title: The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata).
abstract: The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea.
authors.affiliation: Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Gao
authors.affiliation: Department of Life Sciences, Natural History Museum, London SW7 5BD, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: Warren
authors.affiliation: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Gong
authors.affiliation: College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Miao
authors.affiliation: Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Xu
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Yi
authors.affiliation: Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Song
mesh_terms: D016798:Ciliophora / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D010802:Phylogeny; D017422:Sequence Analysis, DNA