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Chi Y, Wei F, Tang D, Mu C, Ma H, Wang Z, Al-Rasheid KAS, Hines HN, Chen X. Exploring the biogeography, morphology, and phylogeny of the condylostomatid ciliates (Alveolata, Ciliophora, Heterotrichea), with establishment of four new Condylostoma species and a revision including redescriptions of five species found in China. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:365-404. [PMID: 39219685 PMCID: PMC11358585 DOI: 10.1007/s42995-024-00223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/12/2024] [Indexed: 09/04/2024]
Abstract
Species of the ciliate class Heterotrichea Stein, 1859 are a cosmopolitan group of unicellular eukaryotic microorganisms, many of which have been widely used as models in various fields of research such as regenerative biology, functional ecology, environmental toxicology, and symbiotic behavior. However, species identification in the heterotrich family Condylostomatidae, especially the most species-rich and type genus Condylostoma Bory de Saint-Vincent, 1824, remains challenging due to incomplete original descriptions, few reliable distinguishing characters, and overlapping features between different species. This study presents an updated revision of Condylostoma and its related genus Condylostomides da Silva Neto, 1994 based on descriptions of five species, including nine populations collected from China, using both morphological and molecular methods. The main findings are as follows: (1) 43 nominal species and about 130 populations are reviewed, resulting in the recognition of 30 valid species of Condylostoma and eight valid species of Condylostomides; (2) keys, synonyms, biogeographic distributions and amended/improved diagnoses of all valid species are provided; (3) based on the available data, four new Condylostoma species (C. marinum sp. nov., C. petzi sp. nov., C. villeneuvei sp. nov., and C. microstomum sp. nov.), one new combination (Condylostomides minimus (Dragesco, 1954) comb. nov. & nom. corr.), and two corrected names (Condylostoma ancestrale Villeneuve-Brachon, 1940 nom. corr. and Condylostomides nigrus (Dragesco, 1960) nom. corr.) are suggested; (4) cryptic species are detected and proposed for the first time to form the Condylostoma curvum species complex; (5) three highly confusing Condylostoma species, C. kris, C. spatiosum, and C. minutum, are redefined for the first time based on modern taxonomic methods; (6) a 'flagship' species, Condylostomides coeruleus, is recorded for the first time from the continent of Asia, substantially expanding its biogeography; (7) ciliature adjacent to the distal end of the paroral membrane within the family Condylostomatidae is uniformly defined as frontal membranelles and is classified into three patterns according to the arrangement of kinetosomes, which serve as important key features. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00223-3.
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Affiliation(s)
- Yong Chi
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
- Institute of Evolution & Marine Biodiversity, and Key Laboratory of Evolution & Marine Biodiversity (Education Ministry), Ocean University of China, Qingdao, 266003 China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, and Key Laboratory of Evolution & Marine Biodiversity (Education Ministry), Ocean University of China, Qingdao, 266003 China
| | - Danxu Tang
- Marine College, Shandong University, Weihai, 264209 China
| | - Changjun Mu
- Weishan Special Aquaculture Base, Jining, 277600 China
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and Key Laboratory of Evolution & Marine Biodiversity (Education Ministry), Ocean University of China, Qingdao, 266003 China
| | - Zhe Wang
- Institute of Evolution & Marine Biodiversity, and Key Laboratory of Evolution & Marine Biodiversity (Education Ministry), Ocean University of China, Qingdao, 266003 China
| | | | - Hunter N. Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Florida, 34946 USA
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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Wang Z, Chi Y, Li T, Song W, Wang Y, Wu T, Zhang G, Liu Y, Ma H, Song W, Al-Rasheid KAS, Warren A, Lu B. Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:429-451. [PMID: 37078082 PMCID: PMC10077249 DOI: 10.1007/s42995-022-00154-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/20/2022] [Indexed: 05/02/2023]
Abstract
Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited. To address this issue, a project to investigate the freshwater ciliates of the Lake Weishan Wetland, Shandong Province, commenced in 2019. Here, we summarize our findings to date on the diversity of ciliates. A total of 187 ciliate species have been found, 94 of which are identified to species-level, 87 to genus-level, and six to family-level. These species show a high morphological diversity and represent five classes, i.e., Heterotrichea, Litostomatea, Prostomatea, Oligohymenophorea, and Spirotrichea. The largest number of species documented are oligohymenophoreans. A comprehensive database of these ciliates, including morphological data, gene sequences, microscope slide specimens and a DNA bank, has been established. In the present study, we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species. Most of these species are recorded in China for the first time and more than 20% are tentatively identified as new to science. Additionally, an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00154-x.
