Molecular Phylogeny Within Three Ciliated Classes Spirotriches, Oligohymenophorea And Prostomatea (Protozoa, Ciliophora)

Ciliated protozoa is the most morphorlogically complex and highly differentiated taxon among single-celled organisms, and plays an important role in eukaryotic evolutionary investigation. Based on the morphology, infraciliature and ontogenetic characters, some classical systems of ciliate classification were proposed. However, the significance of various structures and infraciliatures is rather different according to different investigators,, which caused different systems of classification. And these systems needed careful reconstruction. Recently, the molecular phylogenic analyses have thrown new light on the taxonomy and systematics of ciliates, which reveals phylogenetic relationships at the genic level. However, only one gene marker was chosen for most of the molecular phylogenetic investigations, which caused differences between phylogenetic trees and the "real" ones. Therefore, more investigations are needed to reveal the relatinships among Ciliophora.With molecular biological methods, this work resolved some confusions of morphological taxonomy and systematology of lower taxa within three ciliated classes, viz., Spirotrichea, Oligohymenophorea, Prostomatea, at the genetical level. In order to minimize the differences between molecular phylogenetic trees and "real" trees, we included more species, sequenced more gene marks, and improved the methods of data analyses.The following conclusions could be drawed:1) ITS2 secondary structures of 14 spirotrichean genera and 41 species were predicted. These 14 genera are:Anteholosticha, Apokeronopsis, Bergerilla, Diaxonella, Epiclintes, Holosticha, Metaurostylopsis, Nothoholosticha, Parabirojimia, Psammomitra, Pseudourostyla, Pseudoamphisiella, Pseudokeronopsis, Thigmokeronopsis2) A new suborder was established within the order Urostylida:Parabirojimina Yi et al. 2008; a new improved taxon:Psammomitridae。3) The phylogenetic positions of nine spirotrichean species, whose assignments were historically unclear, have been classified. These nine species are:Apokeronopsis crassa, A. bergeri, Metaurostylopsis struederkypkella, M. salina, M. sinica, Thigmokeronopsis stoecki, Pseudoamphisiella lacazei, P. alveolata, Parabirojimia similis.4) The molecular phylogenetic relationships among the order Euplotida were analysed for the first time. Result showed:(i) the 'typical' euplotids comprised a paraphyletic assemblage composed of two divergent clades (family Uronychiidae and families Euplotidae-Certesiidae-Aspidiscidae-Gastrocirrhidae); (ii) in the family Uronychiidae, the genera Uronychia and Paradiophrys formed a clearly outlined, well-supported clade that seemed to be rather divergent from Diophrys and Diophryopsis, suggesting that the Diophrys-complex may have had a longer and more separate evolutionary history than previously supposed; (iii) inclusion of 12 new SSrRNA sequences in analyses of Euplotidae revealed two new clades of species within the family and cast additional doubt on the present classification of genera within the family; (iv) the intraspecific divergence among five species of Aspidisca was far greater than those of closely related genera. In addition, the ITS1-5.8S-ITS2 coding regions and partial histone H4 genes of six morphospecies in the Diophrys-complex were sequenced along with their SSrRNA genes and used to compare phylogenies constructed from single data sets to those constructed from combined sets. Results indicated that combined analyses could be used to construct more reliable, less ambiguous phylogenies of complex groups like the order Euplotida, because they provide a greater amount and diversity of information.5) The phylogenetic positions of six oligohymenophorean species, whose assignments were historically unclear, have been classified. These six species are:Uronemella filificum, Pleuronema czapikae, P. sinica, Schizocalyptra sp-WYG07060701, S. aeschtae, Paraterahymena sp.6) The variable region 4 secondary structures of SSrRNA gene of twenty oligohymenophorean genera and thirty species were predicted. There are several minor differences among ITS2 secondary structures of four species, while three P. carnea populations are identical. The size of the terminal bulge in Helix E23-7 is probably different for the orders Philasterida and Pleuronematida. These twenty genera are:Homalogastra, Pseudocohnilembus, Metanophrys, Mesanophrys, Anophyroides, Philasterides, Miamiensis, Parauronema, Plagiopyliella, Thyrophylax, Entorhipidium, Entodiscus, Uronema, Uronemella, Paranophrys, Cohnilembus, Schizocaryum, Pleuronema, Schizocalyptra, Cyclidium.7) The possibility of tree construction using combination data constaining morphological characters and gene sequences is discussed.8) The phylogenetic positions of five prostomatean species, whose assignments were historically unclear, have been classified. These five species are:Apocoleps sp-WYG07060702, Apocoleps sp-FXP07101005, Apocoleps magnus, Tiarina fusa, Nolandia sp-WYG07050702. And accuracy improvement of the phylogenetic estimates caused by increased environmental taxa sampling is also proved.In addition, SSrRNA gene of 44 species, ITS-5.8S-ITS2 region of 26 species, alpha-tubulin gene of 15 species, and histon H4 gene of five species are sequenced and submitted.