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University of Gent Faculty of Science Department Nematology Academic Year 2014-2015 BIODIVERSITY ASSESSMENT of MARINE SEDIMENTS
University of Gent Faculty of Science Department Nematology Academic year 2014-2015 BIODIVERSITY ASSESSMENT OF MARINE SEDIMENTS THROUGH DNA BARCODING Xorla Kanfra Promoter: Dr. Sofie Derycke Literature review submitted in partial Co-promoter: Dr. Katja Guilini fulfillment for a degree in Master of Supervisor: Dr. Sofie Derycke Science in Nematology Table of Contents 1 Introduction ................................................................................................................................. 1 1.1 Marine nematode biodiversity ............................................................................................. 1 1.2 Dispersal in nematodes ........................................................................................................ 2 1.3 Nematode taxonomy ............................................................................................................ 4 1.4 Taxonomy: Traditional and molecular approaches ............................................................ 5 1.5 Molecular markers for systematics and identification of marine nematodes ...................... 8 1.5.1 Nuclear genes .......................................................................................................... 9 1.5.2 Mitochondrial genes .............................................................................................. 11 1.6 The DNA barcoding approach ........................................................................................... 12 1.6.1 Application of DNA barcoding: Environmental metagenetics -
Lepidoptera: Tortricidae: Tortricinae) and Evolutionary Correlates of Novel Secondary Sexual Structures
Zootaxa 3729 (1): 001–062 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Monograph ZOOTAXA Copyright © 2013 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3729.1.1 http://zoobank.org/urn:lsid:zoobank.org:pub:CA0C1355-FF3E-4C67-8F48-544B2166AF2A ZOOTAXA 3729 Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures JASON J. DOMBROSKIE1,2,3 & FELIX A. H. SPERLING2 1Cornell University, Comstock Hall, Department of Entomology, Ithaca, NY, USA, 14853-2601. E-mail: [email protected] 2Department of Biological Sciences, University of Alberta, Edmonton, Canada, T6G 2E9 3Corresponding author Magnolia Press Auckland, New Zealand Accepted by J. Brown: 2 Sept. 2013; published: 25 Oct. 2013 Licensed under a Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0 JASON J. DOMBROSKIE & FELIX A. H. SPERLING Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures (Zootaxa 3729) 62 pp.; 30 cm. 25 Oct. 2013 ISBN 978-1-77557-288-6 (paperback) ISBN 978-1-77557-289-3 (Online edition) FIRST PUBLISHED IN 2013 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2013 Magnolia Press 2 · Zootaxa 3729 (1) © 2013 Magnolia Press DOMBROSKIE & SPERLING Table of contents Abstract . 3 Material and methods . 6 Results . 18 Discussion . 23 Conclusions . 33 Acknowledgements . 33 Literature cited . 34 APPENDIX 1. 38 APPENDIX 2. 44 Additional References for Appendices 1 & 2 . 49 APPENDIX 3. 51 APPENDIX 4. 52 APPENDIX 5. -
DNA Barcoding Confirms Polyphagy in a Generalist Moth, Homona Mermerodes (Lepidoptera: Tortricidae)
Molecular Ecology Notes (2007) 7, 549–557 doi: 10.1111/j.1471-8286.2007.01786.x BARCODINGBlackwell Publishing Ltd DNA barcoding confirms polyphagy in a generalist moth, Homona mermerodes (Lepidoptera: Tortricidae) JIRI HULCR,* SCOTT E. MILLER,† GREGORY P. SETLIFF,‡ KAROLYN DARROW,† NATHANIEL D. MUELLER,§ PAUL D. N. HEBERT¶ and GEORGE D. WEIBLEN** *Department of Entomology, Michigan State University, 243 Natural Sciences Building, East Lansing, Michigan 48824, USA, †National Museum of Natural History, Smithsonian Institution, Box 37012, Washington, DC 20013-7012, USA, ‡Department of Entomology, University of Minnesota, 1980 Folwell Avenue, Saint Paul, Minnesota 55108–1095 USA, §Saint Olaf College, 1500 Saint Olaf Avenue, Northfield, MN 55057, USA,¶Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1, **Bell Museum of Natural History and Department of Plant Biology, University of Minnesota, 220 Biological Sciences Center, 1445 Gortner Avenue, Saint Paul, Minnesota 55108–1095, USA Abstract Recent DNA barcoding of generalist insect herbivores has revealed complexes of cryptic species within named species. We evaluated the species concept for a common generalist moth occurring in New Guinea and Australia, Homona mermerodes, in light of host plant records and mitochondrial cytochrome c oxidase I haplotype diversity. Genetic divergence among H. mermerodes moths feeding on different host tree species was much lower than among several Homona species. Genetic divergence between haplotypes from New Guinea and Australia was also less than interspecific divergence. Whereas molecular species identification methods may reveal cryptic species in some generalist herbivores, these same methods may confirm polyphagy when identical haplotypes are reared from multiple host plant families. A lectotype for the species is designated, and a summarized bibliography and illustrations including male genitalia are provided for the first time. -
Mitochondrial Pseudogenes in Insect DNA Barcoding: Differing Points of View on the Same Issue
Biota Neotrop., vol. 12, no. 3 Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue Luis Anderson Ribeiro Leite1,2 1Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná – UFPR, CP 19020, CEP 81531-980, Curitiba, PR, Brasil 2Corresponding author: Luis Anderson Ribeiro Leite, e-mail: [email protected] LEITE, L.A.R. Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue. Biota Neotrop. 12(3): http://www.biotaneotropica.org.br/v12n3/en/abstract?thematic-review+bn02412032012 Abstract: Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes. Keywords: COI, molecular, NUMTs. LEITE, L.A.R. Pseudogenes mitocondriais no DNA barcoding em insetos: diferentes pontos de vista sobre a mesma questão. -
Similarities and Contrasts in the Local Insect Faunas Associated with Ten Forest Tree Species of New Guinea!
