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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

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PROF. SINA ADL (Orcid ID : 0000-0001-6324-6065) PROF. DAVID BASS (Orcid ID : 0000-0002-9883-7823) DR. CÉDRIC BERNEY (Orcid ID : 0000-0001-8689-9907) DR. PACO CÁRDENAS (Orcid ID : 0000-0003-4045-6718) DR. IVAN CEPICKA (Orcid ID : 0000-0002-4322-0754) DR. MICAH DUNTHORN (Orcid ID : 0000-0003-1376-4109) PROF. BENTE EDVARDSEN (Orcid ID : 0000-0002-6806-4807) DR. DENIS H. LYNN (Orcid ID : 0000-0002-1554-7792) DR. EDWARD A.D MITCHELL (Orcid ID : 0000-0003-0358-506X) PROF. JONG SOO PARK (Orcid ID : 0000-0001-6253-5199) DR. GUIFRÉ TORRUELLA (Orcid ID : 0000-0002-6534-4758) Article DR. VASILY V. ZLATOGURSKY (Orcid ID : 0000-0002-2688-3900) Article type : Original Article Corresponding author mail id: [email protected] Adl et al.---Classification of Eukaryotes Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina M. Adla, David Bassb,c, Christopher E. Laned, Julius Lukeše,f, Conrad L. Schochg, Alexey Smirnovh, Sabine Agathai, Cedric Berneyj, Matthew W. Brownk,l, Fabien Burkim, Paco Cárdenasn, Ivan Čepičkao, Ludmila Chistyakovap, Javier del Campoq, Micah Dunthornr,s, Bente Edvardsent, Yana Eglitu, Laure Guillouv, Vladimír Hamplw, Aaron A. Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Sergey Karpovh, Eunsoo Kimx, Martin Koliskoe, Alexander Kudryavtsevh,aa, Daniel J. G. Lahrab, Enrique Laraac,ad, Line Le Gallae, Denis H. Lynnaf,ag, David G. Mannah, Ramon Massana i Moleraq, Edward A. D. Mitchellac,ai , Christine Morrowaj, Jong Soo Parkak, Jan W. Pawlowskial, Martha J. Powellam, Daniel J. Richteran, Sonja Rueckertao, Lora Shadwickap, Satoshi Shimanoaq, Frederick W. Spiegelap, Guifré Torruella i Cortesar, Noha Youssefas, Vasily Zlatogurskyh,at, Qianqian Zhangau,av. This article has been accepted for publication and undergone full peer review but has not Accepted been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/jeu.12691 This article is protected by copyright. All rights reserved. a Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK Canada, and b Dept of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, and c Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, and d Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881 USA, and eInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czechia, and fFaculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia, and gNational Institute for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA, and hDepartment of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia, and iDepartment of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria, and jCNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystèmes Pélagiques, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France, and kDepartment of Biological Sciences, Mississippi State University, MS USA, and lInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS USA, and mDepartment of Organismal Biology, Program in Systematic Biology, Science for Life Laboratory, Article Uppsala University, Uppsala 75236, Sweden, and nPharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, SE-75123 Uppsala, Sweden, and oDepartment of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czechia, and pCore Facility Centre for Culture Collection of Microorganisms, Saint Petersburg State University, 198504 Saint Petersburg, Russia, and q Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49 08003 Barcelona, Catalonia, Spain, and rDepartment of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, D-67663 Kaiserslautern, Germany, and sDepartment of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, D- 45141 Essen, Germany, and tDepartment of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway, and uDepartment of Biology, Dalhousie University, Halifax, NS, Canada, and vSorbonne Université, Université Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff, France, and wDepartment of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czechia, and xDepartment of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024 USA, and ySenckenberg am Meer, DZMB – German Centre for Marine Biodiversity Research, D-26382 Wilhelmshaven, Germany, and z Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA, and aaLaboratory of Parasitic Worms and Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia, and abDepartment of Zoology, Institute of Biosciences, University of Sao Paulo, Matao Travessa 14 Cidade Universitaria, Sao Paulo, 05508-090 SP, Brazil, and acLaboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, Accepted Switzerland, and This article is protected by copyright. All rights reserved. adReal Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain, and aeInstitut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 39 75005, Paris, France, and afDepartment of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph, Ontario N1G 2W1 Canada, and agDepartment of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver, British Columbia V6T 1Z4 Canada, and ahRoyal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom and Institute for Agrifood Research and Technology, C/ Poble Nou km 5.5, Sant Carles de La Ràpita, E-43540 Spain , and aiJardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, CH-2000 Neuchâtel, Switzerland, and ajDepartment of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood BT18 OEU, Northern Ireland, UK, and akDepartment of Oceanography and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Republic of Korea, and alDepartment of Genetics and Evolution, University of Geneva 1211, Geneva 4, Switzerland, and amDepartment of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA, and anInstitut de Biologia Evolutiva (CSIC-Univeritat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain, and aoSchool of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, United Kingdom, and ap Article Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA, and aqScience Research Centre, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo, 102-8160, Japan, and arLaboratoire Evolution et Systématique, Université Paris-XI, 91405 Orsay, France, and asDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074 USA, and atDepartment of Organismal Biology, Systematic Biology Program, Uppsala university, Uppsala, Sweden, and au Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, China, and avInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China. Abstract: This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera, and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have found their home. Sampling soils, deeper marine waters, and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Exavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples. Accepted This article is protected by copyright. All rights reserved. THIS revision of the classification of eukaryotes updates that of the International Society of Protistologists (Adl et al., 2012). Since then, there has been a massive increase in DNA sequence information of phylogenetic relevance from environmental samples. We now have a much better sense of the undescribed biodiversity in our environment (Pawlowski et al., 2012; de Vargas et al., 2015). While significant, it still remains a partial estimation as several continents and soils in general are poorly sampled, and the deeper ocean is hard to reach. This new data clarified phylogenetic relationships and the new information is incorporated
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  • Reconstruction of Protein Domain Evolution Using Single-Cell Amplified

