title: Phylogeny of the photosynthetic euglenophytes inferred from the nuclear SSU and partial LSU rDNA.
abstract: Previous studies using the nuclear SSU rDNA have indicated that the photosynthetic euglenoids are a monophyletic group; however, some of the genera within the photosynthetic lineage are not monophyletic. To test these results further, evolutionary relationships among the photosynthetic genera were investigated by obtaining partial LSU nuclear rDNA sequences. Taxa from each of the external clades of the SSU rDNA-based phylogeny were chosen to create a combined dataset and to compare the individual LSU and SSU rDNA datasets. Conserved areas of the aligned sequences for both the LSU and SSU rDNA were used to generate parsimony, log-det, maximum-likelihood and Bayesian trees. The SSU and LSU rDNA consistently generated the same seven terminal clades; however, the relationship among those clades varied depending on the type of analysis and the dataset used. The combined dataset generated a more robust phylogeny, but the relationships among clades still varied. The addition of the LSU rDNA dataset to the euglenophyte phylogeny supports the view that the genera Euglena, Lepocinclis and Phacus are not monophyletic and substantiates the existence of several well-supported clades. A secondary structural model for the D2 region of the LSU rDNA was proposed on the basis of compensatory base changes found in the alignment.
authors.affiliation: Division of Life Sciences, Rutgers University, Nelson Hall, 604 Allison Road, Piscataway, NJ 08854, USA.
authors.forename: Stacy
authors.initials: S
authors.lastname: Brosnan
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Woongghi
authors.initials: W
authors.lastname: Shin
authors.affiliation: Department of Entomology, Rutgers University, Cook College, Blake Hall, 93 Lipman Drive, New Brunswick, NJ 08901, USA.
authors.forename: Karl M
authors.initials: KM
authors.lastname: Kjer
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Triemer
mesh_terms: D000818:Animals; D001483:Base Sequence; D016054:DNA, Protozoan / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D005055:Euglena / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010788:Photosynthesis; D010802:Phylogeny; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D016053:RNA, Protozoan; D012335:RNA, Ribosomal