Pacific Science (1996), vol. 50, no. 2: 157-183 © 1996 by University of Hawai'i Press. All rights reserved Similarities and Contrasts in the Local Insect Faunas Associated with Ten Forest Tree Species of New Guinea! YVES BASSET,z,3 G. A. SAMUELSON, 2 AND S. E. MILLER 2 ABSTRACT: Insect faunas associated with 10 tree species growing in a sub montane area in Papua New Guinea are described and compared. In total, 75,000 insects were collected on these trees during the day and night by hand collecting, beating, branch clipping, intercept flight traps, and pyrethrum knock down over a l-yr period. Association of chewing insects with the hosts was in ferred from feeding trials. Characteristics of the fauna associated with each tree species are briefly outlined, with an emphasis on chewing insects. Four subsets of data, of decreasing affinity with the host, were analyzed by canonical corre spondence and cluster analyses: (1) specialist leaf-chewers, (2) proven leaf chewers, (3) all herbivores (including transient leaf-chewers and sap-suckers), and (4) all insects (including nonherbivore categories). Analyses of similarity between tree species were performed using number of either species or in dividuals within insect families. Analyses using number ofindividuals appeared more robust than those using number of species, because transient herbivore species artificially inflated the level of similarity between tree species. Thus, it is recommended that number of individuals be used in analyses of this type, par ticularly when the association of insects with their putative host has not been ascertained. Not unexpectedly, the faunal similarity of tree species increased along the sequence (1)-(2)-(3)-(4). -
Four Years of DNA Barcoding: Current Advances and Prospects
Four years of DNA barcoding: current advances and prospects. Lise Frézal, Raphael Leblois To cite this version: Lise Frézal, Raphael Leblois. Four years of DNA barcoding: current advances and prospects.. In- fection, Genetics and Evolution, Elsevier, 2008, 8 (5), pp.727-36. 10.1016/j.meegid.2008.05.005. mnhn-00392451 HAL Id: mnhn-00392451 https://hal-mnhn.archives-ouvertes.fr/mnhn-00392451 Submitted on 8 Jun 2009 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. Frézal, L., Leblois, R. Infection, Genetics and Evolution 1 4 years of DNA barcoding : current advances and prospects 2 3 4 Authors : Lise Frézal 1, Raphael Leblois2* 5 1 Laboratoire de Biologie intégrative des populations, Ecole Pratique des Hautes Etudes, Paris, 6 France 7 2 Unité Origine, Structure et Evolution de la Biodiversité UMR 5202 CNRS/MNHN, Muséum 8 National d'Histoire Naturelle, Paris, France 9 * Corresponding author (Phone: +33 (0)1 40 79 33 49; Fax: +33 (0)1 40 79 33 42; Email: 10 [email protected]) 11 12 13 1 Frézal, L., Leblois, R. Infection, Genetics and Evolution 14 Abstract 15 L. Frézal and R. Leblois – 4 years of DNA barcoding: current advances and prospects - 16 Infection, Genetics and Evolution 17 18 19 Research using cytochrome c oxidase barcoding techniques on zoological specimens was 20 initiated by Hebert et al. -
(Lepidoptera: Tortricidae) Fauna of Seram Island, Indonesia. Acta Zool
Acta zoologica cracoviensia, 56(2): 29-89, Kraków, 30 December, 2013 Ó Institute of Systematics and Evolution of Animals, Pol. Acad. Sci., Kraków doi:10.3409/azc.56_2.29 Zoobank Account: urn:lsid:zoobank.org:pub:34A104A5-22CF-4603-991C-7E25EA849C3A AnassessmentoftheTortricid(Lepidoptera:Tortricidae)fauna ofSeramIsland,Indonesia JózefRAZOWSKI Received: 05 September 2013. Accepted: 30 November 2013. RAZOWSKI J. 2013. An assessment of the Tortricid (Lepidoptera: Tortricidae) fauna of Seram Island, Indonesia. Acta zool. cracov., 56(2): 29-89. Abstract. The tortricid fauna of Seram is comprised of 35 genera and 60 species. Two genera (Kanikehia gen. n., Mersa gen. n.) and 41 species (Reptilisocia gunungana sp. n., Schoeno- tenes peos sp. n., Schoenotenes emmetra sp. n., Schoenotenes elasma sp. n., Metachorista longiseta sp. n., Cornuticlava binaiae sp. n., Cornuticlava kobipoto sp. n., Mimeoclysia mystrion sp. n., Kanikehia kanikehiana sp. n., Mersa metochia sp. n., Homona obtusuncus sp. n., Homona privigena sp. n., Isodemis solea sp. n., Isodemis phloiosignum sp. n., Isote- nes syndesma sp. n., Isotenes latitata sp. n., Zacorisca leura sp. n., Zacorisca helicoces- tum sp. n., Zacorisca seramica sp. n., Zacorisca digna sp. n., Adoxophyes planes sp. n., Adoxophyes meion sp. n., Adoxophyes olethra sp. n., Adoxophyes lacertana sp. n., Adoxo- phyes panurga sp. n., Adoxophyes luctuosa sp. n., Demeijerella palleophyton sp. n., Lobe- sia drasteria sp. n., Rhectogonia sandrae sp. n., Metrioglypha ithuncus sp. n., Aterpia monada sp. n., Asaphistis omora sp. n., Rhodacra leptalea sp. n., Rhopobota jonesiana sp. n., Rhopobota nasea sp. n., Rhopobota grisona sp. n., Peridaedala speculata sp. n., Peri- daedala stenygra sp. -