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Affiliation(s)
- Zhe Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Yong Chi
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Wenya Song
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yunfeng Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tong Wu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Gongaote Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yujie Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Honggang Ma
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Weibo Song
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Marine College, Shandong University, Weihai, 264209 China
- Laoshan Laboratory, Qingdao, 266237 China
| | | | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Borong Lu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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4
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Ye T, Jiang Y, Chen S, Xu Y, Li L, Shin MK, Chen X. The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:471-492. [PMID: 37078084 PMCID: PMC10077228 DOI: 10.1007/s42995-022-00152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/17/2022] [Indexed: 05/03/2023]
Abstract
Ciliates of the heterotrich family Folliculinidae are widespread in various habitats and are distinguished by their transparent loricae of various shapes, conspicuous peristomial lobes, and dimorphic life cycles. They usually attach firmly to the surface of substrates, feed on bacteria and microalgae, and play a significant role in energy flow and material cycling in the microbial food web. However, little is known regarding their biodiversity and systematics. In this work, we establish the terminology of the family Folliculinidae and select six crucial features for genus recognition. Based on previous studies, we revise the classification of Folliculinidae, supply improved diagnoses for each of the 33 folliculinid genera, and provide a key to their identification. Moreover, phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences revealed that the family is monophyletic and comprises two subclades (subclades I II) which can be identified by the flexibility of their peristomial lobes and the sculpturing of their necks. Furthermore, we investigate the evolutionary relationships of folliculinids using the six chosen generic features. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00152-z.
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Affiliation(s)
- Tingting Ye
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Yaohan Jiang
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Shuchang Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
| | - Yixiang Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan, 44610 South Korea
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
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5
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Hao T, Li B, Song Y, Warren A, Pan X. Taxonomy and molecular phylogeny of two new Blepharisma species (Ciliophora, Heterotrichea) from northeastern china. Eur J Protistol 2022; 85:125908. [DOI: 10.1016/j.ejop.2022.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
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6
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Ahsan R, Blanche W, Katz LA. Macronuclear development in ciliates, with a focus on nuclear architecture. J Eukaryot Microbiol 2022; 69:e12898. [PMID: 35178799 DOI: 10.1111/jeu.12898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei varies tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in sexual cycle), the germline micronucleus is transcriptionally-inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally-active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively-fragmented gene-sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes.
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Affiliation(s)
- Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
| | - Wumei Blanche
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
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7
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Ma M, Li Y, Maurer-Alcalá XX, Wang Y, Yan Y. Deciphering phylogenetic relationships in class Karyorelictea (Protista, Ciliophora) based on updated multi-gene information with establishment of a new order Wilbertomorphida n. ord. Mol Phylogenet Evol 2022; 169:107406. [PMID: 35031457 DOI: 10.1016/j.ympev.2022.107406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/07/2021] [Accepted: 01/01/2022] [Indexed: 10/19/2022]
Abstract
The class Karyorelictea, a unique assemblage of ciliates, is a key group in deciphering ciliate evolution history. However, the systematic relationships among members of this class remain poorly understood. Here we newly obtained eight small subunit (SSU) rDNA, 24 large subunit (LSU) rDNA, and 25 ITS1-5.8S-ITS2 sequences (covering 25 species, 10 genera and 4 out of 6 families) to analyze the phylogenetic relationships within Karyorelictea. Our results indicate that: (1) considering its unique morphology and early branching position in the SSU rDNA-based tree, the family Wilbertomorphidae represents a new taxon at order level, hence the new order Wilbertomorphida n. ord. is established; (2) all five families with available molecular information are monophyletic, as expected, and the orders Loxodida and Protostomatida show a closer relationship than with Protoheterotrichida; (3) in Trachelocercidae, the compound circumoral kineties is believed to be a plesiomorphic feature while the single circumoral kinety is synapomorphic; and (4) the freshwater genus Loxodes could be derived from the marine Remanella and both share most morphological features. Taken together, these muti-gene analyses provide further insights into the phylogeny of the diverse clades in Karyorelictea.
