The Revised Classification of Eukaryotes
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A Six-Gene Phylogeny Provides New Insights Into Choanoflagellate Evolution Martin Carr, Daniel J
A six-gene phylogeny provides new insights into choanoflagellate evolution Martin Carr, Daniel J. Richter, Parinaz Fozouni, Timothy J. Smith, Alexandra Jeuck, Barry S.C. Leadbeater, Frank Nitsche To cite this version: Martin Carr, Daniel J. Richter, Parinaz Fozouni, Timothy J. Smith, Alexandra Jeuck, et al.. A six- gene phylogeny provides new insights into choanoflagellate evolution. Molecular Phylogenetics and Evolution, Elsevier, 2017, 107, pp.166 - 178. 10.1016/j.ympev.2016.10.011. hal-01393449 HAL Id: hal-01393449 https://hal.archives-ouvertes.fr/hal-01393449 Submitted on 7 Nov 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Molecular Phylogenetics and Evolution 107 (2017) 166–178 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A six-gene phylogeny provides new insights into choanoflagellate evolution ⇑ Martin Carr a, ,1, Daniel J. Richter b,1,2, Parinaz Fozouni b,3, Timothy J. Smith a, Alexandra Jeuck c, Barry S.C. Leadbeater d, Frank Nitsche c a School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK b Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA c University of Cologne, Biocentre, General Ecology, Zuelpicher Str. -
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Laura Wegener Parfrey University of Massachusetts Amherst Jessica Grant Smith College Yonas I. Tekle Smith College Erica Lasek-Nesselquist Marine Biological Laboratory Hilary G. Morrison Marine Biological Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; and Katz, Laura A., "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life" (2010). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/126 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Authors Laura Wegener Parfrey, Jessica Grant, Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison, Mitchell L. Sogin, David J. Patterson, and Laura A. Katz This article is available at Smith ScholarWorks: https://scholarworks.smith.edu/bio_facpubs/126 Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1,JESSICA GRANT2,YONAS I. TEKLE2,6,ERICA LASEK-NESSELQUIST3,4, 3 3 5 1,2, HILARY G. -
Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. -
A Revised Classification of Naked Lobose Amoebae (Amoebozoa
Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility. -
Clerissi-2018-Frontiersmicrobi
Protists Within Corals: The Hidden Diversity Camille Clerissi, Sébastien Brunet, Jeremie Vidal-Dupiol, Mehdi Adjeroud, Pierre Lepage, Laure Guillou, Jean-Michel Escoubas, Eve Toulza To cite this version: Camille Clerissi, Sébastien Brunet, Jeremie Vidal-Dupiol, Mehdi Adjeroud, Pierre Lepage, et al.. Protists Within Corals: The Hidden Diversity. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.2043. 10.3389/fmicb.2018.02043. hal-01887637 HAL Id: hal-01887637 https://hal.archives-ouvertes.fr/hal-01887637 Submitted on 7 Aug 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-09-02043 August 30, 2018 Time: 10:39 # 1 ORIGINAL RESEARCH published: 31 August 2018 doi: 10.3389/fmicb.2018.02043 Protists Within Corals: The Hidden Diversity Camille Clerissi1*, Sébastien Brunet2, Jeremie Vidal-Dupiol3, Mehdi Adjeroud4, Pierre Lepage2, Laure Guillou5, Jean-Michel Escoubas6 and Eve Toulza1* 1 Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France, 2 McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada, 3 IFREMER, IHPE UMR 5244, Univ. Perpignan Via Domitia, CNRS, Univ. Montpellier, Montpellier, France, 4 Institut de Recherche pour le Développement, UMR 9220 ENTROPIE & Laboratoire d’Excellence CORAIL, Université de Perpignan, Perpignan, France, 5 CNRS, UMR 7144, Sorbonne Universités, Université Pierre et Marie Curie – Paris 6, Station Biologique de Roscoff, Roscoff, France, 6 CNRS, IHPE UMR 5244, Univ. -
Protistology an International Journal Vol
Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb. -
A Guide to 1.000 Foraminifera from Southwestern Pacific New Caledonia
Jean-Pierre Debenay A Guide to 1,000 Foraminifera from Southwestern Pacific New Caledonia PUBLICATIONS SCIENTIFIQUES DU MUSÉUM Debenay-1 7/01/13 12:12 Page 1 A Guide to 1,000 Foraminifera from Southwestern Pacific: New Caledonia Debenay-1 7/01/13 12:12 Page 2 Debenay-1 7/01/13 12:12 Page 3 A Guide to 1,000 Foraminifera from Southwestern Pacific: New Caledonia Jean-Pierre Debenay IRD Éditions Institut de recherche pour le développement Marseille Publications Scientifiques du Muséum Muséum national d’Histoire naturelle Paris 2012 Debenay-1 11/01/13 18:14 Page 4 Photos de couverture / Cover photographs p. 1 – © J.-P. Debenay : les foraminifères : une biodiversité aux formes spectaculaires / Foraminifera: a high biodiversity with a spectacular variety of forms p. 4 – © IRD/P. Laboute : îlôt Gi en Nouvelle-Calédonie / Island Gi in New Caledonia Sauf mention particulière, les photos de cet ouvrage sont de l'auteur / Except particular mention, the photos of this book are of the author Préparation éditoriale / Copy-editing Yolande Cavallazzi Maquette intérieure et mise en page / Design and page layout Aline Lugand – Gris Souris Maquette de couverture / Cover design Michelle Saint-Léger Coordination, fabrication / Production coordination Catherine Plasse La loi du 1er juillet 1992 (code de la propriété intellectuelle, première partie) n'autorisant, aux termes des alinéas 2 et 3 de l'article L. 122-5, d'une part, que les « copies ou reproductions strictement réservées à l'usage privé du copiste et non destinées à une utilisation collective » et, d'autre part, que les analyses et les courtes citations dans un but d'exemple et d'illustration, « toute représentation ou reproduction intégrale ou partielle, faite sans le consentement de l'auteur ou de ses ayants droit ou ayants cause, est illicite » (alinéa 1er de l'article L. -