Population Genetics of Ecological Communities with DNA Barcodes: an Example from New Guinea Lepidoptera
Population genetics of ecological communities with DNA barcodes: An example from New Guinea Lepidoptera Kathleen J. Crafta, Steffen U. Paulsb, Karolyn Darrowc, Scott E. Millerc, Paul D. N. Hebertd, Lauren E. Helgenc, Vojtech Novotnye, and George D. Weiblena,1 Departments of aPlant Biology and bEntomology, University of Minnesota, Saint Paul, MN 55108; cNational Museum of Natural History, Smithsonian Institution, Washington, DC 20013; dBiodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada; and eInstitute of Entomology, Czech Academy of Sciences and Department of Zoology, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic Communicated by Hans R. Herren, Millennium Institute, Arlington, VA, January 5, 2010 (received for review November 23, 2008) Comparative population genetics of ecological guilds can reveal specialists, and may in fact confirm polyphagy (9). Population generalities in patterns of differentiation bearing on hypotheses genetic analyses of entire herbivorous insect communities are regarding the origin and maintenance of community diversity. needed to understand the extent of host-associated differ- Contradictory estimates of host specificity and beta diversity in entiation (10); no such studies have yet been reported in the tropical Lepidoptera (moths and butterflies) from New Guinea and tropics, however. the Americas have sparked debate on the role of host-associated Population genetic analyses also can test biogeographic divergence and geographic isolation in explaining -
DNA Barcoding Confirms Polyphagy in a Generalist Moth, Hontona Mermerodes (Lepidoptera: Tortricidae)
Molecular Ecology Notes (2007) 7,549-557 doi: 10.1111/j.1471-8286.2007.01786.x BARCODING DNA barcoding confirms polyphagy in a generalist moth, Hontona mermerodes (Lepidoptera: Tortricidae) JIRI HULCR,*SCOTT E. MILLER,t GREGORY P. SETLIFFJ KAROLYN DARROW,t NATHANIEL D. MUELLER,§ PAUL D. N. HEBERTl andGEORGE D. WEIBLEN" *Department of Entomology, Michigan State University, 243 Natural Sciences Building, East Lansing, Michigan 48824, USA, fNational Museum of Natural History, Smithsonian Institution, Box 37012, Washington, DC 20013-7012, USA, •^Department of Entomology, University of Minnesota, 1980 F olwell Avenue, Saint Paul, Minnesota 55108-1095 USA, §Saint Olaf College, 1500 Saint Olaf Avenue, Northfield, MN 55057, USA,fDepartment of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1, **Bell Museum of Natural History and Department of Plant Biology, University of Minnesota, 220 Biological Sciences Center, 1445 Gortner Avenue, Saint Paul, Minnesota 55108-1095, USA Abstract Recent DNA barcoding of generalist insect herbivores has revealed complexes of cryptic species within named species. We evaluated the species concept for a common generalist moth occurring in New Guinea and Australia, Hontona mermerodes, in light of host plant records and mitochondrial cytochrome c oxidase I haplotype diversity. Genetic divergence among H. mermerodes moths feeding on different host tree species was much lower than among several Homo«« species. Genetic divergence between haplotypes from New Guinea and Australia was also less than interspecific divergence. Whereas molecular species identification methods may reveal cryptic species in some generalist herbivores, these same methods may confirm polyphagy when identical haplotypes are reared from multiple host plant families. A lectotype for the species is designated, and a summarized bibliography and illustrations including male genitalia are provided for the first time. -
Pheromone Production, Male Abundance, Body Size, and the Evolution of Elaborate Antennae in Moths Matthew R