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Affiliation(s)
- Mingzhen Ma
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuqing Li
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland; Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Ying Yan
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Morphology, Life Cycle, and SSU rDNA-based Phylogeny of Two Folliculinid Ciliates (Ciliophora, Heterotrichea, Folliculinidae) Collected from Subtropical Coastal Wetlands of China. Protist 2021; 172:125844. [PMID: 34916151 DOI: 10.1016/j.protis.2021.125844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
Most ciliates of the heterotrich family Folliculinidae are flagship periphytic species. They are characterized by their transparent lorica, conspicuous peristomial lobes, and dimorphic life cycle. However, the understanding of their biodiversity and systematics is relatively poor. In the present study, we investigate the morphology and phylogenetic affinities of Ampullofolliculina lageniformis Hadži, 1951 and Metafolliculina producta (Wright, 1859) Dons, 1934, collected from subtropical coastal wetlands in China. An integrative approach combining investigations of their morphology, life cycle and ecology was used. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences showed that: all folliculinid genera form a monophyletic clade; the two genera with flexible peristomial lobes, Metafolliculina and Eufolliculina, are closely related; the other three genera with inflexible peristomial lobes, Ampullofolliculina, Diafolliculina and Folliculina, group together.
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9
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Jin D, Zhao X, Ye T, Huang J, Warren A, Al-Farraj SA, Chen X. Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp. Front Microbiol 2021; 12:719360. [PMID: 34557172 PMCID: PMC8453171 DOI: 10.3389/fmicb.2021.719360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/06/2021] [Indexed: 11/25/2022] Open
Abstract
The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48-67, mean about 56 vs. 26-51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.
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Affiliation(s)
- Didi Jin
- School of Marine Sciences, Ningbo University, Ningbo, China
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xuetong Zhao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Tingting Ye
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Saleh A. Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, China
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10
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Campello-Nunes PH, Fernández LD, Paiva TS, Soares CAG, Silva-Neto ID, Fernandes NM. Macronuclear Plasticity in Two South American Populations of Spirostomum (Ciliophora, Heterotrichea) Warns About its Use for Species Classification: Revision and New Insights. Protist 2021; 172:125803. [PMID: 33940500 DOI: 10.1016/j.protis.2021.125803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 11/15/2022]
Abstract
Spirostomum is a widely distributed heterotrichean genus composed of well-known species with described ecology and phylogenetic affinities. The morphological classification of Spirostomum species is mostly based on the body size/shape, number of cortical granule rows and macronuclear characteristics. These features along with molecular phylogenies based on ribosomal genes divide the genus into two phylogroups, one including species with a compact macronucleus, and another including species with a moniliform macronucleus. Here, we present our observations on atypical Spirostomum specimens with unusually two distinct macronuclei and shortened adoral zone of membranelles. These atypical forms appeared in the cultures of S. minus and S. yagiui, sampled at different sites in South America (Chile and Brazil) and associated with unrelated substrate types. Morphological observations of living and stained cells, 18S rRNA gene analyses, and a thorough investigation of the literature suggest that the atypical phenotype may be a result of uncommon pathways during the conjugative process. Thus, we demonstrate that studies of ciliate natural populations and their morphological variations, especially from undersampled biogeographical regions, can reveal the boundaries of widely used morphological characters for Spirostomum taxonomy and species identification.
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Affiliation(s)
- Pedro H Campello-Nunes
- Laboratório de Protistologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | - Thiago S Paiva
- Laboratório de Protistologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil
| | - Carlos A G Soares
- Laboratório de Genética Molecular de Eucariontes e Simbiontes, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil
| | - Inácio D Silva-Neto
- Laboratório de Protistologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil
| | - Noemi M Fernandes
- Laboratório de Protistologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil.
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Hoshina R, Tsukii Y, Harumoto T, Suzaki T. Characterization of a green Stentor with symbiotic algae growing in an extremely oligotrophic environment and storing large amounts of starch granules in its cytoplasm. Sci Rep 2021; 11:2865. [PMID: 33536497 PMCID: PMC7859197 DOI: 10.1038/s41598-021-82416-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The genus Stentor is a relatively well-known ciliate owing to its lucid trumpet shape. Stentor pyriformis represents a green, short, and fat Stentor, but it is a little-known species. We investigated 124 ponds and wetlands in Japan and confirmed the presence of S. pyriformis at 23 locations. All these ponds were noticeably oligotrophic. With the improvement of oligotrophic culture conditions, we succeeded in long-term cultivation of three strains of S. pyriformis. The cytoplasm of S. piriformis contains a large number of 1-3 μm refractive granules that turn brown by Lugol's staining. The granules also show a typical Maltese-cross pattern by polarization microscopy, strongly suggesting that the granules are made of amylopectin-rich starch. By analyzing the algal rDNA, it was found that all S. pyriformis symbionts investigated in this study were Chlorella variabilis. This species is known as the symbiont of Paramecium bursaria and is physiologically specialized for endosymbiosis. Genetic discrepancies between C. variabilis of S. pyriformis and P. bursaria may indicate that algal sharing was an old incident. Having symbiotic algae and storing carbohydrate granules in the cytoplasm is considered a powerful strategy for this ciliate to withstand oligotrophic and cold winter environments in highland bogs.
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Affiliation(s)
- Ryo Hoshina
- grid.419056.f0000 0004 1793 2541Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829 Japan
| | - Yuuji Tsukii
- grid.257114.40000 0004 1762 1436Laboratory of Biological Science, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo 102-8160 Japan
| | - Terue Harumoto
- grid.174568.90000 0001 0059 3836Research Group of Biological Sciences, Division of Natural Sciences, Nara Women’s University, Kitauoya-Nishimachi, Nara 630-8506 Japan
| | - Toshinobu Suzaki
- grid.31432.370000 0001 1092 3077Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 Japan
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12
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Mukhtar I, Wu S, Wei S, Chen R, Cheng Y, Liang C, Chen J. Transcriptome Profiling Revealed Multiple rquA Genes in the Species of Spirostomum (Protozoa: Ciliophora: Heterotrichea). Front Microbiol 2021; 11:574285. [PMID: 33469448 PMCID: PMC7813818 DOI: 10.3389/fmicb.2020.574285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Adaptation to life at different oxygen tensions plays a role in protozoan ecology and controls the distribution of different species in anoxic habitats. The ciliate genus Spirostomum inhabiting fresh or low salinity water globally where these species are considered as bioindicators. Under anaerobic or low oxygen conditions, the rhodoquinol-dependent pathway has been reported in the species from the class Heterotrichea. With the help of RNA sequencing (RNAseq) data, Spirostomum spp., are suitable for deep molecular investigations on rquA for rhodoquinone (RQ) biosynthesis. In this study, Spirostomum ambiguum, Spirostomum subtilis, and Spirostomum teres collected from densely vegetated freshwater habitat in Fuzhou, China, explored the evidence of rquA. Based on transcriptome analysis, two to three RquA proteins were identified in S. ambiguum, S. teres, and S. subtilis, respectively. The presence of a key Motif-I of RquA and mitochondrial targeting signals (MTS), also confirmed the identity of these as RquA. Furthermore, Spirostomum RquA proteins could be sorted into two groups based on their conserved amino acid (CAA) residues. Phylogenetic analysis also exhibited RquA division into two subclades contained RquA1 and RquA2/RquA3 and supports two to three paralogs of rquA genes in the genomes Spirostomum spp. Additional transcriptomes and genomes analysis of Blepharisma spp., and Stentor spp., respectively, also revealed at least two paralogs of rquA in members of the class Heterotrichea. The present study provides evidence for the presence of RquA and rhodoquinol dependent fumarate reduction pathway in Spirostomum species potentially use to respire in the oxygen-depleted habitats and two to three diverse rquA genes.
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Affiliation(s)
- Irum Mukhtar
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Siyi Wu
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Shurong Wei
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Ruanni Chen
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Yunying Cheng
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Chen Liang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jianming Chen
- Institute of Oceanography, Minjiang University, Fuzhou, China
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13
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New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses. SCIENCE CHINA-LIFE SCIENCES 2020; 64:606-620. [PMID: 33068287 DOI: 10.1007/s11427-020-1817-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/06/2020] [Indexed: 01/15/2023]
Abstract
Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology, regenerative biology, and toxicology. In the present study, we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea. The main results include: (1) 96 new ribosomal DNA sequences from 36 populations, representing eight families and 13 genera, including three poorly annotated genera, Folliculinopsis, Ampullofolliculina and Linostomella; (2) the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree, but the family Peritromidae probably represents the basal lineage based on its possession of many "primitive" morphological characters; (3) some findings in molecular trees are not supported by morphological evidence, such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close; (4) the systematic positions of Condylostomatidae, Climacostomidae, and Gruberiidae remain uncertain based either on morphological or molecular data; and (5) the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees, except for Blepharisma in the SSU rDNA tree and Folliculina in the ITS1-5.8S-ITS2 tree.
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14
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Chi Y, Li Y, Zhang Q, Ma M, Warren A, Chen X, Song W. New contributions to two ciliate genera (Ciliophora, Heterotrichea) based on morphological and molecular analyses, with description of a new Gruberia species. BMC Microbiol 2020; 20:297. [PMID: 33008292 PMCID: PMC7531149 DOI: 10.1186/s12866-020-01879-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heterotrichous ciliates are common members of microeukaryote communities which play important roles in both the transfer of material and the flow of energy in aquatic food webs. This group has been known for over two centuries due to their large body size and cosmopolitan distribution. Nevertheless, species identification and phylogenetic relationships of heterotrichs remain challenging due to the lack of accurate morphological information and insufficient molecular data. RESULTS The morphology and phylogeny of two heterotrichous ciliates, namely Gruberia foissneri spec. nov. and Linostomella vorticella (Ehrenberg, 1833) Aescht in Foissner et al., 1999, were studied using rigorous methods (living morphology, stained preparations, and small subunit rDNA sequence data). Gruberia foissneri spec. nov. is morphologically very similar to G. uninucleata Kahl, 1932, however, it can be distinguished from the latter by having more ciliary rows (about 32 vs. about 20) and macronuclear shape (sausage-shaped vs. ellipsoid). Based on a combination of previous and present studies, an improved diagnosis of L. vorticella is supplied and several taxonomic anomalies are clarified. In addition, phylogenetic analyses based on SSU rDNA sequence data support the generic assignment of these two species. CONCLUSIONS Modern ciliate taxonomy should be performed by means of detailed living observation, stained preparations and molecular information. For those species that have been reported in previous studies, it is necessary to provide as much useful information as possible using state-of-the-art methods in order to resolve taxonomic anomalies.
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Affiliation(s)
- Yong Chi
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Yuqing Li
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Mingzhen Ma
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Weibo Song
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.
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15
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Kabir AS, Bharti D, Kumar S, Shazib SUA, Shin MK. Redescription of Rigidohymena inquieta (Stokes, 1887) Berger, 2011 as Metahymena inquieta gen. nov., comb. nov. (Ciliophora, Hypotricha) Based on Morphology, Morphogenesis, and Molecular Phylogeny. J Eukaryot Microbiol 2020; 67:541-554. [PMID: 32396978 DOI: 10.1111/jeu.12801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 11/28/2022]
Abstract
The morphology and morphogenesis of Rigidohymena inquieta (Stokes, 1887) Berger, 2011, isolated from a lawn soil in the campus of the University of Ulsan, Korea, was studied, using live observation and protargol impregnation. The molecular phylogeny was studied based on the SSU rRNA gene sequences. The morphology of the Korean population of R. inquieta matches the previously known populations; however, the morphogenetic pattern shows differences to the species R. candens in the involvement of cirrus V/3 in the anlagen formation. A novel genus namely Metahymena gen. nov. has been erected for the present species based on the ontogenetic difference, and the new combination Metahymena inquieta gen. nov., comb. nov. is proposed. The morphology, morphogenesis, distribution, and phylogeny of M. inquieta are presented. The morphologic and morphogenetic data corroborate the phylogenetic analyses as M. inquieta clusters among the stylonychid ciliates in a clade distant from Rigidohymena candens.
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Affiliation(s)
- Ahmed Salahuddin Kabir
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan, 44610, South Korea
| | - Daizy Bharti
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan, 44610, South Korea.,Zoological Survey of India, Prani Vigyan Bhawan, M-Block, New Alipore, Kolkata, 700053, India
| | - Santosh Kumar
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan, 44610, South Korea.,Zoological Survey of India, Prani Vigyan Bhawan, M-Block, New Alipore, Kolkata, 700053, India
| | - Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan, 44610, South Korea
| | - Mann Kyoon Shin
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan, 44610, South Korea
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16
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Campello-Nunes PH, Fernandes NM, Szokoli F, Fokin SI, Serra V, Modeo L, Petroni G, Soares CA, Paiva TDS, Silva-Neto IDD. Parablepharisma (Ciliophora) is not a Heterotrich: A Phylogenetic and Morphological Study with the Proposal of New Taxa. Protist 2020; 171:125716. [DOI: 10.1016/j.protis.2020.125716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 12/13/2022]
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17
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Chi Y, Duan L, Luo X, Cheng T, Warren A, Huang J, Chen X. A new contribution to the taxonomy and molecular phylogeny of three, well-known freshwater species of the ciliate genus Spirostomum (Protozoa: Ciliophora: Heterotrichea). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz115] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractMembers of the heterotrich genus Spirostomum are commonly found in freshwater or low salinity biotopes. In the present study, three species (S. minus, S. subtilis and S. teres) collected from freshwater habitats in Qingdao, China, are investigated using morphological and molecular methods. Detailed morphometric data are documented and improved diagnosis are supplied based on a combination of previous and present studies. In addition, small subunit ribosomal DNA (SSU rDNA) sequences are obtained from the clonal cultures. Phylogenetic analyses show that all three species are placed in the Spirostomum clade. However, isolates of the morphospecies S. minus are divided into two paraphyletic clades, while ‘populations’ of the nominal species, S. teres, are placed in at least four separate groups in the tree. After comparing morphological and molecular differences in closely related forms available, we hypothesized that S. minus and S. teres might represent species complexes. A key to the identification of the ten valid species of Spirostomum is also supplied.
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Affiliation(s)
- Yong Chi
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Lili Duan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaotian Luo
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ting Cheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, China
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18
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Shazib SUA, Vďačný P, Slovák M, Gentekaki E, Shin MK. Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Sci Rep 2019; 9:16360. [PMID: 31704993 PMCID: PMC6841689 DOI: 10.1038/s41598-019-52722-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
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Affiliation(s)
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, 845 23, Bratislava, Slovakia.,Department of Botany, Charles University, 128 01, Prague, Czech Republic
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, 44610, South Korea.
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19
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Chen X, Li J, Xu K. Multigene‐based phylogeny analyses of the controversial family Condylostomatidae (Ciliophora, Heterotrichea). ZOOL SCR 2019. [DOI: 10.1111/zsc.12383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xumiao Chen
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao China
- Center for Ocean Mega‐Science Chinese Academy of Sciences Qingdao 266071 China
| | - Ju Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Kuidong Xu
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao China
- University of Chinese Academy of Sciences Beijing China
- Center for Ocean Mega‐Science Chinese Academy of Sciences Qingdao 266071 China
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20
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Luo J, Ma M, Lu B, Li X, Warren A, Shi Y, Chen X. The Taxonomy and Phylogeny of the Poorly known Heterotrich Ciliate Ampullofolliculina lageniformis Hadži, 1951 (Ciliophora: Heterotrichea). J Eukaryot Microbiol 2019; 66:925-936. [PMID: 31112318 DOI: 10.1111/jeu.12743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/29/2019] [Accepted: 05/14/2019] [Indexed: 11/27/2022]
Abstract
Ampullofolliculina Hadži, 1951 is a monotypic genus, the only species being A. lageniformis which was first discovered in estuarine habitats in the U.S. and has never been redescribed. In the present study, we investigated the taxonomy and phylogeny of A. lageniformis Hadži, 1951 based on analyses of a population collected from a brackish wetland in Ningbo, China. The main characteristics of this species are as follows: trophont about 450-700 μm long in vivo with two short, rounded peristomial lobes of equal size; lorica flask-shaped, transparent and smooth with a short, wide neck at the base of which two transparent valves are asymmetrically inserted; cortex with brownish to reddish cortical granules and greenish pigment granules; about 80 somatic kineties evenly arranged; moniliform macronucleus with 4-8 ellipsoidal nodules; swarmer dark green, vermiform in shape, about 200-350 μm long in vivo, with about 60 adoral membranelles and 85 somatic kineties, no mouth nor paroral membrane. Phylogenetic analyses inferred from SSU rDNA sequences show that A. lageniformis is closely related to Folliculina and Eufolliculina which nest within a large clade that comprises five families, i.e. Stentoridae, Blepharismidae, Fabreidae, Maristentoridae, and Folliculinidae.
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Affiliation(s)
- Jun Luo
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Mingzhen Ma
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Borong Lu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinghao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Yuhong Shi
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
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21
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Hines HN, Onsbring H, Ettema TJ, Esteban GF. Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records. Protist 2018; 169:875-886. [DOI: 10.1016/j.protis.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 11/26/2022]
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22
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Boscaro V, Santoferrara LF, Zhang Q, Gentekaki E, Syberg-Olsen MJ, Del Campo J, Keeling PJ. EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates. Environ Microbiol 2018; 20:2218-2230. [PMID: 29727060 DOI: 10.1111/1462-2920.14264] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Abstract
High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Luciana F Santoferrara
- Department of Marine Sciences, University of Connecticut, Stamford, CT, USA.,Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, USA
| | - Qianqian Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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23
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Campello-Nunes PH, Fernandes NM, Szokoli F, Petroni G, da Silva-Neto ID. Morphology and Phylogenetic Position of Gruberia lanceolata (Gruber 1884) (Ciliophora, Heterotrichea) from Rio de Janeiro, Brazil. J Eukaryot Microbiol 2018; 65:902-912. [PMID: 29779265 DOI: 10.1111/jeu.12636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022]
Abstract
Ciliates of the genus Gruberia are poorly studied. Consequently, most species lack detailed morphological descriptions, and all gene sequences in GenBank are not classified at the species level. In this study, a detailed morphological description of a population of G. lanceolata from Brazil is presented, based on live and protargol-stained organisms. We also present the 18S rRNA gene sequence and the phylogenetic position of this species. The primary characteristics of G. lanceolata from the Maricá Lagoon are as follows: an elongate fusiform body 280-870 × 40-160 μm in size; rosy cortical granules; a peristome occupying approximately 1/3-1/2 of body length; an adoral zone comprising 115-330 membranelles; a paroral membrane in 35-50 fragments; and a moniliform macronucleus with 11-16 nodules. Based on our observations and data from pertinent literature, we suggest G. beninensis to be a junior synonym of G. lanceolata.
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Affiliation(s)
- Pedro H Campello-Nunes
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Noemi M Fernandes
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Franziska Szokoli
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany.,Dipartimento di Biologia, Università di Pisa, via A. Volta 4-6, Pisa, 56126, Italy
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, via A. Volta 4-6, Pisa, 56126, Italy
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
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24
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Chen X, Shazib SUA, Kim JH, Kim MS, Shin MK. New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae). Eur J Protistol 2018; 65:16-30. [PMID: 29793141 DOI: 10.1016/j.ejop.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length. However, our molecular analyses of four different genetic markers - three nuclear DNA markers (18S rDNA, ITS1-5.8S-ITS2 region, D1D2 of 28S rDNA) and one mitochondrial (mt) marker (CO1 gene) - indicated that all Korean populations examined were the same species. Based on our present findings and historic works, we propose that G. calkinsi, G. aculeata, and G. beninensis are junior synonyms of G. lanceolata.
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Affiliation(s)
- Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | | | - Ji Hye Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Min Seok Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Nakdong River Environment Research Center, Goryeong-gun, Gyeongbuk 40103, South Korea
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea.
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25
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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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26
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Pan H, Stoeck T. Redescription of the halophile ciliate, Blepharisma halophilum Ruinen, 1938 (Ciliophora, Heterotrichea, Heterotrichida) shows that the genus Blepharisma is non-monophyletic. Eur J Protistol 2017; 61:20-28. [DOI: 10.1016/j.ejop.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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27
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Chen X, Kim JH, Shazib SUA, Kwon CB, Shin MK. Morphology and molecular phylogeny of three heterotrichid species (Ciliophora, Heterotrichea), including a new species of Anigsteinia. Eur J Protistol 2017; 61:278-293. [DOI: 10.1016/j.ejop.2017.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022]
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28
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Kim MS, Kim JH, Shin MK. First Record of Two Spirostomum Species (Spirostomatidae, Heterotrichida, Heterotrichea) of Ciliates from Jindo Island in Korea. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2016. [DOI: 10.5635/ased.2016.sin9.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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29
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Kim JY, Jung JH. Taxonomic survey on ciliate diversity in eastern area of Kangwon-province, Korea: Brief records of fifteen species unrecorded from Korea. ACTA ACUST UNITED AC 2016. [DOI: 10.12651/jsr.2016.5.3.333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Mol Phylogenet Evol 2016; 102:128-44. [DOI: 10.1016/j.ympev.2016.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022]
