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Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

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Classification of the Phylum Ciliophora (Eukaryota, Alveolata) 1! The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised 2! Classification of the Phylum Ciliophora (Eukaryota, Alveolata) 3! 4! Feng Gao a, Alan Warren b, Qianqian Zhang c, Jun Gong c, Miao Miao d, Ping Sun e, 5! Dapeng Xu f, Jie Huang g, Zhenzhen Yi h,* & Weibo Song a,* 6! 7! a Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 8! China; b Department of Life Sciences, Natural History Museum, London, UK; c Yantai 9! Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; d 10! College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; 11! e Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, 12! Xiamen University, Xiamen, China; f State Key Laboratory of Marine Environmental 13! Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 14! China; g Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; h 15! School of Life Science, South China Normal University, Guangzhou, China. 16! 17! Running Head: Phylogeny and evolution of Ciliophora 18! *!Address correspondence to Zhenzhen Yi, [email protected]; or Weibo Song, 19! [email protected] 20! ! ! 1! Table S1. List of species for which SSU rDNA, 5.8S rDNA, LSU rDNA, and alpha-tubulin were newly sequenced in the present work. ! ITS1-5.8S- Class Subclass Order Family Speicies Sample sites SSU rDNA LSU rDNA a-tubulin ITS2 A freshwater pond within the campus of 1 COLPODEA Colpodida Colpodidae Colpoda inflata the South China Normal University, KM222106 KM222071 KM222160 Guangzhou (23° 09′N, 113° 22′ E) Climacostomum No. 2 Bathing Beach, Qingdao (36° 03′ N, 2 HETEROTRICHEA Heterotrichida Climacostomidae KM222165 KM221978 virens 120° 21′ E) Mariculture pond, Weifang (37°06′′N, 3 HETEROTRICHEA Heterotrichida Climacostomidae Fabrea salina KM222110 KM222078 KM222167 KM222005 119°30′′) Condylostoma Wanggezhuang mudflats, Qingdao (36° 17′ 4 HETEROTRICHEA Heterotrichida Condylostomatidae KM222108 KM222076 KM222163 KM221981 magnum N, 120° 39′ E) Folliculina Zhongyuan Dock, Qingdao (36° 03′ N, 5 HETEROTRICHEA Heterotrichida Folliculinidae KM222079 KM222168 KM221977 simplex 120° 19′ E) Estuary of Baisha River, Qingdao (36° 15′ 6 HETEROTRICHEA Heterotrichida Peritromidae Peritromus faurei KM222080 KM222169 N, 120° 19′ E) Anigsteinia No. 1 Bathing Beach, Qingdao (36° 03′ N, 7 HETEROTRICHEA Heterotrichida Spirostomidae KM222109 KM222077 KM222166 KM221982 clarissima 120° 21′ E) A freshwater pond within the campus of 8 HETEROTRICHEA Heterotrichida Spirostomidae Spirostomum sp. the South China Normal University, KM222081 KM222170 KM222008 Guangzhou (23° 09′N, 113° 22′ E) Huguangyan scenic spot, Zhanjiang (21° 9 HETEROTRICHEA Heterotrichida Stentoridae Stentor sp. KM222111 KM222082 KM222171 KM222003 09′ N, 110° 18′ E) Loxodes cf. Seagull Island, Guagnzhou (22° 59′ N, 10 KARYORELICTEA Loxodida Loxodidae KM222107 KM222075 KM222162 striatus 113° 32′ E) Remanella Sculpture Park Bathing Beach, Qingdao 11 KARYORELICTEA Loxodida Loxodidae KM221984 granulosa (36° 05′N, 120° 27′ E) Protoheterotrichi No. 1 Bathing Beach, Qingdao (36° 03′ N, 12 KARYORELICTEA