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Song W, Jiao H, Yang J, Tang D, Ye T, Li L, Yang L, Li L, Song W, Al-Farraj SA, Hines HN, Liu W, Chen X. New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora). Mol Phylogenet Evol 2023; 188:107911. [PMID: 37648182 DOI: 10.1016/j.ympev.2023.107911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.
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Affiliation(s)
- Wen Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Huixin Jiao
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Juan Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Danxu Tang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Tingting Ye
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lu Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lei Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hunter N Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China.
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Suzhou Research Institute of Shandong University, Suzhou 215123, China.
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Song W, Xu D, Chen X, Warren A, Shin MK, Song W, Li L. Overview of the Diversity, Phylogeny and Biogeography of Strombidiid Oligotrich Ciliates (Protista, Ciliophora), With a Brief Revision and a Key to the Known Genera. Front Microbiol 2021; 12:700940. [PMID: 34603227 PMCID: PMC8481829 DOI: 10.3389/fmicb.2021.700940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids.
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Affiliation(s)
- Wen Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, South Korea
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
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Küppers GC, da Silva Paiva T, do Nascimento Borges B, Alfaro ER, Claps MC. A new oligotrich (Ciliophora, Oligotrichia) from Argentina, with redefinition of Novistrombidium Song and Bradbury. Eur J Protistol 2019; 69:20-36. [PMID: 30870724 DOI: 10.1016/j.ejop.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 02/05/2019] [Accepted: 02/11/2019] [Indexed: 11/27/2022]
Abstract
A new oligotrich similar to Novistrombidium was discovered in plankton samples from an artificial tributary of the Salado River, Buenos Aires province, Argentina, in summer 2010. Propecingulum fistoleramalliei sp. n. has an obovate and anteriorly truncated body, with a conspicuous ventral furrow, is flattened ventrally, and has a prominent right apical protrusion. It temporarily attaches to the substratum by a posterior mucous thread. Rod-shaped extrusomes arranged equidistantly and insert directly above the girdle kinety. The macronucleus is globular to ellipsoidal. The contractile vacuole is located in the left, anterior quarter of the cell and the adoral zone is composed of 30-35 collar, 9-14 buccal, and two thigmotactic membranelles. The girdle kinety is dextrally spiraled and ventrally open; the ventral kinety is posterior to anterior end of the girdle kinety. The oral primordium develops posterior to the right thigmotactic membranelle and anterior the stripe of extrusomes above left, lateral portion of the girdle kinety. The SSUrDNA phylogeny confirms one more time that Novistrombidium is not monophyletic; consequently, we elevate the subgenus Propecingulum up to genus rank and redefine the genus Novistrombidium.
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Affiliation(s)
- Gabriela Cristina Küppers
- División Invertebrados, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina.
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Bárbara do Nascimento Borges
- Laboratório de Biologia Molecular "Francisco Mauro Salzano", Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Elisa Raquel Alfaro
- División Invertebrados, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - María Cristina Claps
- Instituto de Limnología "Dr. R. A. Ringuelet", La Plata, Buenos Aires, Argentina
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Gao F, Li J, Song W, Xu D, Warren A, Yi Z, Gao S. Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora). Mol Phylogenet Evol 2016; 105:241-50. [PMID: 27582373 DOI: 10.1016/j.ympev.2016.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/17/2016] [Accepted: 08/26/2016] [Indexed: 11/23/2022]
Abstract
Phylogenetic analyses of ciliated protists are frequently based on single molecular markers, usually the small subunit ribosomal RNA gene (SSU rDNA), despite the well-known limitations of this approach. Here, 78 new sequences of three linked genes (SSU rDNA, ITS1-5.8S rDNA-ITS2, LSU rDNA) were characterized and applied to phylogenetic analyses of oligotrichs (s. str.). It was found that: (1) three taxa, that is tontoniids, pelagostrombidiids and cyrtostrombidiids should be split from the family Strombidiidae (s. l.), which supports Agatha's classification based on morphological characters; (2) the families Tontoniidae and Cyrtostrombidiidae are both monophyletic whereas Strombidiidae is polyphyletic; (3) the positions of the families Cyrtostrombidiidae and Pelagostrombidiidae varied in different trees although with low support values; (4) the close relationship between Varistrombidium and Apostrombidium is confirmed, which updates the evolutionary hypothesis for oligotrichs based on ciliary patterns; and (5) two relatively stable clades were found in the family Strombidiidae.
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