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31
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Yan Y, Fan Y, Chen X, Li L, Warren A, Al-Farraj SA, Song W. Taxonomy and phylogeny of three heterotrich ciliates (Protozoa, Ciliophora), with description of a newBlepharismaspecies. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12369] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Yan
- School of Marine Sciences; Ningbo University; Ningbo 315211 China
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Yangbo Fan
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Xiangrui Chen
- School of Marine Sciences; Ningbo University; Ningbo 315211 China
| | - Lifang Li
- Marine College; Shandong University; Weihai 264209 China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | | | - Weibo Song
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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32
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Chen X, Shazib SUA, Kim JH, Jang SW, Shin MK. Morphological Description and Molecular Phylogeny of Two Species of Levicoleps (Ciliophora, Prostomatida), L. taehwae nov. spec. and L. biwae jejuensis nov. subspec., collected in Korea. J Eukaryot Microbiol 2016; 63:471-80. [PMID: 26679511 DOI: 10.1111/jeu.12291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 11/29/2022]
Abstract
Two colepid ciliates, Levicoleps taehwae nov. spec. and L. biwae jejuensis nov. subspec., were collected from the brackish water of the Taehwa River and a small freshwater pond in Jeju Island, South Korea, respectively. Their living morphology, infraciliature, and small subunit (SSU) rRNA gene sequences were determined using standard methods. Barrel-shaped L. taehwae nov. spec. is a small ciliate with an average size of 45 × 25 μm in vivo, about 15 ciliary rows each composed of 12 monokinetids and two perioral dikinetids, and two 20 μm-long caudal cilia. The sequence length and GC content of the SSU rRNA gene are 1,669 bp, 44.5%. This novel species is similar in body size to Coleps hirtus, and has six armor tiers and hirtus-type tier plates, and the same number of ciliary rows as C. hirtus; however, it can be distinguished from the latter by the absence of armor spines and its sequence similarity of SSU rRNA gene is about 92.8% which indicates that it is a distinct form. Levicoleps biwae jejuensis nov. subspec., is a medium colepid ciliate which has a barrel-shaped body, about 22 somatic kineties and 16 transverse ciliary rows, three mini adoral organelles, and four 15 μm-long caudal cilia. The sequence length and GC content of the SSU rRNA gene are 1,666 bp and 44.4%.
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Affiliation(s)
- Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | | | - Ji Hye Kim
- Department of Biological Sciences, University of Ulsan, Ulsan, 44610, South Korea
| | - Seok Won Jang
- Department of Biological Sciences, University of Ulsan, Ulsan, 44610, South Korea
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan, 44610, South Korea
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33
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Fernandes NM, Paiva TDS, da Silva-Neto ID, Schlegel M, Schrago CG. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data. Mol Phylogenet Evol 2015; 95:229-46. [PMID: 26549427 DOI: 10.1016/j.ympev.2015.10.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.
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Affiliation(s)
- Noemi M Fernandes
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil; Laboratório de Biologia Molecular "Francisco Mauro Salzano", Instituto de Ciências Biológicas, Universidade Federal do Pará, Brazil
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany
| | - Carlos G Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
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34
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Kim JH, Shin MK. Novel Discovery of Two Heterotrichid Ciliates, Climacostomum virens and Fabrea salina (Ciliophora: Heterotrichea: Heterotrichida) in Korea. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2015. [DOI: 10.5635/ased.2015.31.3.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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35
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Fernandes NM, Dias RJP, Schrago CG, Silva-Neto ID. Redescription and Phylogenetic Position of Condylostoma arenarium
Spiegel, 1926 (Ciliophora, Heterotrichea) from Guanabara Bay, Brazil. J Eukaryot Microbiol 2015; 62:722-32. [DOI: 10.1111/jeu.12228] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/14/2015] [Accepted: 03/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Noemi M. Fernandes
- Laboratório de Biologia Evolutiva Teórica e Aplicada; Dept. de Genética; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro; CEP: 21941-617 Ilha do Fundão Rio de Janeiro - RJ Brazil
| | - Roberto J. P. Dias
- Laboratório de Protozoologia; Dept. de Zoologia; ICB; Universidade Federal de Juiz de Fora; CEP: 36036-900 Juiz de Fora - MG Brazil
| | - Carlos G. Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada; Dept. de Genética; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro; CEP: 21941-617 Ilha do Fundão Rio de Janeiro - RJ Brazil
| | - Inácio D. Silva-Neto
- Laboratório de Protistologia; Dept. de Zoologia; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro - UFRJ; CEP: 21941-590 Ilha do Fundão Rio de Janeiro - RJ Brazil
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36
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Morphology and molecular phylogeny of three marine Condylostoma species from China, including two new ones (Ciliophora, Heterotrichea). Eur J Protistol 2015; 51:66-78. [DOI: 10.1016/j.ejop.2014.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 11/22/2022]
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