Author
Frederick W. Spiegel
Other affiliations: Miami University
Bio: Frederick W. Spiegel is an academic researcher from University of Arkansas. The author has contributed to research in topics: Amoebozoa & Protosteloid. The author has an hindex of 24, co-authored 67 publications receiving 5432 citations. Previous affiliations of Frederick W. Spiegel include Miami University.
Topics: Amoebozoa, Protosteloid, Species richness, Monophyly, Slime mold
Papers published on a yearly basis
Papers
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Dalhousie University1, University of Georgia2, Bigelow Laboratory For Ocean Sciences3, Ontario Veterinary College4, New York State Department of Health5, Blaise Pascal University6, Bedford Institute of Oceanography7, University of Louisiana at Lafayette8, Duke University9, Pedagogical University10, Colorado State University11, University of Toronto12, University of Connecticut13, United States Forest Service14, University of Guelph15, Royal Botanic Garden Edinburgh16, Academy of Natural Sciences of Drexel University17, Michigan State University18, University of Copenhagen19, George Mason University20, University of Illinois at Urbana–Champaign21, Saint Petersburg State University22, University of Arkansas23, University of British Columbia24
TL;DR: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists, and proposes a scheme that is based on nameless ranked systematics.
Abstract: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
1,620 citations
Dalhousie University1, University of Saskatchewan2, University of Rhode Island3, Sewanee: The University of the South4, Natural History Museum5, New York State Department of Health6, University of British Columbia7, Kaiserslautern University of Technology8, Charles University in Prague9, University of Guelph10, Le Moyne College11, Georgia College & State University12, University of Colorado Boulder13, University of Geneva14, Edinburgh Napier University15, University of Arkansas16, Saint Petersburg State University17
TL;DR: This revision of the classification of eukaryotes retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees.
Abstract: This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
1,414 citations
University of Saskatchewan1, Natural History Museum2, Centre for Environment, Fisheries and Aquaculture Science3, University of Rhode Island4, Academy of Sciences of the Czech Republic5, Sewanee: The University of the South6, National Institutes of Health7, Saint Petersburg State University8, University of Salzburg9, Centre national de la recherche scientifique10, Mississippi State University11, Science for Life Laboratory12, Uppsala University13, Charles University in Prague14, Spanish National Research Council15, University of Duisburg-Essen16, Kaiserslautern University of Technology17, University of Oslo18, Dalhousie University19, Pierre-and-Marie-Curie University20, American Museum of Natural History21, University of Michigan22, University of Warsaw23, University of São Paulo24, University of Paris25, University of British Columbia26, University of Guelph27, Royal Botanic Garden Edinburgh28, Kyungpook National University29, University of Geneva30, University of Alabama31, Pompeu Fabra University32, Edinburgh Napier University33, University of Arkansas34, Hosei University35, Oklahoma State University–Stillwater36, Chinese Academy of Sciences37
TL;DR: It is confirmed that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista, and suggested primer sets for DNA sequences from environmental samples that are effective for each clade are provided.
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 ...
750 citations
TL;DR: An overview of the enormous morphological, taxonomical and functional diversity of soil protists is provided, and current challenges and opportunities in soil protistology are discussed.
Abstract: Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.
297 citations
Dalhousie University1, University of Oxford2, New York State Department of State3, Blaise Pascal University4, University of Georgia5, Pedagogical University6, United States Forest Service7, RWTH Aachen University8, Michigan State University9, Saint Petersburg State University10, University of Arkansas11
TL;DR: Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ -fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models, plus a phylogenetic foundation for comparative mammalian genomics is evaluated.
Abstract: the origin of echolocation and flight in bats. Nature 403:188– 192. van Rheede, T., T. Bastiaans, D. N. Boone, S. B. Hedges, W. W. de Jong, and O. Madsen. 2006. The platypus in its place: nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23:587–597. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141– 154. Waddell, P. J., N. Okada, and M. Hasegawa. 1999. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48:1–5. Waddell, P. J., and S. Shelley. 2003. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ -fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28:197–224.
261 citations
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TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
18,256 citations
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
14,171 citations
TL;DR: In this paper, the authors present a set of methods for soil sampling and analysis, such as: N.H.Hendershot, H.M.Hettiarachchi, C.C.De Freitas Arbuscular Mycorrhiza, Y.K.Soon and W.J.
