Species Concepts and the Evolutionary Paradigm in Modern Nematology
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History and Philosophy of Systematic Biology
History and Philosophy of Systematic Biology Bock, W. J. (1973) Philosophical foundations of classical evolutionary classification Systematic Zoology 22: 375-392 Part of a general symposium on "Contemporary Systematic Philosophies," there are some other interesting papers here. Brower, A. V. Z. (2000) Evolution Is Not a Necessary Assumption of Cladistics Cladistics 16: 143- 154 Dayrat, Benoit (2005) Ancestor-descendant relationships and the reconstruction of the Tree of Lif Paleobiology 31: 347-353 Donoghue, M.J. and J.W. Kadereit (1992) Walter Zimmermann and the growth of phylogenetic theory Systematic Biology 41: 74-84 Faith, D. P. and J. W. H. Trueman (2001) Towards an inclusive philosophy for phylogenetic inference Systematic Biology 50: 331-350 Gaffney, E. S. (1979) An introduction to the logic of phylogeny reconstruction, pp. 79-111 in Cracraft, J. and N. Eldredge (eds.) Phylogenetic Analysis and Paleontology Columbia University Press, New York. Gilmour, J. S. L. (1940) Taxonomy and philosophy, pp. 461-474 in J. Huxley (ed.) The New Systematics Oxford Hull, D. L. (1978) A matter of individuality Phil. of Science 45: 335-360 Hull, D. L. (1978) The principles of biological classification: the use and abuse of philosophy Hull, D. L. (1984) Cladistic theory: hypotheses that blur and grow, pp. 5-23 in T. Duncan and T. F. Stuessy (eds.) Cladistics: Perspectives on the Reconstruction of Evolutionary History Columbia University Press, New York * Hull, D. L. (1988) Science as a process: an evolutionary account of the social and conceptual development of science University of Chicago Press. An already classic work on the recent, violent history of systematics; used as data for Hull's general theories about scientific change. -
Supplementary Data Sterner, Beckett* and Scott Lidgard. (Under Revision
Supplementary Data Sterner, Beckett* and Scott Lidgard. (Under revision) “Moving Past the Systematics Wars.” Journal of the History of Biology. *Corresponding author E-mail: [email protected] Table S1 Examples of additive coding procedures used in conjuction with both phenetic & cladistic methodologies. Methods Taxa & Characters Use of additive Publication coding phenetic hyphomycetes fungi; phenetic Kendrick & Proctor morphology 1964 phenetic helminthosporium phenetic Ibrahim & Threlfall fungi; morphology, 1966 pathogenicity, physiology, biochemistry phenetic Listeria, Streptococci, phenetic Davis et al. 1969 related bacteria; morphology, biochemistry, sediment phenetic Agrobacterium; phenetic Kesters et al. 1973 morphology, biochemistry phenetic fossil nummulitid phenetic Barnett 1974 foraminifera; morphology phenetic anaerobic bacteria; phenetic Holmberg & Nord morphology, 1975 biochemistry phenetic actinomycete bacteria; phenetic Goodfellow et al. morphology, 1979 biochemistry phenetic freshwater sediment phenetic Mallory & Sayler bacteria; morphology, 1984 biochemistry phenetic nemerteans; phenetic Sundberg 1985 morphology, ecology, development phenetic rhodococci bacteria; phenetic Goodfellow et al. morphology, 1990 biochemistry phenetic actinomycete bacteria; phenetic O'Donnell et al. 1993 morphology, biochemistry phenetic Bacillus bacteria; phenetic Nielsen et al. 1995 biochemistry, DNA base composition phenetic fossil crinoids; skeletal phenetic Deline & Ausich 2011 morphology phenetic fossil crinoids; skeletal phenetic -
Species Concepts and the Evolutionary Paradigm in Modern Nematology
