title: Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes.
abstract: The phylogenetic positions of the primary photosynthetic eukaryotes, or Archaeplastida (green plants, red algae, and glaucophytes) and the secondary photosynthetic chromalveolates, Haptophyta, vary depending on the data matrices used in the previous nuclear multigene phylogenetic studies. Here, we deduced the phylogeny of three groups of Archaeplastida and Haptophyta on the basis of sequences of the multiple slowly evolving nuclear genes and reduced the gaps or missing data, especially in glaucophyte operational taxonomic units (OTUs). The present multigene phylogenetic analyses resolved that Haptophyta and two other groups of Chromalveolata, stramenopiles and Alveolata, form a monophyletic group that is sister to the green plants and that the glaucophytes and red algae are basal to the clade composed of green plants and Chromalveolata. The bootstrap values supporting these phylogenetic relationships increased with the exclusion of long-branched OTUs. The close relationship between green plants and Chromalveolata is further supported by the common replacement in two plastid-targeted genes.
authors.affiliation: Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nozaki@biol.s.u-tokyo.ac.jp
authors.forename: Hisayoshi
authors.initials: H
authors.lastname: Nozaki
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Maruyama
authors.forename: Motomichi
authors.initials: M
authors.lastname: Matsuzaki
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakada
authors.forename: Syou
authors.initials: S
authors.lastname: Kato
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Misawa
mesh_terms: D056893:Alveolata / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D019143:Evolution, Molecular; D016013:Likelihood Functions; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics*; D000461:Rhodophyta / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA