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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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2
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Yuasa T, Takahashi O. Ultrastructural morphology of the reproductive swarmers of Sphaerozoum punctatum (Huxley) from the East China Sea. Eur J Protistol 2014; 50:194-204. [DOI: 10.1016/j.ejop.2013.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/10/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
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3
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Yi Z, Dunthorn M, Song W, Stoeck T. Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea). Mol Phylogenet Evol 2010; 57:937-41. [DOI: 10.1016/j.ympev.2010.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/15/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
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4
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Gilg IC, Amaral-Zettler LA, Countway PD, Moorthi S, Schnetzer A, Caron DA. Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. Protist 2009; 161:197-211. [PMID: 20044311 DOI: 10.1016/j.protis.2009.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 09/19/2009] [Indexed: 10/20/2022]
Abstract
Incomplete knowledge of acantharian life cycles has hampered their study and limited our understanding of their role in the vertical flux of carbon and strontium. Molecular tools can help identify enigmatic life stages and offer insights into aspects of acantharian biology and evolution. We inferred the phylogenetic position of acantharian sequences from shallow water, as well as acantharian-like clone sequences from 500 and 880 m in the San Pedro Channel, California. The analyses included validated acantharian and polycystine sequences from public databases with environmental clone sequences related to acantharia and used Bayesian inference methods. Our analysis demonstrated strong support for two branches of unidentified organisms that are closely related to, but possibly distinct from the Acantharea. We also found evidence of acantharian sequences from mesopelagic environments branching within the chaunacanthid clade, although the morphology of these organisms is presently unknown. HRP-conjugated probes were developed to target Acantharea and phylotypes from Unidentified Clade 1 using Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) on samples collected at 500 m. Our CARD-FISH experiments targeting phylotypes from an unidentified clade offer preliminary glimpses into the morphology of these protists, while a morphology for the aphotic acantharian lineages remains unknown at this time.
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Affiliation(s)
- Ilana C Gilg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy AHF 301, Los Angeles, CA 90089-0371, USA.
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5
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6
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Breiner HW, Foissner W, Stoeck T. The search finds an end: colpodidiids belong to the Class Nassophorea (ciliophora). J Eukaryot Microbiol 2008; 55:100-2. [PMID: 18318862 DOI: 10.1111/j.1550-7408.2008.00307.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At its discovery in 1982, the ciliate genus Colpodidium was assigned to the Class Colpodea. Redescriptions of the type species Colpodidium caudatum caused the establishment of a new family (Colpodidiidae). Based on ontogenetic data, eventually a new order-Colpodidiida-was established and hypothesized to belong to the Class Nassophorea. Despite a remarkable increase in the number of colpodidiid species, no sequence data were available to confirm or reject either class assignment or to assess the phylogenetic validity of the Colpodidiidae and the Colpodidiida. We here retrieved and phylogenetically analyzed the SSrDNA sequences of C. caudatum from a Namibian soil and an as-yet undescribed colpodidiid ciliate from the Chobe River floodplain, Botswana. Bayesian inference methods and evolutionary distance analyses confirmed the assignment of these taxa to the class Nassophorea.
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Affiliation(s)
- Hans-Werner Breiner
- University of Kaiserslautern, Department of Ecology, D-67663 Kaiserslautern, Germany
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7
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Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol Phylogenet Evol 2007; 44:255-66. [DOI: 10.1016/j.ympev.2006.11.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 10/11/2006] [Accepted: 11/02/2006] [Indexed: 11/16/2022]
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8
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Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ Microbiol 2007; 9:1233-52. [PMID: 17472637 DOI: 10.1111/j.1462-2920.2007.01247.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 microm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function.
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Affiliation(s)
- Fabrice Not
- Marine Biology and Fisheries Division, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
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9
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Lovejoy C, Massana R, Pedrós-Alió C. Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl Environ Microbiol 2006; 72:3085-95. [PMID: 16672445 PMCID: PMC1472370 DOI: 10.1128/aem.72.5.3085-3095.2006] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed microbial eukaryote diversity in perennially cold arctic marine waters by using 18S rRNA gene clone libraries. Samples were collected during concurrent oceanographic missions to opposite sides of the Arctic Ocean Basin and encompassed five distinct water masses. Two deep water Arctic Ocean sites and the convergence of the Greenland, Norwegian, and Barents Seas were sampled from 28 August to 2 September 2002. An additional sample was obtained from the Beaufort Sea (Canada) in early October 2002. The ribotypes were diverse, with different communities among sites and between the upper mixed layer and just below the halocline. Eukaryotes from the remote Canada Basin contained new phylotypes belonging to the radiolarian orders Acantharea, Polycystinea, and Taxopodida. A novel group within the photosynthetic stramenopiles was also identified. One sample closest to the interior of the Canada Basin yielded only four major taxa, and all but two of the sequences recovered belonged to the polar diatom Fragilariopsis and a radiolarian. Overall, 42% of the sequences were <98% similar to any sequences in GenBank. Moreover, 15% of these were <95% similar to previously recovered sequences, which is indicative of endemic or undersampled taxa in the North Polar environment. The cold, stable Arctic Ocean is a threatened environment, and climate change could result in significant loss of global microbial biodiversity.
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Affiliation(s)
- C Lovejoy
- Québec Océan and Département de Biologie, Université Laval, Quebec, QC, Canada G1K 7P4.
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10
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Kunitomo Y, Sarashina I, Iijima M, Endo K, Sashida K. Molecular phylogeny of acantharian and polycystine radiolarians based on ribosomal DNA sequences, and some comparisons with data from the fossil record. Eur J Protistol 2006; 42:143-53. [PMID: 17070759 DOI: 10.1016/j.ejop.2006.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 04/13/2006] [Accepted: 04/15/2006] [Indexed: 10/24/2022]
Abstract
Polycystines (spumellarians, nassellarians, and collodarians), phaeodarians, and acantharians are marine planktonic protists that have been conventionally and collectively called "radiolaria". Recent molecular phylogenetic studies revealed radiolarian polyphyly with phaeodarians being a separate offshoot. Collodarians and nassellarians are also shown to form a monophyletic group, but other aspects of radiolarian phylogeny, such as interrelations among polycystines and acantharians, remained uncertain. Here, we present molecular phylogenetic analyses including new ribosomal RNA sequences from ten spumellarians and nine nassellarians, based on Bayesian and maximum-likelihood methods. Results indicate that the Polycystinea is a paraphyletic group, with Bayesian analysis suggesting that spumellarians form a clade with acantharians. The heliozoan-like protist Sticholonche appears as a sister to the spumellarian clade. The nassellarian Eucyrtidium is located outside the clade including the other nassellarians and collodarians. The mineralogy of the test of extant radiolarians and the tree topology obtained in this work suggest that acantharians and spumellarians evolved from an ancestor with a siliceous skeleton. Collodarians and nassellarians form a well-supported clade and one might infer from the fossil record that they may have diverged between the Jurassic and the Eocene.
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Affiliation(s)
- Yoshiki Kunitomo
- Doctoral Program in Earth Evolution Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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11
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Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS. A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 2006; 157:31-43. [PMID: 16431157 DOI: 10.1016/j.protis.2005.10.004] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 10/30/2005] [Indexed: 11/28/2022]
Abstract
The Cariaco Basin off the Venezuelan coast in the Caribbean Sea is the world's largest truly marine body of anoxic water. The first rRNA survey of microbial eukaryotes in this environment revealed a number of novel lineages, but sampled only a fraction of the entire diversity. The goal of this study was to significantly improve recovery of protistan rRNA from the Basin. This was achieved by a systematic application of multiple PCR primer sets and substantially larger sequencing efforts. We focused on the most diverse habitat in the basin, anoxic waters approximately 100m below the oxic-anoxic interface, and detected novel lineages that escaped the single PCR primer approach. All clones obtained proved unique. A 99% sequence similarity cut-off value combined these clones into operational taxonomic units (OTUs), over 75% of which proved novel. Some of these OTUs form deep branches within established protistan groups. Others signify discovery of novel protistan lineages that appear unrelated to any known microeukaryote. Surprisingly, even this large-scale multi-primer rRNA approach still missed a substantial part of the samples' rRNA diversity. The overlap between the species lists obtained with different primers is low, with only 4% of OTUs shared by all three libraries, and the number of species detected only once is large (55%). This strongly indicates that, at least in anoxic environments, protistan diversity may be much larger than is commonly thought. A single sample appears to contain thousands of largely novel protistan species. Multiple PCR primer combinations may be needed to capture these species.
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Affiliation(s)
- Thorsten Stoeck
- Department of Ecology, Technical University Kaiserslautern, Kaiserslautern, Germany
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12
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Yuasa T, Takahashi O, Honda D, Mayama S. Phylogenetic analyses of the polycystine Radiolaria based on the 18s rDNA sequences of the Spumellarida and the Nassellarida. Eur J Protistol 2005. [DOI: 10.1016/j.ejop.2005.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Sakaguchi M, Nakayama T, Hashimoto T, Inouye I. Phylogeny of the Centrohelida inferred from SSU rRNA, tubulins, and actin genes. J Mol Evol 2005; 61:765-75. [PMID: 16211424 DOI: 10.1007/s00239-005-0006-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Amoeboid protists are major targets of recent molecular phylogeny in connection with reconstruction of global phylogeny of eukaryotes as well as the search for the root of eukaryotes. The Centrohelida are one of the major groups of Heliozoa, classified in the Actinopodida, whose evolutionary position is not well understood. To clarify the relationships between the Centrohelida and other eukaryotes, we sequenced SSU rRNA, alpha-tubulin, and beta-tubulin genes from a centroheliozoan protist, Raphidiophrys contractilis. The SSU rRNA phylogeny showed that the Centrohelida are not closely related to other heliozoan groups, Actinophryida, Desmothoracida, or Taxopodida. Maximum likelihood analyses of the combined phylogeny using a concatenate model for an alpha- + beta-tubulin + actin data set, and a separate model for SSU rRNA, alpha- and beta-tubulin, and actin gene data sets revealed the best tree, in which the Centrohelida have a closer relationship to Rhodophyta than to other major eukaryotic groups. However, both weighted Shimodaira-Hasegawa and approximately unbiased tests for the concatenate protein phylogeny did not reject alternative trees in which Centrohelida were constrained to be sisters to the Amoebozoa. Moreover, alternative trees in which Centrohelida were placed at the node branching before and after Amoebozoa or Viridiplantae were not rejected by the WSH tests. These results narrowed the possibilities for the position of Centrohelida to a sister to the Rhodophyta, to the Amoebozoa, or to an independent branch between the branchings of Amoebozoa and Rhodophyta (or possibly Plantae) at the basal position within the bikonts clade in the eukaryotic tree.
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Affiliation(s)
- Miako Sakaguchi
- Institute of Biological Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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Yuan J, Chen MY, Shao P, Zhou H, Chen YQ, Qu LH. Genetic diversity of small eukaryotes from the coastal waters of Nansha Islands in China. FEMS Microbiol Lett 2005; 240:163-70. [PMID: 15522504 DOI: 10.1016/j.femsle.2004.09.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 09/20/2004] [Accepted: 09/21/2004] [Indexed: 11/21/2022] Open
Abstract
Population structures and genetic diversity of the small eukaryotic plankton from the coastal waters of the Nansha Islands in China were investigated. Two genes libraries using 18S rDNA of the marine small eukaryotes were constituted, and 323 clones were identified within alveolates (more than 43%), acanthareas, viridiplantaes, and stramenopiles. Many novel clones were detected in the two libraries, including two groups of alveolates and two clades related to both acanthareas and polycystineas. Several sequences unrelated to any other known eukaryotes may represent early branches in the phylogenetic tree. Our results reveal that there is a high diversity and abundance of small eukaryotes in the marine regions of China.
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Affiliation(s)
- Jie Yuan
- Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
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Moreira D, Rodríguez-Valera F, López-García P. Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environ Microbiol 2004; 6:959-69. [PMID: 15305921 DOI: 10.1111/j.1462-2920.2004.00644.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have sequenced and analysed a 39.5 kbp genome fragment of a marine Group II euryarchaeote identified in a metagenomic library of 500 m deep plankton at the Antarctic Polar Front. The clone contains a 16S rRNA gene that is separated from the 23S rRNA gene in the genome. This appears to be a trait shared by Thermoplasmatales and Group II euryarchaeota. This genome fragment exhibits a compact organization, including a few overlapping genes in the canonical spectinomycin-like (spc) operon for ribosomal proteins that is immediately upstream the 16S rDNA. Most open reading frames (ORFs) encoded proteins involved in housekeeping processes and, as expected, exhibited a phylogenetic distribution congruent with that of the 16S rRNA. A considerable number of proteins with predicted transmembrane helices was identified. Among those, two proteins encoded by genes likely forming an operon appear to be part of a membrane terminal electron transport chain. One of these proteins has an unusual domain arrangement including ferredoxin, flavodoxin and one succinate dehydrogenase/fumarate reductase subunit. These proteins probably constitute a new succinate dehydrogenase-like oxidoreductase involved in what could be a novel pathway for energy metabolism in Group II euryarchaeota.
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Affiliation(s)
- David Moreira
- UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France
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Berney C, Pawlowski J. Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol 2004; 57 Suppl 1:S120-7. [PMID: 15008408 DOI: 10.1007/s00239-003-0015-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
There is accumulating evidence that the general shape of the ribosomal DNA-based phylogeny of Eukaryotes is strongly biased by the long-branch attraction phenomenon, leading to an artifactual basal clustering of groups that are probably highly derived. Among these groups, Foraminifera are of particular interest, because their deep phylogenetic position in ribosomal trees contrasts with their Cambrian appearance in the fossil record. A recent actin-based phylogeny of Eukaryotes has proposed that Foraminifera might be closely related to Cercozoa and, thus, branch among the so-called crown of Eukaryotes. Here, we reanalyze the small-subunit ribosomal RNA gene (SSU rDNA) phylogeny by removing all long-branching lineages that could artifactually attract foraminiferan sequences to the base of the tree. Our analyses reveal that Foraminifera branch together with the marine testate filosean Gromia oviformis as a sister group to Cercozoa, in agreement with actin phylogeny. Our study confirms the utility of SSU rDNA as a phylogenetic marker of megaevolutionary history, provided that the artifacts due to the heterogeneity of substitution rates in ribosomal genes are circumvented.
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Affiliation(s)
- Cédric Berney
- Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland.
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17
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Berney C, Fahrni J, Pawlowski J. How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol 2004; 2:13. [PMID: 15176975 PMCID: PMC428588 DOI: 10.1186/1741-7007-2-13] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 06/04/2004] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Over the past few years, the use of molecular techniques to detect cultivation-independent, eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA) gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them represent novel diversity in known eukaryotic groups, mainly stramenopiles and alveolates. Others do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to review the evolutionary importance of this novel high-level eukaryotic diversity critically, and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES), we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the small river, the Seymaz (Geneva, Switzerland). RESULTS Based on a detailed screening of an exhaustive alignment of eukaryotic SSU rRNA gene sequences and the phylogenetic re-analysis of previously published environmental sequences using Bayesian methods, our results suggest that the number of novel higher-level taxa revealed by previously published EES was overestimated. Three main sources of errors are responsible for this situation: (1) the presence of undetected chimeric sequences; (2) the misplacement of several fast-evolving sequences; and (3) the incomplete sampling of described, but yet unsequenced eukaryotes. Additionally, EES give a biased view of the diversity present in a given biotope because of the difficult amplification of SSU rRNA genes in some taxonomic groups. CONCLUSIONS Environmental DNA surveys undoubtedly contribute to reveal many novel eukaryotic lineages, but there is no clear evidence for a spectacular increase of the diversity at the kingdom level. After re-analysis of previously published data, we found only five candidate lineages of possible novel high-level eukaryotic taxa, two of which comprise several phylotypes that were found independently in different studies. To ascertain their taxonomic status, however, the organisms themselves have now to be identified.
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Affiliation(s)
- Cédric Berney
- Department of Zoology and Animal Biology, University of Geneva, CH – 1211 Geneva 4, Switzerland
| | - José Fahrni
- Department of Zoology and Animal Biology, University of Geneva, CH – 1211 Geneva 4, Switzerland
| | - Jan Pawlowski
- Department of Zoology and Animal Biology, University of Geneva, CH – 1211 Geneva 4, Switzerland
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18
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Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, Mylnikov AP, Aleshin VV, Petrov NB, Pawlowski J. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci U S A 2004; 101:8066-71. [PMID: 15148395 PMCID: PMC419558 DOI: 10.1073/pnas.0308602101] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent molecular phylogenetic studies revealed the extraordinary diversity of single-celled eukaryotes. However, the proper assessment of this diversity and accurate reconstruction of the eukaryote phylogeny are still impeded by the lack of molecular data for some major groups of easily identifiable and cultivable protists. Among them, amoeboid eukaryotes have been notably absent from molecular phylogenies, despite their diversity, complexity, and abundance. To partly fill this phylogenetic gap, we present here combined small-subunit ribosomal RNA and actin sequence data for the three main groups of "Heliozoa" (Actinophryida, Centrohelida, and Desmothoracida), the heliozoan-like Sticholonche, and the radiolarian group Polycystinea. Phylogenetic analyses of our sequences demonstrate the polyphyly of heliozoans, which branch either as an independent eukaryotic lineage (Centrohelida), within stramenopiles (Actinophryida), or among cercozoans (Desmothoracida), in broad agreement with previous ultrastructure-based studies. Our data also provide solid evidence for the existence of the Rhizaria, an emerging supergroup of mainly amoeboid eukaryotes that includes desmothoracid heliozoans, all radiolarians, Sticholonche, and foraminiferans, as well as various filose and reticulose amoebae and some flagellates.
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Affiliation(s)
- Sergey I Nikolaev
- A. N. Belozersky Institute of Physico-Chemical Biology, Department of Evolutionary Biochemistry, Moscow State University, Moscow 119992, Russia
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19
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López-García P, Brochier C, Moreira D, Rodríguez-Valera F. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol 2003; 6:19-34. [PMID: 14686938 DOI: 10.1046/j.1462-2920.2003.00533.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures.
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MESH Headings
- Chromosomes, Archaeal/genetics
- Conserved Sequence
- Crenarchaeota/genetics
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Gene Order
- Gene Transfer, Horizontal
- Genes, Archaeal
- Molecular Sequence Data
- Open Reading Frames
- Phylogeny
- Recombination, Genetic
- Sequence Analysis, DNA
- Water Microbiology
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Affiliation(s)
- Purificación López-García
- UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay, France.
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20
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Abstract
Most cultivated and characterized eukaryotes can be confidently assigned to one of eight major groups. After a few false starts, we are beginning to resolve relationships among these major groups as well. However, recent developments are radically revising this picture again, particularly (i) the discovery of the likely antiquity and taxonomic diversity of ultrasmall eukaryotes, and (ii) a fundamental rethinking of the position of the root. Together these data suggest major gaps in our understanding simply of what eukaryotes are or, when it comes to the tree, even which end is up.
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Affiliation(s)
- S L Baldauf
- Department of Biology, University of York, Box 373, Heslington, York YO10 5YW, UK.
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21
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Abstract
Comparative analyses of multiple genes suggest most known eukaryotes can be classified into half a dozen 'super-groups'. A new investigation of the distribution of a fused gene pair amongst these 'super-groups' has greatly narrowed the possible positions of the root of the eukaryote tree, clarifying the broad outlines of early eukaryote evolution.
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Affiliation(s)
- Alastair G B Simpson
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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22
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Abstract
In spite of the great success of small-subunit ribosomal RNA (SSU rRNA)-based studies for the analysis of environmental prokaryotic diversity, this molecular approach has seldom been applied to microbial eukaryotes. Recent molecular surveys of the smallest eukaryotic planktonic fractions at different oceanic surface regions and in deep-sea Antarctic samples revealed an astonishing protist diversity. Many of the phylotypes found in the photic region affiliate with photosynthetic groups that are known to contain picoeukaryotic representatives in the range 1-2 microm. Surprisingly, a vast diversity of presumably heterotrophic or mixotrophic lineages is also found. Among these, several novel lineages of heterokonts, and a large diversity of alveolates clustering in two major groups (Groups I and II), are present at all depths in the water column. Many of these new phylotypes appear biogeographically ubiquitous. These initial studies suggest that a wide diversity of small eukaryotes remains to be discovered not only in the ocean but also in other environments. For both ecology and evolutionary studies, it is predicted that environmental molecular identification of eukaryotes will have a profound impact in the immediate future.
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Affiliation(s)
- David Moreira
- Université Pierre et Marie Curie, UMR 7622, 9, quai St Bernard, 75005 Paris, France.
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