JOURNAL OF NEMATOLOGY VOLUME 30 MARCH 1998 NUMBER 1 Journal of Nematology 30 (1) :1-21. 1998. © The Society of Nematologists 1998. Species Concepts and the Evolutionary Paradigm in Modern Nematology BYRON J. ADAMS 1 Abstract: Given the task of recovering and representing evolutionary history, nematode taxonomists can choose from among several species concepts. All species concepts have theoretical and (or) opera- tional inconsistencies that can result in failure to accurately recover and represent species. This failure not only obfuscates nematode taxonomy but hinders other research programs in hematology that are dependent upon a phylogenetically correct taxonomy, such as biodiversity, biogeography, cospeciation, coevolution, and adaptation. Three types of systematic errors inherent in different species concepts and their potential effects on these research programs are presented. These errors include overestimating and underestimating the number of species (type I and II error, respectively) and misrepresenting their phylogenetic relationships (type III error). For research programs in hematology that utilize recovered evolutionary history, type II and III errors are the most serious. Linnean, biological, evolutionary, and phylogenefic species concepts are evaluated based on their sensitivity to systematic error. Linnean and biologica[ species concepts are more prone to serious systematic error than evolutionary or phylogenetic concepts. As an alternative to the current paradigm, an amalgamation of evolutionary and phylogenetic species concepts is advocated, along with a set of discovery operations designed to minimize the risk of making systematic errors. Examples of these operations are applied to species and isolates of Heterorhab- ditis. Key words: adaptation, biodiversity, biogeography, coevolufion, comparative method, cospeciation, evolution, nematode, philosophy, species concepts, systematics, taxonomy. -
Western Tiger Salamander,Ambystoma Mavortium
COSEWIC Assessment and Status Report on the Western Tiger Salamander Ambystoma mavortium Southern Mountain population Prairie / Boreal population in Canada Southern Mountain population – ENDANGERED Prairie / Boreal population – SPECIAL CONCERN 2012 COSEWIC status reports are working documents used in assigning the status of wildlife species suspected of being at risk. This report may be cited as follows: COSEWIC. 2012. COSEWIC assessment and status report on the Western Tiger Salamander Ambystoma mavortium in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. xv + 63 pp. (www.registrelep-sararegistry.gc.ca/default_e.cfm). Previous report(s): COSEWIC. 2001. COSEWIC assessment and status report on the tiger salamander Ambystoma tigrinum in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. vi + 33 pp. (www.sararegistry.gc.ca/status/status_e.cfm). Schock, D.M. 2001. COSEWIC assessment and status report on the tiger salamander Ambystoma tigrinum in Canada, in COSEWIC assessment and status report on the tiger salamander Ambystoma tigrinum in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. 1-33 pp. Production note: COSEWIC would like to acknowledge Arthur Whiting for writing the status report on the Western Tiger Salamander, Ambystoma mavortium, in Canada, prepared under contract with Environment Canada. This report was overseen and edited by Kristiina Ovaska, Co-chair of the COSEWIC Amphibians and Reptiles Specialist Subcommittee. For additional copies contact: COSEWIC Secretariat c/o Canadian Wildlife Service Environment Canada Ottawa, ON K1A 0H3 Tel.: 819-953-3215 Fax: 819-994-3684 E-mail: COSEWIC/[email protected] http://www.cosewic.gc.ca Également disponible en français sous le titre Ếvaluation et Rapport de situation du COSEPAC sur la Salamandre tigrée de l’Ouest (Ambystoma mavortium) au Canada. -
Loggerhead Shrike, Migrans Subspecies (Lanius Ludovicianus Migrans), in Canada
