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The phylogenetic position of Koliella , a chlorophyte characterized by Klebsormidium type cell division, was inferred from analyses of partial 18S rDNA and partial 16S rDNA. Parsimony and distance analyses of separate and combined data sets indicated that the members of Koliella belonged to Trebouxiophyceae, and high decay indices and bootstrap values supported this affinity. However, the genus appeared to be polyphyletic. Koliella spiculiformis , the nomenclatural type of the genus, was allied with Nannochloris eucaryota and the "true" chlorellas ( Chlorella vulgaris , C. lobophora , C. sorokiniana , and C. kessleri ). The close relatives of Koliella longiseta ( ϵ Raphidonema longiseta ) and Koliella sempervirens appeared to be Stichococcus bacillaris and some species traditionally classified in Chlorella that were characterized by the production of secondary carotenoids under nitrogendeficient conditions. This clade was also supported by the presence of a relatively phylogenetically stable group I intron (1506) in the 18S rRNA gene. Because of the presence of Klebsormidium type cell division, some authors regarded the members of Koliella as closely related to charophytes. Molecular analyses, however, did not confirm this affinity and suggested that a Klebsormidium type cell division is homoplastic in green plants.

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear-encoded genes (nSSU, nLSU, hsp90), one chloroplast-encoded gene (cpSSU) and one nuclear-encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well-defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.

Morphological studies of 16 strains belonging to the genus Monomorphina revealed a single, parietal, orbicular chloroplast in their cells. The chloroplast has a tendency to be perforated and disintegrates in aging populations and thus may appear to be many chloroplasts under the light microscope. A single chloroplast in the cells of Cryptoglena skujae is also parietally located and highly perforated. It never forms a globular and closed structure, but is open from the side of the furrow, resembling the letter C. We have verified the Monomorphina pyrum group (M. pyrum-like) on the basis of phylogenetic analysis of SSU rDNA and morphological data. The strain CCAC 0093 (misidentified as M. reeuwykiana) diverges first on the SSU rDNA phylogenetic tree. The rest of the M. pyrum-like strains form a tight cluster, subdivided into several smaller ones. Because morphological differences between the M. pyrum-like strains (including the strain CCAC 0093) do not conform to the tree topology, we suggest that they all (except the strain CCAC 0093) belong to M. pyrum. We designate a new species, M. pseudopyrum, for the strain CCAC 0093, solely on the basis of molecular characters. We also suggest that M. reeuwykiana and similar species should stay in Phacus and Lepocinclis unless detailed molecular and morphological studies show otherwise. Emended diagnoses of the genera Monomorphina and Cryptoglena and the species M. aenigmatica are also proposed, as well as the delimitation of an epitype for M. pyrum, the type species for the genus Monomorphina.

Eighteen new 16S rDNA and 16 new 18S rDNA sequences from 24 strains, representing 23 species of photoautotrophic euglenoids, were obtained in nearly their entire length. Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on separate data (39 sequences of 16S rDNA and 58 sequences of 18S rDNA), as well as on combined data sets (37 sequences). All methods of sequence analysis gave similar results in those cases in which the clades received substantial support. However, the combined data set produced several additional wellsupported clades, not encountered before in the analyses of green euglenoids. There are three main well-defined clades (A, B/C/D, and G) on trees from the combined data set. Clade G diverges first, while clades A and B/C/D form sister groups. Clade A consists of Euglena species sensu stricto and is divided into three sub-clades (A1, A2, and A3). Clade A3 (composed of E. deses and E. mutabilis) branches off first; then, two sister clades emerge: A1 (composed of E. viridis-like species) and A2 (consisting of E. agilis and E. gracilis species). Clade B/C/D consists of the Strombomonas, Trachelomonas, Cryptoglena, Monomorphina, and Colacium genera. Clade G comprises Phacus and Lepocinclis, as well as the Discoglena species of Euglena, with Discoglena branching off first, and then Phacus and Lepocinclis emerging as sister groups.