Pheromone production, male abundance, body size, and the evolution of elaborate antennae in moths Matthew R. E. Symonds1,2, Tamara L. Johnson1 & Mark A. Elgar1 1Department of Zoology, University of Melbourne, Victoria 3010, Australia 2Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia. Keywords Abstract Antennal morphology, forewing length, Lepidoptera, phylogenetic generalized least The males of some species of moths possess elaborate feathery antennae. It is widely squares, sex pheromone. assumed that these striking morphological features have evolved through selection for males with greater sensitivity to the female sex pheromone, which is typically Correspondence released in minute quantities. Accordingly, females of species in which males have Matthew R. E. Symonds, School of Life and elaborate (i.e., pectinate, bipectinate, or quadripectinate) antennae should produce Environmental Sciences, Deakin University, 221 the smallest quantities of pheromone. Alternatively, antennal morphology may Burwood Highway, Burwood, Victoria 3125, Australia. Tel: +61 3 9251 7437; Fax: +61 3 be associated with the chemical properties of the pheromone components, with 9251 7626; E-mail: elaborate antennae being associated with pheromones that diffuse more quickly (i.e., [email protected] have lower molecular weights). Finally, antennal morphology may reflect population structure, with low population abundance selecting for higher sensitivity and hence Funded by a Discovery Project grant from the more elaborate antennae. We conducted a phylogenetic comparative analysis to test Australian Research Council (DP0987360). these explanations using pheromone chemical data and trapping data for 152 moth species. Elaborate antennae are associated with larger body size (longer forewing Received: 13 September 2011; Revised: 23 length), which suggests a biological cost that smaller moth species cannot bear. -
Redalyc.Mitochondrial Pseudogenes in Insect DNA Barcoding: Differing
Biota Neotropica ISSN: 1676-0611 [email protected] Instituto Virtual da Biodiversidade Brasil Ribeiro Leite, Luis Anderson Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue Biota Neotropica, vol. 12, núm. 3, septiembre, 2012, pp. 301-308 Instituto Virtual da Biodiversidade Campinas, Brasil Available in: http://www.redalyc.org/articulo.oa?id=199124391029 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Biota Neotrop., vol. 12, no. 3 Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue Luis Anderson Ribeiro Leite1,2 1Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná – UFPR, CP 19020, CEP 81531-980, Curitiba, PR, Brasil 2Corresponding author: Luis Anderson Ribeiro Leite, e-mail: [email protected] LEITE, L.A.R. Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue. Biota Neotrop. 12(3): http://www.biotaneotropica.org.br/v12n3/en/abstract?thematic-review+bn02412032012 Abstract: Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. -
Insects on Plants: Explaining the Paradox of Low Diversity Within Specialist Herbivore Guilds
vol. 179, no. 3 the american naturalist march 2012 Insects on Plants: Explaining the Paradox of Low Diversity within Specialist Herbivore Guilds Vojtech Novotny,1,* Scott E. Miller,2 Jan Hrcek,1 Leontine Baje,3 Yves Basset,4 Owen T. Lewis,5 Alan J. A. Stewart,6 and George D. Weiblen7 1. Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic; 2. National Museum of Natural History, Smithsonian Institution, Washington, DC 20008; 3. New Guinea Binatang Research Center, P.O. Box 604, Madang, Papua New Guinea; 4. Smithsonian Tropical Research Institute, Apartado 0843- 03092, Balboa, Ancon, Panama; 5. Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom; 6. School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom; 7. Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108 Submitted July 24, 2011; Accepted November 7, 2011; Electronically published January 25, 2012 Online enhancement: appendix. Dryad data: http://dx.doi.org/10.5061/dryad.rg155q32. moted where specialized herbivores or pathogens have abstract: Classical niche theory explains the coexistence of species density-dependent effects on plant growth and fitness, put- through their exploitation of different resources. Assemblages of her- bivores coexisting on a particular plant species are thus expected to be ting locally rare plant species at an advantage (the Janzen- dominated by species from host-specific guilds with narrow, coexis- Connell hypothesis, reviewed in Leigh et al. 2004). High tence-facilitating niches rather than by species from generalist guilds.