation: Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
authors.forename: Dayana E
authors.initials: DE
authors.lastname: Salas-Leiva
authors.forename: Alan W
authors.initials: AW
authors.lastname: Meerow
authors.forename: Michael
authors.initials: M
authors.lastname: Calonje
authors.forename: M Patrick
authors.initials: MP
authors.lastname: Griffith
authors.forename: Javier
authors.initials: J
authors.lastname: Francisco-Ortega
authors.forename: Kyoko
authors.initials: K
authors.lastname: Nakamura
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.forename: Carl E
authors.initials: CE
authors.lastname: Lewis
authors.forename: Sandra
authors.initials: S
authors.lastname: Namoff
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D032462:Cycadopsida / Q000145:classification* / Q000235:genetics*; D018628:Gene Dosage / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D058974:Phylogeography; D011110:Polymorphism, Genetic; D013045:Species Specificity; D013997:Time Factors; D014197:Trees / Q000235:genetics*
keywords: Biogeography; Bowenia; Cycadales; Dioon; Stangeria; gymnosperms; molecular systematics