PROPOSED Species at Risk Act Recovery Strategy Series Recovery Strategy for the Loggerhead Shrike, migrans subspecies (Lanius ludovicianus migrans), in Canada Loggerhead Shrike, migrans subspecies © Manitoba Conservation 2010 About the Species at Risk Act Recovery Strategy Series What is the Species at Risk Act (SARA)? SARA is the Act developed by the federal government as a key contribution to the common national effort to protect and conserve species at risk in Canada. SARA came into force in 2003, and one of its purposes is “to provide for the recovery of wildlife species that are extirpated, endangered or threatened as a result of human activity.” What is recovery? In the context of species at risk conservation, recovery is the process by which the decline of an endangered, threatened or extirpated species is arrested or reversed, and threats are removed or reduced to improve the likelihood of the species’ persistence in the wild. A species will be considered recovered when its long-term persistence in the wild has been secured. What is a recovery strategy? A recovery strategy is a planning document that identifies what needs to be done to arrest or reverse the decline of a species. It sets objectives and broad strategies to attain them and identifies the main areas of activities to be undertaken. Detailed planning is done at the action plan stage. Recovery strategy development is a commitment of all provinces and territories and of three federal agencies — Environment Canada, Parks Canada Agency and Fisheries and Oceans Canada — under the Accord for the Protection of Species at Risk. -
Historical Review of Systematic Biology and Nomenclature - Alessandro Minelli
BIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS – Vol. II - Historical Review of Systematic Biology and Nomenclature - Alessandro Minelli HISTORICAL REVIEW OF SYSTEMATIC BIOLOGY AND NOMENCLATURE Alessandro Minelli Department of Biology, Via U. Bassi 58B, I-35131, Padova,Italy Keywords: Aristotle, Belon, Cesalpino, Ray, Linnaeus, Owen, Lamarck, Darwin, von Baer, Haeckel, Sokal, Sneath, Hennig, Mayr, Simpson, species, taxa, phylogeny, phenetic school, phylogenetic school, cladistics, evolutionary school, nomenclature, natural history museums. Contents 1. The Origins 2. From Classical Antiquity to the Renaissance Encyclopedias 3. From the First Monographers to Linnaeus 4. Concepts and Definitions: Species, Homology, Analogy 5. The Impact of Evolutionary Theory 6. The Last Few Decades 7. Nomenclature 8. Natural History Collections Glossary Bibliography Biographical Sketch Summary The oldest roots of biological systematics are found in folk taxonomies, which are nearly universally developed by humankind to cope with the diversity of the living world. The logical background to the first modern attempts to rationalize the classifications was provided by Aristotle's logic, as embodied in Cesalpino's 16th century classification of plants. Major advances were provided in the following century by Ray, who paved the way for the work of Linnaeus, the author of standard treatises still regarded as the starting point of modern classification and nomenclature. Important conceptual progress was due to the French comparative anatomists of the early 19th century UNESCO(Cuvier, Geoffroy Saint-Hilaire) – andEOLSS to the first work in comparative embryology of von Baer. Biological systematics, however, was still searching for a unifying principle that could provide the foundation for a natural, rather than conventional, classification.SAMPLE This principle wasCHAPTERS provided by evolutionary theory: its effects on classification are already present in Lamarck, but their full deployment only happened in the 20th century. -
Mecoptera: Meropeidae): Simply Dull Or Just Inscrutable?
