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Jiang L, Wang C, Al-Farraj SA, Hines HN, Hu X. Morphological and molecular examination of the ciliate family Lagynusidae (Protista, Ciliophora, Prostomatea) with descriptions of two new genera and two new species from China. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:178-195. [PMID: 37275546 PMCID: PMC10232704 DOI: 10.1007/s42995-023-00174-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/12/2023] [Indexed: 06/07/2023]
Abstract
Ciliates in the class Prostomatea play an important role in the global microbial loop due to their significant abundances and broad feeding strategies at the foundation of food webs. Despite their importance in ecosystems, the taxonomy and systematics of this group of ciliates has long been poorly understood, with this being especially true for members of the family Lagynusidae. Here we examine four lagynusids collected from sandy beaches in China, using silver-staining and 18S rRNA gene sequencing techniques. These investigations revealed two new genera and two new species and provided details for two little known forms: Penardella marina gen. nov., sp. nov., Apolagynus cucumis (as reported by Penard. Études sur les infusoires d'eau douce. Georg and Cie, Genève, 1922) gen. nov., comb. nov., Lagynus minutus sp. nov., and Lagynus elegans (Engelmann in Z Wiss Zool 11:347-393, 1862) Quennerstedt (Acta Univ Lund 4:1-48, 1867). Penardella gen. nov. can be morphologically distinguished by having more than three dikinetidal perioral kineties. Apolagynus gen. nov. differs from the closely related genus Lagynus in the absence of a conspicuous neck-like region. The ciliature of Apolagynus cucumis is revealed here for the first time, which demonstrates the classification of this species within Lagynusidae. Furthermore, Apolagynus binucleatus (Jiang et al., 2021) comb. nov. is established according to the new finding. The results of our phylogenetic analyses based on the 18S rRNA gene support the establishment of two new genera and indicate that Lagynusidae is monophyletic, which further strengthens its valid taxonomic status.
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Affiliation(s)
- Limin Jiang
- College of Fisheries, and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Congcong Wang
- College of Fisheries, and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Saleh A. Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451 Saudi Arabia
| | - Hunter N. Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34982 USA
| | - Xiaozhong Hu
- College of Fisheries, and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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2
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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3
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Omar A, Moon JH, Jung JH. Molecular phylogeny of a new gonostomatid ciliate revealing a discrepancy between interphasic and cell divisional patterns (Ciliophora, Hypotricha). Eur J Protistol 2021; 79:125794. [PMID: 33975056 DOI: 10.1016/j.ejop.2021.125794] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/07/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The morphology, ontogenesis, and molecular phylogeny of a new ciliate, Gonostomum koreanum n. sp., discovered in a terrestrial moss sample from South Korea, were investigated. Morphologically, it is characterized by a gonostomatid oral apparatus, two macronuclear nodules, six frontoventral rows, the two rightmost of which (frontoventral rows V and VI) extend posteriorly to near pretransverse and transverse cirri, and three dorsal kineties each with a single caudal cirrus posteriorly. The new species is easily confused with members of the genus Metagonostomum because of the long frontoterminal cirral row but differs mainly in the de novo (vs. intrakinetal) origin of anlage VI, a character found only in Gonostomum and Paragonostomum. To solve the discrepancy between the interphasic and ontogenetic patterns, we additionally performed morphological and multigene analyses on three gonostomatid species, namely Gonostomum koreanum n. sp. and its morphologically (M. gonostomoida) and ontogenetically (G. kuehnelti) most similar species. The multigene analyses show that the new species is closely related to G. kuehnelti and the core gonostomatids consists of five groups based on the origin of the frontoventral rows.