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    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 ’.
  • Protozoologica ACTA Doi:10.4467/16890027AP.17.016.7497 PROTOZOOLOGICA

    Protozoologica ACTA Doi:10.4467/16890027AP.17.016.7497 PROTOZOOLOGICA

    Acta Protozool. (2017) 56: 181–189 www.ejournals.eu/Acta-Protozoologica ACTA doi:10.4467/16890027AP.17.016.7497 PROTOZOOLOGICA Allovahlkampfia minuta nov. sp., (Acrasidae, Heterolobosea, Excavata) a New Soil Amoeba at the Boundary of the Acrasid Cellular Slime Moulds Alvaro DE OBESO FERNADEZ DEL VALLE, Sutherland K. MACIVER Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Scotland, UK Abstract. We report the isolation of a new species of Allovahlkampfia, a small cyst-forming heterolobosean soil amoeba. Phylogenetic analysis of the 18S rDNA and the internal transcribed spacers indicates that Allovahlkampfia is more closely related to the acrasids than to other heterolobosean groups and indicates that the new strain (GF1) groups with Allovahlkampfia tibetiensisand A. nederlandiensis despite being significantly smaller than these and any other described Allovahlkampfia species. GF1 forms aggregated cyst masses similar to the early stages of Acrasis sorocarp development, in agreement with the view that it shares ancestry with the acrasids. Time-lapse video mi- croscopy reveals that trophozoites are attracted to individuals that have already begun to encyst or that have formed cysts. Although some members of the genus are known to be pathogenic the strain GF1 does not grow above 28oC nor at elevated osmotic conditions, indicating that it is unlikely to be a pathogen. INTRODUCTION and habit. The heterolobosean acrasid slime moulds are very similar to the amoebozoan slime moulds too in life cycle, but these remarkable similarities in ap- The class heterolobosea was first created on mor- pearance and function are most probably due to parallel phological grounds to unite the schizopyrenid amoe- bae/amoeboflagellates with the acrasid slime moulds evolution.
  • Supporting Material

    Supporting Material

    Supporting Text Recursions. We developed a model to investigate the evolution of ploidy levels in the presence of host-parasite interactions between a focal and nonfocal species. The focal species is assumed to have two loci, a ploidy modifier locus with alleles C1 and C2 and an interaction locus with alleles A and a. Thus there are four haploid gamete types in the focal species: AC1 with frequency X1, aC1 with frequency X2, AC2 with frequency X3, and aC2 with frequency X4. The modifier locus influences ploidy levels by altering the timing of meiosis; diploid zygotes of genotype CiCj have a probability, dij, of undergoing meiosis late in life, thus experiencing host-parasite selection as a diploid, versus early in life, thus experiencing selection as a haploid (Fig. 2). The nonfocal species is assumed to be a sexual diploid, having only a brief haploid stage, although results derived with a haploid nonfocal species were similar. For clarity, we assume that the A locus in the focal species interacts with a B locus in the nonfocal species, with alleles B and b. Note that Table 1 differs from this convention by referring to alleles in both species as A and a. We use a different notation here to avoid additional subscripts in the equations. The frequencies of alleles are denoted by pA, pa, pC1, and pC2 in the focal species and pB and pb in the nonfocal species, all measured at the gamete stage of the life cycle (Fig. 2). Also measured at this stage is D = (X1 X4 - X2 X3), the disequilibrium between the modifier and selected loci in the focal species.