title: Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.
abstract: OBJECTIVE
  The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial.
  
  
  METHODS
  Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated.
  
  
  RESULTS
  The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent.
  
  
  CONCLUSIONS
  Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
authors.affiliation: Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark. oles@snm.ku.dk
authors.forename: Ole
authors.initials: O
authors.lastname: Seberg
authors.forename: Gitte
authors.initials: G
authors.lastname: Petersen
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.forename: Mark W
authors.initials: MW
authors.lastname: Chase
authors.forename: Michael F
authors.initials: MF
authors.lastname: Fay
authors.forename: Dion S
authors.initials: DS
authors.lastname: Devey
authors.forename: Tina
authors.initials: T
authors.lastname: Jørgensen
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Sytsma
authors.forename: Yohan
authors.initials: Y
authors.lastname: Pillon
mesh_terms: D001483:Base Sequence; D061125:Genes, Chloroplast / Q000235:genetics*; D050259:Genes, Mitochondrial / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D016013:Likelihood Functions; D019668:Liliaceae / Q000235:genetics*; D010802:Phylogeny; D014197:Trees / Q000235:genetics