Abstract: SOIL SAMPLING AND HANDLING, G.T. Patterson and M.R. Carter Soil Sampling Designs, D. Pennock, T. Yates, and J. Braidek Sampling Forest Soils, N. Belanger and K.C.J. Van Rees Measuring Change in Soil Organic Carbon Storage, B.H. Ellert, H.H. Janzen, A.J. VandenBygaart, and E. Bremer Soil Sample Handling and Storage, S.C. Sheppard and J.A. Addison Quality Control in Soil Chemical Analysis, C. Swyngedouw and R. Lessard DIAGNOSTIC METHODS for SOIL and ENVIRONMENTAL MANAGEMENT, J.J. Schoenau and I.P. O'Halloran Nitrate and Exchangeable Ammonium Nitrogen, D.G. Maynard, Y.P. Kalra, and J.A. Crumbaugh Mehlich 3 Extractable Elements, N. Ziadi and T. Sen Tran Sodium Bicarbonate Extractable Phosphorus, J.J. Schoenau and I. P. O'Halloran Boron, Molybdenum and Selenium, G. M. Hettiarachchi and U. C. Gupta Trace Element Assessment, W.H. Hendershot, H. Lalande, D. Reyes, and D. MacDonald Readily Soluble Aluminum and Manganese in Acid Soils, Y.K. Soon, N. Belanger, and W.H. Hendershot Lime Requirement, N. Ziadi and T. Sen Tran Ion Supply Rates Using Ion Exchange Resins, P. Qian, J.J. Schoenau, and N. Ziadi Environmental Soil Phosphorus Indices, A.N. Sharpley, P.J.A. Kleinman and J.L. Weld Electrical Conductivity and Soluble Ions, J.J. Miller and D. Curtin SOIL CHEMICAL ANALYSES, Y.K. Soon and W.H. Hendershot Soil Reaction and Exchangeable Acidity, W.H. Hendershot, H. Laland,e and M. Duquette Collection and Characterization of Soil Solutions, J.D. MacDonald, N. Belanger, S. Sauve, F. Courchesne, and W.H. Hendershot Ion Exchange and Exchangeable Cations, W.H. Hendershot, H. Lalande, and M. Duquette Non-Exchangeable Ammonium, Y.K. Soon and B.C. Liang Carbonates, T.B. Goh and A.R. Mermut Total and Organic Carbon, J.O. Skjemstad and J.A. Baldock Total Nitrogen, P.M. Rutherford, W.B. McGill, C.T. Figueiredo, and J.M. Arocena Chemical Characterization of Soil Sulphur, C.G. Kowalenko and M. Grimmett Total and Organic Phosphorus, I.P. O'Halloran and B.J. Cade-Menum Characterization of Available P by Sequential Extraction, H. Tiessen and J.O. Moir Extractable Al, Fe, Mn, and Si, F. Courchesne and M.C. Turmel Determining Nutrient Availability in Forest Soils, N. Belanger, David Pare, and W.H. Hendershot Chemical Properties of Organic Soils, A. Karam SOIL BIOLOGICAL ANALYSES, E. Topp and C.A. Fox Cultural Methods for Soil and Root Associated Microorganisms, J.J. Germida and J.R. de Freitas Arbuscular Mycorrhiza, Y. Dalpe and C. Hamel Root Nodule Bacteria and Symbiotic Nitrogen Fixation, D. Prevost and H. Antoun Microarthropods, J.P Winter and V.M. Behan-Pelletier Nematodes, T.A. Forge and J. Kimpinski Earthworms, M.J. Clapperton, G.H. Baker and C.A. Fox Enchytraeids, S.M. Adl Protozoa, S.M. Adl, D. Acosta-Mercado, and D.H. Lynn Denitrification Techniques for Soils, C.F. Drury, D.D. Myrold, E.G. Beauchamp, and W.D.Reynolds Nitrification Techniques in Soil Systems, C.F. Drury, S.C. Hart, and X.M. Yang Substrate-Induced Respiration and Selective Inhibition as Measures of Microbial Biomass in Soils, V.L. Bailey, J.L. Smith, and H. Bolton Jr. Assessment of Soil Biological Activity, R.P.Beyaert and C.A. Fox Soil ATP, R.P. Voroney, G. Wen, and R.P. Beyaert Lipid-Based Community Analysis, K.E. Dunfield Bacterial Community Analyses by Denaturing Gradient Gel Electrophoresis (DGGE), E. Topp, Y.-C. Tien, and A. Hartmann Indicators of Soil Food Web Properties, T.A. Forge and M. Tenuta SOIL ORGANIC MATTER ANALYSES, E.G. Gregorich and M.H. Beare Carbon Mineralization, D.W. Hopkins Mineralizable Nitrogen, Denis Curtin and C.A. Campbell Physically Uncomplexed Organic Matter, E.G. Gregorich and M.H. Beare Extraction and Characterization of Dissolved Organic Matter, M.H. Chantigny, D.A. Angers, K. Kaiser, and K. Kalbitz Soil Microbial Biomass C, N, P and S, R.P. Voroney, P.C. Brookes, and R.P. Beyaert Carbohydrates, M.H. Chantigny and D.A. Angers Organic Forms of Nitrogen, D.C. Olk Soil Humus Fractions, D.W. Anderson and J.J Schoenau Soil Organic Matter Analysis by Solid-State 13C Nuclear Magnetic Resonance Spectroscopy, M. J. Simpson and C. M. Preston Stable Isotopes in Soil and Environmental Research, B.H. Ellert and L. Rock SOIL PHYSICAL ANALYSES, D.A. Angers and F.J. Larney