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Affiliation(s)
- Atef Omar
- Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea; Department of Zoology, Al Azhar University, Assiut 71524, Egypt
| | - Ji Hye Moon
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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4
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Vďačný P, Foissner W. Morphology and ontogenesis of two new Hemiholosticha species (Ciliophora, Hypotrichia, Hemiholostichidae nov. fam.). Eur J Protistol 2020; 77:125763. [PMID: 33307357 DOI: 10.1016/j.ejop.2020.125763] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 11/29/2022]
Abstract
The morphology and ontogenesis of two new hypotrich ciliates, Hemiholosticha solitaria and Hemiholosticha germanica, were studied using live observation, protargol impregnation, and scanning electron microscopy. Both species share a medium-sized, almost globular body with a short anterior projection; two macronuclear nodules with a single micronucleus in between; a central contractile vacuole; three or four ventral, one postoral, one right and one left marginal cirral row; and three dorsal kineties extending along ribs. However, H. germanica is distinguished from congeners by a higher number of cirri in ventral rows R1 and R2 (3-6 vs. 2 cirri in each row). Hemiholosticha solitaria differs from congeners by having four (vs. three) ventral cirral rows and by the lack (vs. presence) of intracellular green algae. The ontogenesis of H. solitaria follows the H. pantanalensis mode in that (i) the oral primordium develops in a deep pouch and generates the first two cirral streaks in addition to adoral membranelles and undulating membranes, (ii) the undulating membrane anlage does not produce any cirri, and (iii) the longitudinal ventral cirral row R3 originates from two anlagen. The ontogenetic peculiarities along with the 18S rRNA gene phylogenies suggest classification of Hemiholosticha, Psilotrichides, and Urospinula into a new family, Hemiholostichidae.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Wilhelm Foissner
- Department of Biosciences, Faculty of Natural Sciences, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
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Xu J, Wilkinson M, Chen M, Zhang Q, Yang R, Yi Z. Concatenated data and dense taxon sampling clarify phylogeny and ecological transitions within Hypotricha. ZOOL SCR 2020. [DOI: 10.1111/zsc.12459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Mark Wilkinson
- Department of Life Sciences Natural History Museum London UK
| | - Miaoying Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Qi Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
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The affiliation of Hexasterias problematica and Halodinium verrucatum sp. nov. to ciliate cysts based on molecular phylogeny and cyst wall composition. Eur J Protistol 2018; 66:115-135. [DOI: 10.1016/j.ejop.2018.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 11/17/2022]
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Chen L, Wu W, El-Serehy HA, Hu X, Clamp JC. Morphology, morphogenesis, and phylogeny of an Anteholosticha intermedia (Ciliophora, Urostylida) population from the United States. Eur J Protistol 2018; 65:1-15. [DOI: 10.1016/j.ejop.2018.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
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8
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Park DS, Worthington S, Xi Z. Taxon sampling effects on the quantification and comparison of community phylogenetic diversity. Mol Ecol 2018; 27:1296-1308. [PMID: 29423927 DOI: 10.1111/mec.14520] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/12/2017] [Accepted: 01/02/2018] [Indexed: 11/26/2022]
Abstract
Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These "inferred community phylogenies" are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.
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Affiliation(s)
- Daniel S Park
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Steven Worthington
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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9
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Gao F, Huang J, Zhao Y, Li L, Liu W, Miao M, Zhang Q, Li J, Yi Z, El-Serehy HA, Warren A, Song W. Systematic studies on ciliates (Alveolata, Ciliophora) in China: Progress and achievements based on molecular information. Eur J Protistol 2017; 61:409-423. [DOI: 10.1016/j.ejop.2017.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/25/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
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10
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Integrative taxonomy of ciliates: Assessment of molecular phylogenetic content and morphological homology testing. Eur J Protistol 2017; 61:388-398. [DOI: 10.1016/j.ejop.2017.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/06/2017] [Indexed: 11/18/2022]
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11
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Selvatti AP, Galvão A, Pereira AG, Pedreira Gonzaga L, Russo CADM. An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae). Mol Biol Evol 2017; 34:483-499. [PMID: 28069777 DOI: 10.1093/molbev/msw250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.
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Affiliation(s)
- Alexandre Pedro Selvatti
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Ana Galvão
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anieli Guirro Pereira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Luiz Pedreira Gonzaga
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Lu BR, Ma MZ, Gao F, Shi YH, Chen XR. Morphology and molecular phylogeny of two colepid species from China, Coleps amphacanthus Ehrenberg, 1833 and Levicoleps biwae jejuensis Chen et al., 2016 (Ciliophora, Prostomatida). DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2017; 37:176-85. [PMID: 27265656 DOI: 10.13918/j.issn.2095-8137.2016.3.176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Two colepid ciliates, Coleps amphacanthus Ehrenberg, 1833 and Levicoleps biwae jejuensis Chen et al., 2016, were first recorded in China. Their living morphology, infraciliature and small subunit (SSU) rRNA gene sequences were determined using standard methods. The improved diagnosis of Coleps amphacanthus is as follows:cell size about 100×50 μm in vivo, barrel-shaped; 22-28 ciliary rows each composed of about 14-21 monokinetids and two perioral dikinetids; 5-10 caudal cilia; and one terminal contractile vacuole. Levicoleps biwae jejuensis was also investigated, with an improved diagnosis given based on previous and present work. The phylogenetic analyses based on SSU rRNA gene sequences revealed that all Coleps species were grouped together, except for Coleps amphacanthus, which was grouped into a clade of the genus Levicoleps.
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Affiliation(s)
- Bo-Rong Lu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Ming-Zhen Ma
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Yu-Hong Shi
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiang-Rui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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13
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Chen L, Zhao X, Shao C, Miao M, Clamp JC. Morphology and phylogeny of two new ciliates, Sterkiella sinica sp. nov. and Rubrioxytricha tsinlingensis sp. nov. (Protozoa, Ciliophora, Hypotrichia) from north-west China. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1219426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lingyun Chen
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaolu Zhao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Chen Shao
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - John C. Clamp
- Department of Biology, North Carolina Central University, Durham, 1801 Fayetteville St., North Carolina 27707, USA
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14
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Mordret S, Romac S, Henry N, Colin S, Carmichael M, Berney C, Audic S, Richter DJ, Pochon X, de Vargas C, Decelle J. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.). THE ISME JOURNAL 2016; 10:1424-36. [PMID: 26684730 PMCID: PMC5029185 DOI: 10.1038/ismej.2015.211] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 12/11/2022]
Abstract
Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.
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Affiliation(s)
- Solenn Mordret
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Sarah Romac
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Henry
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Sébastien Colin
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Margaux Carmichael
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Cédric Berney
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Audic
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Daniel J Richter
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Colomban de Vargas
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Johan Decelle
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
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Gao F, Warren A, Zhang Q, Gong J, Miao M, Sun P, Xu D, Huang J, Yi Z, Song W. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata). Sci Rep 2016; 6:24874. [PMID: 27126745 PMCID: PMC4850378 DOI: 10.1038/srep24874] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/05/2016] [Indexed: 11/17/2022] Open
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.
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Affiliation(s)
- Feng Gao
- Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Miao Miao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Weibo Song
- Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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16
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Tekle YI. DNA barcoding in amoebozoa and challenges: the example of Cochliopodium. Protist 2014; 165:473-84. [PMID: 24945930 DOI: 10.1016/j.protis.2014.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/15/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022]
Abstract
The diversity of microbial eukaryotes in general and amoeboid lineages in particular is poorly documented. Even though amoeboid lineages are among the most abundant microbes, taxonomic progress in the group has been hindered by the limitations of traditional taxonomy and technical difficultly in studying them. Studies using molecular approaches such as DNA barcoding with cytochrome oxidase I (COI) gene are slowly trickling in for Amoebozoa, and they hopefully will aid in unveiling the true diversity of the group. In this study a retrospective approach is used to test the utility of COI gene in a scale-bearing amoeba, Cochliopodium, which is morphologically well defined. A total of 126 COI sequences and 62 unique haplotypes were generated from 9 Cochliopodium species. Extensive analyses exploring effects of sequence evolution models and length of sequence on genetic diversity computations were conducted. The findings show that COI is a promising marker for Cochliopodium, except in one case where it failed to delineate two morphologically well-defined cochliopodiums. Two species delimitation approaches also recognize 8 genetic lineages out of 9 species examined. The taxonomic implications of these findings and factors that may confound COI as a barcode marker in Cochliopodium and other amoebae are discussed.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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17
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Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Stock A, Kauff F, Stoeck T. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol 2014; 31:993-1009. [PMID: 24473288 DOI: 10.1093/molbev/msu055] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
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Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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18
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Zhang Q, Yi Z, Fan X, Warren A, Gong J, Song W. Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora). Mol Phylogenet Evol 2014; 70:162-70. [DOI: 10.1016/j.ympev.2013.09.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 10/26/2022]
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19
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Yi Z, Strüder-Kypke M, Hu X, Lin X, Song W. Sampling strategies for improving tree accuracy and phylogenetic analyses: a case study in ciliate protists, with notes on the genus Paramecium. Mol Phylogenet Evol 2013; 71:142-8. [PMID: 24315865 DOI: 10.1016/j.ympev.2013.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 11/20/2013] [Accepted: 11/24/2013] [Indexed: 11/28/2022]
Abstract
In order to assess how dataset-selection for multi-gene analyses affects the accuracy of inferred phylogenetic trees in ciliates, we chose five genes and the genus Paramecium, one of the most widely used model protist genera, and compared tree topologies of the single- and multi-gene analyses. Our empirical study shows that: (1) Using multiple genes improves phylogenetic accuracy, even when their one-gene topologies are in conflict with each other. (2) The impact of missing data on phylogenetic accuracy is ambiguous: resolution power and topological similarity, but not number of represented taxa, are the most important criteria of a dataset for inclusion in concatenated analyses. (3) As an example, we tested the three classification models of the genus Paramecium with a multi-gene based approach, and only the monophyly of the subgenus Paramecium is supported.
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Affiliation(s)
- Zhenzhen Yi
- Key Laboratory of Ecology and Environment Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China; Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Michaela Strüder-Kypke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario NIG 2W1, Canada
| | - Xiaozhong Hu
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaofeng Lin
- Key Laboratory of Ecology and Environment Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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20
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Pan Y, Li J, Li L, Hu X, Al-Rasheid KA, Warren A. Ontogeny and molecular phylogeny of a new marine ciliate genus, Heterokeronopsis g. n. (Protozoa, Ciliophora, Hypotricha), with description of a new species. Eur J Protistol 2013; 49:298-311. [DOI: 10.1016/j.ejop.2012.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/16/2022]
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21
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Pan H, Gao F, Lin X, Warren A, Song W. Three New Loxophyllum
Species (Ciliophora: Pleurostomatida) from China with a Brief Review of the Marine and Brackish Loxophyllum
Species. J Eukaryot Microbiol 2012. [DOI: 10.1111/jeu.12005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongbo Pan
- Laboratory of Protozoology; Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education; South China Normal University; Guangzhou 510631 China
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
- College of Fisheries and Life science; Shanghai Ocean University; Shanghai 201306 China
| | - Feng Gao
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Xiaofeng Lin
- Laboratory of Protozoology; Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education; South China Normal University; Guangzhou 510631 China
| | - Alan Warren
- Department of Zoology; The Natural History Museum; Cromwell Road London SW7 5BD United Kingdom
| | - Weibo Song
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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22
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Assessing whether alpha-tubulin sequences are suitable for phylogenetic reconstruction of Ciliophora with insights into its evolution in euplotids. PLoS One 2012; 7:e40635. [PMID: 22808216 PMCID: PMC3393704 DOI: 10.1371/journal.pone.0040635] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/11/2012] [Indexed: 11/19/2022] Open
Abstract
The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA genealogies are not useful for resolution of some branches within Ciliophora. Since congruence between multiple loci is the best tool to determine evolutionary history, we assessed the usefulness of alpha-tubulin gene, a protein-coding gene that is frequently sequenced, for ciliate phylogeny. Here, we generate alpha-tubulin gene sequences of 12 genera and 30 species within the order Euplotida, one of the most frequently encountered ciliate clades with numerous apparently cosmopolitan species, as well as four genera within its putative sister order Discocephalida. Analyses of the resulting data reveal that: 1) the alpha-tubulin gene is suitable phylogenetic marker for euplotids at the family level, since both nucleotide and amino acid phylogenies recover all monophyletic euplotid families as defined by both morphological criteria and SSU-rDNA trees; however, alpha-tubulin gene is not a good marker for defining species, order and subclass; 2) for seven out of nine euplotid species for which paralogs are detected, gene duplication appears recent as paralogs are monophyletic; 3) the order Euplotida is non-monophyletic, and the family Uronychiidae with sequences from four genera, is non-monophyletic; and 4) there is more genetic diversity within the family Euplotidae than is evident from dargyrome (geometrical pattern of dorsal “silverline system” in ciliates) patterns, habit and SSU-rDNA phylogeny, which indicates the urgent need for taxonomic revision in this area.
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23
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Soares AE, Schrago CG. The influence of taxon sampling and tree shape on molecular dating: an empirical example from Mammalian mitochondrial genomes. Bioinform Biol Insights 2012; 6:129-43. [PMID: 22693422 PMCID: PMC3370833 DOI: 10.4137/bbi.s9677] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Over the last decade, molecular dating methods have been among the most studied subjects in statistical phylogenetics. Although the evolutionary modelling of substitution rates and the handling of calibration information are the primary focus of species divergence time research, parameters that influence topological estimation, such as taxon sampling and tree shape, also have the potential to influence evolutionary age estimates. However, the impact of topological parameters on chronological estimates is rarely considered. In this study, we use mitochondrial genomes to evaluate the influence of tree shape and taxon sampling on the divergence times of selected nodes of the mammalian tree. Our results show that taxon sampling affects divergence time estimates; the credibility intervals for age estimates decrease as taxonomic sampling increases (i.e., estimates become more precise). The influence of taxonomic sampling was not observed on nodes that lay deep in the mammalian phylogeny, although the means of the posterior distributions tend to converge with increased taxon sampling, an effect that is independent of the location of the node. In the majority of cases, the effect of tree shape was negligible.
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Affiliation(s)
- André E.R. Soares
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G. Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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24
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Zhou L, Li J, Lin X, Al-Rasheid KAS. Use of RAPD to detect DNA damage induced by nitrofurazone in marine ciliate, Euplotes vannus (Protozoa, Ciliophora). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2011; 103:225-232. [PMID: 21481819 DOI: 10.1016/j.aquatox.2011.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 03/02/2011] [Accepted: 03/07/2011] [Indexed: 05/30/2023]
Abstract
The random amplified polymorphic DNA (RAPD) assay was evaluated as a potential tool to detect the ecotoxicity induced by nitrofurazone in marine ciliate, Euplotes vannus. The data revealed a reduction in viability of the test ciliates with increasing nitrofurazone concentration in the range of 0-24 mgl(-1) and time of exposure from 24 to 96 h. The nitrofurazone treated ciliates were subjected to DNA damage analysis by RAPD assay. Among the 33 test RAPD primers used in this study, 11 primers with 60-70% GC content produced unique polymorphic band patterns. A total of 213 bands of 155-3317 bp in molecular size range were observed in the untreated cells. In comparison with the control ciliates, the nitrofurazone treated groups showed differences in RAPD profiles with respect to the band intensity, disappearance of bands and appearance of new bands of amplified DNA. The variation of RAPD profiles showed both the time- and concentration-dependent relationships. The data suggested significant genomic template instability, which corresponds well with the viability of the test ciliates. Thus the results demonstrated the potential of the RAPD assay for application as a powerful tool for detecting genotoxicity induced by fishy drugs in aquatic environment.
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Affiliation(s)
- Liang Zhou
- Laboratory of Protozoology, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou 510631, Guangdong, China
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25
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Chen X, Gao S, Liu W, Song W, Al-Rasheid KAS, Warren A. Taxonomic descriptions of three marine colepid ciliates, Nolandia sinica spec. nov., Apocoleps caoi spec. nov. and Tiarina fusa (Claparede & Lachmann, 1858) Bergh, 1881 (Ciliophora, Prorodontida). Int J Syst Evol Microbiol 2011; 62:735-744. [PMID: 21515708 DOI: 10.1099/ijs.0.026302-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The morphology of three marine colepid ciliates, Nolandia sinica spec. nov., Apocoleps caoi spec. nov. and Tiarina fusa (Claparède & Lachmann, 1858) Bergh, 1881, isolated from Chinese coastal waters, was investigated. N. sinica spec. nov. may be separated from its congeners by the structure of its armour plates, each of which may have up to five reniform windows. A. caoi spec. nov. is characterized by its large body with broad anterior end and by having 10-12 long, sharp posterior spines. New data and an improved diagnosis are supplied for Tiarina fusa (Claparède & Lachmann, 1858) Bergh, 1881, which has a spindle-shaped body, about 16 ciliary rows and a single adoral organelle. Sequence similarities with other available colepid species were determined.
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Affiliation(s)
- Xiangrui Chen
- College of Life Science and Biotechnology, Ningbo University, Ningbo 315211, PR China.,Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Shan Gao
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Weiwei Liu
- Laboratory of Protozoology, South China Normal University, Guangzhou 510631, PR China
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | | | - Alan Warren
- Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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