Geleiidae Geleia sinica KM222074 KM222161 da 120° 21′ E) Kentrophoros No. 6 Bathing Beach, Qingdao (36° 03′ N, 13 KARYORELICTEA Protostomatida Kentrophoridae KM222029 gracilis 120° 19′ E) Licnophora cf. Daya Bay, Guangzhou (22° 36′N, 114° 33′ 77 LICNOPHORIEA Licnophorida Licnophoridae FJ876955 KM222164 KM222007 lyngbycola E) Daya Bay, Guangzhou (22° 36′N, 114° 33′ 14 LITOSTOMATEA Haptoria Haptorida Acropisthiidae Chaenea sp. KM222059 KM222153 E) Helicoprorodon Sculpture Park Bathing Beach, Qingdao 15 LITOSTOMATEA Haptoria Haptorida Helicoprorodontidae KM222102 KM222061 KM222154 KM221989 maximus (36° 05′N, 120° 27′ E) A freshwater pond within the campus of 16 LITOSTOMATEA Haptoria Haptorida Tracheliidae Dileptus sp. the South China Normal University, KM222100 KM222152 KM221975 Guangzhou (23° 09′N, 113° 22′ E) Circulating water system of a fish culture, 17 LITOSTOMATEA Haptoria Pleurostomatida Amphileptidae Amphileptus songi FJ876974 KM222058 Qingdao (36° 04′N, 120° 21′ E) Mesodinium Wanggezhuang mudflats, Qingdao (36° 17′ 18 MESODINIEA Mesodiniida Mesodiniidae KM222101 acarus N, 120° 39′ E) Discotricha Stone man bathing beach, Qingdao (36° 06′ 19 NASSOPHOREA Discotrichida Discotrichidae KM222067 papillifera N, 120° 29′ E) A freshwater pond in Changfeng 20 NASSOPHOREA Nassulida Furgasoniidae Parafurgasonia sp. Park, Shanghai, China (31° 14′ N, 121° 24′ KM222070 KM222159 E). Daya Bay, Guangzhou (22° 36′N, 114° 33′ 21 NASSOPHOREA Nassulida Nassulidae Nassula labiata KM222069 E) Daya Bay, Guangzhou (22° 36′N, 114° 33′ 22 OLIGOHYMENOPHOREA Peniculia Paranassulida Paranassulidae Paranassula sp. KM222068 E) Frontonia Huguangyan scenic spot, Zhanjiang (21° 23 OLIGOHYMENOPHOREA Peniculia Peniculida Frontoniidae KM222112 KM222083 KM222172 KM222002 canadensis 09′ N, 110° 18′ E) Huguangyan scenic spot, Zhanjiang (21° 24 OLIGOHYMENOPHOREA Peniculia Peniculida Lembadionidae Lembadion sp. KM222113 KM222084 KM222173 09′ N, 110° 18′ E) Mangrove Reserve, Shenzhen (22° 32′N, 25 OLIGOHYMENOPHOREA Peritrichia Sessilida Epistylididae Epistylis sp. KM222114 KM222085 KM222174 KM222025 114° 00′ E) Pseudepistylis Nan'ao Island, Shantou (23° 28′N, 117° 06′ 26 OLIGOHYMENOPHOREA Peritrichia Sessilida Epistylididae KM222115 KM222086 KM222175 KM222023 songi E) Mangrove Reserve, Shenzhen (22° 32′N, 27 OLIGOHYMENOPHOREA Peritrichia Sessilida Opisthonectidae Opisthonecta sp. KM222119 KM222090 KM222179 KM222024 114° 00′ E) Pseudovorticella Donghai Island, Zhanjiang (21°05′N, 110° 28 OLIGOHYMENOPHOREA Peritrichia Sessilida Vorticellidae KM222116 KM222087 KM222176 KM222020 shii 32′ E) Daya Bay, Guangzhou (22° 36′N, 114° 33′ 29 OLIGOHYMENOPHOREA Peritrichia Sessilida Vorticellidae Vorticella chiangi KM222117 KM222088 KM222177 KM222021 E) Zoothamnium Mipu Reserve, Hongkong (22° 30′N, 114° 30 OLIGOHYMENOPHOREA Peritrichia Sessilida Zoothamniidae KM222118 KM222089 KM222178 KM222022 hentscheli 04′ E) Zoothamnopsis Seawater along the coast of Yellow Sea, 31 OLIGOHYMENOPHOREA Peritrichia Sessilida Zoothamniidae KM222031 sinica Qingdao (36° 03′ N, 120° 22′ E) Cinetochilum 32 OLIGOHYMENOPHOREA Scuticociliatia Loxocephalida Cinetochilidae A port in Qingdao (36° 05′ N, 120° 19′ E) KM221956 ovale Pseudoplatynemat No. 1 Bathing Beach, Qingdao (36° 03′ N, 33 OLIGOHYMENOPHOREA Scuticociliatia Loxocephalida Cinetochilidae KM221967 um denticulatum 120° 21′ E) Sathrophilus Stone man bathing beach, Qingdao (36° 06′ 34 OLIGOHYMENOPHOREA Scuticociliatia Loxocephalida Cinetochilidae KM221968 holtae N, 120° 29′ E) Cardiostomatella Taiping Bay, Qingdao (36° 03′ N, 120° 22′ 35 OLIGOHYMENOPHOREA Scuticociliatia Loxocephalida Loxocephalidae KM221955 vermiformis E) Paratetrahymena Daya Bay, Guangzhou (22° 36′N, 114° 33′ 36 OLIGOHYMENOPHOREA Scuticociliatia Loxocephalida Loxocephalidae KM221963 wassi E) Metanophrys Mariculture pond, Weifang (37°06′′N, 37 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Orchitophryidae KM221961 sinensis 119°30′′) Mariculture pond, Weifang (37°06′′N, 38 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Parauronematidae Miamiensis avidus KM221962 119°30′′) Philasterides No. 6 Bathing Beach, Qingdao (36° 03′ N, 39 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Philasteridae KM221964 armatalis 120° 19′ E) Pseudocohnilembu Nansan Island, Zhanjiang (21° 11′ N, 110° 40 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Pseudocohnilembidae KM221966 s hargisi 27′ E) Seawater along the coast of Yellow Sea, 41 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Uronematidae Uronema marinum KM221969 Qingdao (36°18′ N, 120°43′ E) Mesanophrys Clear Water Bay, Hong Kong (22° 20′ N, 42 OLIGOHYMENOPHOREA Scuticociliatia Philasterida Orchitophryidae KM221960 carcini 114°17′ E) Ancistrum From the mantle cavity of the marine 43 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Ancistridae KM221953 crassum mollusk Ruditapes philippinarum, Qingdao (36° 04′ N, 120° 23′ E) Hippocomos Yangkou sandy beach, Qingdao (36º14'N, 44 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Ctedoctematidae KM221959 salinus 120º40'E) No. 1 Bathing Beach, Qingdao (36° 03′ N, 45 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Cyclidiidae Cristigera media KM221957 120° 21′ E) Protocyclidium Estuary of Baisha River, Qingdao (36° 15′ 46 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Cyclidiidae KM221958 citrullus N, 120° 19′ E) Sculpture Park Bathing Beach, Qingdao 47 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Eurystomateliidae Wilbertia typica KM221970 (36° 05′N, 120° 27′ E) From the mantle cavity of the marine Boveria 48 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Hemispeiridae mollusk Pinna pectinata, Qingdao (36° 04′ KM221954 subcyclindrica N, 120° 23′ E) Pleuronema 49 OLIGOHYMENOPHOREA Scuticociliatia Pleuronematida Pleuronematidae A port in Qingdao (36° 05′ N, 120° 19′ E) KM221965 setigerum Trithigmostoma Longxue Island, Guangzhou (22° 42′ N, 50 PHYLLOPHARYNGEA Cyrtophoria Chlamydodontida Chilodonellidae KM222063 KM222156 KM221985 cucullulus 113° 39′ E) Chlamydodon Nansha Port, Guangzhou (22° 48′N, 113° 51 PHYLLOPHARYNGEA Cyrtophoria Chlamydodontida Chlamydodontidae KM221986 mnemosyne 36′ E) Chlamydonella Daya Bay, Guangzhou (22° 36′N, 114° 33′ 52 PHYLLOPHARYNGEA Cyrtophoria Chlamydodontida Lynchellidae KM222001 pseudochilodon E) Mai Island, Qingdao (36° 04′ N, 120° 27′ 53 PHYLLOPHARYNGEA Cyrtophoria Dysteriida Dysteriidae Dysteria derouxi KM222105 KM222064
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