Particle Size Distribution, D. Kroetsch and C. Wang Soil Shrinkage, C.D. Grant Soil Density and Porosity, X. Hao, B.C. Ball, J.L.B. Culley, M.R. Carter, and G.W. Parkin Soil Consistency: Upper and Lower Plastic Limits, R.A. McBride Compaction and Compressibility, P. Defossez, T. Keller and G. Richard Field Soil Strength, G.C. Topp and D.R. Lapen Air Permeability, C.D. Grant and P.H. Groenevelt Aggregate Stability to Water, D.A. Angers, M.S. Bullock, and G.R. Mehuys Dry Aggregate Size Distribution, F.J. Larney Soil Air, R.E. Farrell and J.A. Elliott Soil-Surface Gas Emissions, P. Rochette and N. Bertrand Bulk Density Measurement in Forest Soils, D.G. Maynard and M.P. Curran Physical Properties of Organic Soils and Growing Media: Particle Size and Degree of Decomposition, L.E. Parent and J. Caron Physical Properties of Organic Soils and Growing Media: Water and Air Storage and Flow Dynamics, J. Caron, D.E. Elrick, J.C. Michel, and R. Naasz SOIL WATER ANALYSES, W.D. Reynolds and G.C. Topp Soil Water Analyses: Principles and Parameters, W.D. Reynolds and G.C. Topp Soil Water Content, G.C. Topp, G.W. Parkin, and Ty P.A Ferre Soil Water Potential, N.J. Livingston and G.C. Topp Soil Water Desorption and Imbibition: Tension and Pressure Techniques, W.D. Reynolds and G.C. Topp Soil Water Desorption and Imbibition: Long Column, W.D. Reynolds and G.C. Topp Soil Water Desorption and Imbibition: Psychrometry, W.D. Reynolds and G.C. Topp Saturated Hydraulic Properties: Laboratory Methods, W.D. Reynolds Saturated Hydraulic Properties: Well Permeameter, W.D. Reynolds Saturated Hydraulic Properties: Ring Infiltrometer, W.D. Reynolds Saturated Hydraulic Properties: Auger-Hole, G.C. Topp Saturated Hydraulic Properties: Piezometer, G.C. Topp Unsaturated Hydraulic Properties: Laboratory Tension Infiltrometer, F.J. Cook Unsaturated Hydraulic Properties: Laboratory Evaporation, O.O. B. Wendroth and N. Wypler Unsaturated Hydraulic Properties: Field Tension Infiltrometer, W.D. Reynolds Unsaturated Hydraulic Properties: Instantaneous Profile, W.D. Reynolds Estimation of Soil Hydraulic Properties, F.J. Cook and H.P. Cresswell Analysis of Soil Variability, B.C. Si, R.G. Kachanoski, and W.D. Reynolds APPENDIX Site Description, G.T. Patterson and J.A. Brierley General Safe Laboratory Operation Procedures, P. St-Georges INDEX
4,631 citations
American Museum of Natural History1, University of Tartu2, University of Gothenburg3, James Hutton Institute4, University of Aberdeen5, Cooperative Institute for Research in Environmental Sciences6, University of California, Berkeley7, Aberystwyth University8, Estonian University of Life Sciences9, Spanish National Research Council10, Royal Botanic Gardens11, Academy of Sciences of the Czech Republic12, Swedish University of Agricultural Sciences13, University of Tennessee14, University of Helsinki15, Stanford University16, Ludwig Maximilian University of Munich17, University of Toronto18, University of Florida19, University of New Mexico20, University of Tübingen21
TL;DR: All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type, and the term ‘species hypothesis’ (SH) is introduced for the taxa discovered in clustering on different similarity thresholds.
Abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
2,605 citations
American Museum of Natural History1, University of Tartu2, University of Colombo3, Royal Netherlands Academy of Arts and Sciences4, University of Florida5, University of Palermo6, Goethe University Frankfurt7, Hobart Corporation8, Nakhon Phanom University9, University of Bamenda10, University of Gothenburg11, Naturalis12, Swedish University of Agricultural Sciences13, Royal Botanic Gardens14, Universiti Malaysia Sabah15, United States Department of Agriculture16, Forest Research Institute Malaysia17, Humboldt State University18, Chinese Academy of Sciences19, Landcare Research20, University of Western Australia21, Estonian University of Life Sciences22, University of Southern Queensland23, Botanic Garden Meise24, Manchester Metropolitan University25, James Cook University26
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Abstract: Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
2,346 citations