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Center for Systematic Entomology, Gainesville, Insecta Mundi Florida 8-24-2007 Etymology of the earwigfly, Merope tuber Newman (Mecoptera: Meropeidae): Simply dull or just inscrutable? Louis A. Somma University of Florida, [email protected] James C. Dunford University of Florida, Gainesville, FL Follow this and additional works at: https://digitalcommons.unl.edu/insectamundi Part of the Entomology Commons Somma, Louis A. and Dunford, James C., "Etymology of the earwigfly, Merope tuber Newman (Mecoptera: Meropeidae): Simply dull or just inscrutable?" (2007). Insecta Mundi. 65. https://digitalcommons.unl.edu/insectamundi/65 This Article is brought to you for free and open access by the Center for Systematic Entomology, Gainesville, Florida at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Insecta Mundi by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. INSECTA MUNDI A Journal of World Insect Systematics 0013 Etymology of the earwigfly, Merope tuber Newman (Mecoptera: Meropeidae): Simply dull or just inscrutable? Louis A. Somma Department of Zoology PO Box 118525 University of Florida Gainesville, FL 32611-8525 [email protected] James C. Dunford Department of Entomology and Nematology PO Box 110620, IFAS University of Florida Gainesville, FL 32611-0620 [email protected] Date of Issue: August 24, 2007 CENTER FOR SYSTEMATIC ENTOMOLOGY, INC., Gainesville, FL Louis A. Somma and James C. Dunford Etymology of the earwigfly, Merope tuber Newman (Mecoptera: Meropeidae): Simply dull or just inscrutable? Insecta Mundi 0013: 1-5 Published in 2007 by Center for Systematic Entomology, Inc. P. O. Box 147100 Gainesville, FL 32604-7100 U. -
Towards a Global Names Architecture: the Future of Indexing Scientific Names
A peer-reviewed open-access journal ZooKeys 550: 261–281Towards (2016) a Global Names Architecture: The future of indexing scientific names 261 doi: 10.3897/zookeys.550.10009 RESEARCH ARTICLE http://zookeys.pensoft.net Launched to accelerate biodiversity research Towards a Global Names Architecture: The future of indexing scientific names Richard L. Pyle1 1 Bernice Pauahi Bishop Museum, 1525 Bernice Street, Honolulu, HI 96817, USA Corresponding author: Richard L. Pyle (email address) Academic editor: Ellinor Michel | Received 19 May 2015 | Accepted 20 May 2015 | Published 7 January 2016 http://zoobank.org/AD5B8CE2-BCFC-4ABC-8AB0-C92DEC7D4D85 Citation: Pyle RL (2016) Towards a Global Names Architecture: The future of indexing scientific names. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 261–281. doi: 10.3897/zookeys.550.10009 Abstract For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly, the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inacces- sible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit micro- scopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all – which we are still in the midst of, and which has not yet been fully realized – is the means by which taxonomists manage and communicate the information of their trade. -
Hibbett Et Al 2011 Fung Biol
fungal biology reviews 25 (2011) 38e47 journal homepage: www.elsevier.com/locate/fbr Plenary Paper Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences David S. HIBBETTa,*, Anders OHMANa, Dylan GLOTZERa, Mitchell NUHNa, Paul KIRKb, R. Henrik NILSSONc,d aBiology Department, Clark University, Worcester, MA 01610, USA bCABI UK, Bakeham Lane, Egham, Surrey TW20 9TY, UK cDepartment of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Goteborg,€ Sweden dDepartment of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005 Tartu, Estonia article info abstract Article history: Fungal taxonomy seeks to discover, describe, and classify all species of Fungi and provide Received 14 December 2010 tools for their identification. About 100,000 fungal species have been described so far, but it Accepted 3 January 2011 has been estimated that there may be from 1.5 to 5.1 million extant fungal species. Over the last decade, about 1200 new species of Fungi have been described in each year. At that Keywords: rate, it may take up to 4000 y to describe all species of Fungi using current specimen-based Biodiversity approaches. At the same time, the number of molecular operational taxonomic units Classification (MOTUs) discovered in ecological surveys has been increasing dramatically. We analyzed Environmental sequences ribosomal RNA internal transcribed spacer (ITS) sequences in the GenBank nucleotide data- Molecular ecology base and classified them as “environmental” or “specimen-based”. We obtained 91,225 MOTU sequences, of which 30,217 (33 %) were of environmental origin. Clustering at an average Taxonomy 93 % identity in extracted ITS1 and ITS2 sequences yielded 16,969 clusters, including 6230 (37 %) clusters with only environmental sequences, and 2223 (13 %) clusters with both envi- ronmental and specimen-based sequences. -