The Revised Classification of Eukaryotes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/231610049 The Revised Classification of Eukaryotes Article in Journal of Eukaryotic Microbiology · September 2012 DOI: 10.1111/j.1550-7408.2012.00644.x · Source: PubMed CITATIONS READS 961 2,825 25 authors, including: Sina M Adl Alastair Simpson University of Saskatchewan Dalhousie University 118 PUBLICATIONS 8,522 CITATIONS 264 PUBLICATIONS 10,739 CITATIONS SEE PROFILE SEE PROFILE Christopher E Lane David Bass University of Rhode Island Natural History Museum, London 82 PUBLICATIONS 6,233 CITATIONS 464 PUBLICATIONS 7,765 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Biodiversity and ecology of soil taste amoeba View project Predator control of diversity View project All content following this page was uploaded by Smirnov Alexey on 25 October 2017. The user has requested enhancement of the downloaded file. The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. -
Reconstruction of Protein Domain Evolution Using Single-Cell Amplified
Reconstruction of protein domain evolution using single-cell amplified royalsocietypublishing.org/journal/rstb genomes of uncultured choanoflagellates sheds light on the origin of animals Research David López-Escardó 1,2 , Xavier Grau-Bové 1,3,4 , Amy Guillaumet-Adkins 5,6 , Marta Gut 5,6 , Michael E. Sieracki 7 and Iñaki Ruiz-Trillo 1,3,8 Cite this article: López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, 1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Ruiz-Trillo I. 2019 Reconstruction of protein 08003 Barcelona, Catalonia, Spain 2Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain domain evolution using single- cell amplified 3Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain genomes of uncultured choanoflagellates sheds 4Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK light on the origin of animals. Phil. 5CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Trans. R. Soc. B 374 : 20190088. Barcelona, Spain 6Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain http://dx.doi.org/10.1098/rstb.2019.0088 7National Science Foundation, Arlington, VA 22314, USA 8ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain Accepted: 15 June 2019 DL-E, 0000-0002-9122-6771; XG-B, 0000-0003-1978-5824; IR-T, 0000-0001-6547-5304 One contribution of 18 to a discussion meeting Understanding the origins of animal multicellularity is a fundamental biologi- cal question. Recent genome data have unravelled the role that co-option of issue ‘Single cell ecology ’. -
Author's Manuscript (764.7Kb)
1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. -
Aquatic Ecosystems Bibliography Compiled by Robert C. Worrest
Aquatic Ecosystems Bibliography Compiled by Robert C. Worrest Abboudi, M., Jeffrey, W. H., Ghiglione, J. F., Pujo-Pay, M., Oriol, L., Sempéré, R., . Joux, F. (2008). Effects of photochemical transformations of dissolved organic matter on bacterial metabolism and diversity in three contrasting coastal sites in the northwestern Mediterranean Sea during summer. Microbial Ecology, 55(2), 344-357. Abboudi, M., Surget, S. M., Rontani, J. F., Sempéré, R., & Joux, F. (2008). Physiological alteration of the marine bacterium Vibrio angustum S14 exposed to simulated sunlight during growth. Current Microbiology, 57(5), 412-417. doi: 10.1007/s00284-008-9214-9 Abernathy, J. W., Xu, P., Xu, D. H., Kucuktas, H., Klesius, P., Arias, C., & Liu, Z. (2007). Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis BMC Genomics, 8, 176. Abseck, S., Andrady, A. L., Arnold, F., Björn, L. O., Bomman, J. F., Calamari, D., . Zepp, R. G. (1998). Environmental effects of ozone depletion: 1998 assessment. Journal of Photochemistry and Photobiology B: Biology, 46(1-3), 1-108. doi: Doi: 10.1016/s1011-1344(98)00195-x Adachi, K., Kato, K., Wakamatsu, K., Ito, S., Ishimaru, K., Hirata, T., . Kumai, H. (2005). The histological analysis, colorimetric evaluation, and chemical quantification of melanin content in 'suntanned' fish. Pigment Cell Research, 18, 465-468. Adams, M. J., Hossaek, B. R., Knapp, R. A., Corn, P. S., Diamond, S. A., Trenham, P. C., & Fagre, D. B. (2005). Distribution Patterns of Lentic-Breeding Amphibians in Relation to Ultraviolet Radiation Exposure in Western North America. Ecosystems, 8(5), 488-500. Adams, N. -
Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483).