On the Probabilities of Branch Durations and Stratigraphic Gaps in Phylogenies of Fossil Taxa When Rates of Diversification Vary
Peter J. Wagner Expected Divergences given Varying Diversification & Sampling 1 On the Probabilities of Branch Durations and Stratigraphic Gaps in 2 Phylogenies of Fossil Taxa when Rates of Diversification Vary over 3 Time 4 Peter J. Wagner 5 Dept. of Earth & Atmospheric Sciences, and School of Biological Sciences 6 316 Bessey Hall 7 University of Nebraska, Lincoln USA 8 [email protected] 9 10 Abstract 11 The time separating the first appearances of species from their divergences from related taxa 12 affects assessments of macroevolutionary hypotheses about rates of anatomical or ecological 13 change. Branch durations necessarily posit stratigraphic gaps in sampling within a clade over 14 which we have failed to sample predecessors (ancestors) and over which there are no 15 divergences leading to sampled relatives (sister-taxa). The former reflects only sampling rates 16 whereas the latter reflects sampling, origination and extinction rates. Because all three rates vary 17 over time, the probability of a branch duration of any particular length will differ depending on 18 when in the Phanerozoic that branch duration spans. Here, I present a birth-death-sampling 19 model allowing interval-to-interval variation in diversification and sampling rates. Increasing 20 either origination or sampling rates increases the probability of finding sister taxa that diverge 21 both during and before intervals of high sampling/origination. Conversely, elevated extinction 22 reduces the probability of divergences from sampled sister-taxa before and during intervals of 1 Peter J. Wagner Expected Divergences given Varying Diversification & Sampling 23 elevated extinction. In the case of total extinction, a Signor-Lipps will reduce expected sister- 24 taxa leading up to the extinction, with the possible effect stretching back many millions of years 25 when sampling is low. -
American Ornithologists' Union
m eeting PrOgrAm 129th Stated Meeting of the AmericAn OrnithOlOgists’ UniOn 24-29 July, 2011 hyatt Regency JackSonville RiveRfRont JackSonville, floRida, uSa Co-hosted by the University of Florida and the Florida Ornithological Society. Jacksonville, florida a merican ornithologists’ union Co ntents Ogi r An Zers .................................................................................................................................................................................2 meeting hOsts ...........................................................................................................................................................................2 registrAtiOn AnD generAl inFOrmAtiOn ............................................................................................................................3 Registration/information desk .................................................................................................................................................................................................3 Message/job board .....................................................................................................................................................................................................................3 Parking ..........................................................................................................................................................................................................................................3 Internet, fax, -
When Mycologists Describe New Species, Not All Relevant
A peer-reviewed open-access journal MycoKeys 72: 109–128 (2020) Mycological species descriptions over time 109 doi: 10.3897/mycokeys.72.56691 RESEARCH ARTICLE MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research When mycologists describe new species, not all relevant information is provided (clearly enough) Louisa Durkin1, Tobias Jansson1, Marisol Sanchez2, Maryia Khomich3, Martin Ryberg4, Erik Kristiansson5, R. Henrik Nilsson1 1 Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden 2 Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden 3 Nofima – Norwegian Institute of Food, Fisheries and Aquaculture Research, P.O. Box 210, 1431 Ås, Norway 4 Department of Organismal Biology, Uppsala University, Uppsala, Sweden 5 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden Corresponding author: R. Henrik Nilsson ([email protected]) Academic editor: T. Lumbsch | Received 19 July 2020 | Accepted 24 August 2020 | Published 10 September 2020 Citation: Durkin L, Jansson T, Sanchez M, Khomich M, Ryberg M, Kristiansson E, Nilsson RH (2020) When mycologists describe new species, not all relevant information is provided (clearly enough). MycoKeys 72: 109–128. https://doi.org/10.3897/mycokeys.72.56691 Abstract Taxonomic mycology struggles with what seems to be a perpetual shortage