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Dna Barcodes, Partitioned Phylogenetic Models, And
LARGE DATASETS AND TRICHOPTERA PHYLOGENETICS: DNA BARCODES, PARTITIONED PHYLOGENETIC MODELS, AND THE EVOLUTION OF PHRYGANEIDAE By PAUL BRYAN FRANDSEN A dissertation submitted to the Graduate School-New Brunswick Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Entomology Written under the direction of Karl M. Kjer And approved by _____________________________________ _____________________________________ _____________________________________ _____________________________________ New Brunswick, New Jersey OCTOBER 2015 ABSTRACT OF THE DISSERTATION Large datasets and Trichoptera phylogenetics: DNA barcodes, partitioned phylogenetic models, and the evolution of Phryganeidae By PAUL BRYAN FRANDSEN Dissertation Director: Karl M. Kjer Large datasets in phylogenetics—those with a large number of taxa, e.g. DNA barcode data sets, and those with a large amount of sequence data per taxon, e.g. data sets generated from high throughput sequencing—pose both exciting possibilities and interesting analytical problems. The analysis of both types of large datasets is explored in this dissertation. First, the use of DNA barcodes in phylogenetics is investigated via the generation of phylogenetic trees for known monophyletic clades. Barcodes are found to be useful in shallow scale phylogenetic analyses when given a well-supported scaffold on which to place them. One of the analytical challenges posed by large phylogenetic datasets is the selection of appropriate partitioned models of molecular evolution. The most commonly used model partitioning strategies can fail to characterize the true variation of the evolutionary process and this effect can be exacerbated when applied to large datasets. A new, scalable algorithm for the automatic selection ! ii! of partitioned models of molecular evolution is proposed with an eye toward reducing systematic error in phylogenomics. -
Morphological Taxonomy, DNA Barcoding, and Species Diversity in Southern Rocky Mountain Headwater Streams Author(S): Brian A
Morphological taxonomy, DNA barcoding, and species diversity in southern Rocky Mountain headwater streams Author(s): Brian A. Gill, Rachel A. Harrington, Boris C. Kondratieff, Kelly R. Zamudio, N. LeRoy Poff and W. Chris Funk Source: Freshwater Science , Vol. 33, No. 1 (March 2014), pp. 288-301 Published by: The University of Chicago Press on behalf of Society for Freshwater Science Stable URL: https://www.jstor.org/stable/10.1086/674526 JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at https://about.jstor.org/terms The University of Chicago Press and Society for Freshwater Science are collaborating with JSTOR to digitize, preserve and extend access to Freshwater Science This content downloaded from 24.9.112.12 on Sun, 25 Aug 2019 21:17:06 UTC All use subject to https://about.jstor.org/terms MOLECULAR APPROACHES IN FRESHWATER ECOLOGY Morphological taxonomy, DNA barcoding, and species diversity in southern Rocky Mountain headwater streams Brian A. Gill1,4, Rachel A. Harrington1,5, Boris C. Kondratieff2,6, Kelly R. Zamudio3,7, N. LeRoy Poff1,8, and W. Chris Funk1,9 1Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523 USA 2Department of Bioagricultural Sciences and Pest Management and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523 USA 3Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853 USA Abstract: Elevation gradients allow scientists to observe changes in fauna over a range of abiotic conditions. -
Taxonomy and Systematics: Contributions to Benthology and J-NABS
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy J. N. Am. Benthol. Soc., 2010, 29(1):147–169 ’ 2010 by The North American Benthological Society DOI: 10.1899/08-065.1 Published online: 5 February 2010 Taxonomy and systematics: contributions to benthology and J-NABS 1,2 3 4 Ralph W. Holzenthal , Desiree R. Robertson , Steffen U. Pauls , AND Patina K. Mendez5 Department of Entomology, University of Minnesota, 1980 Folwell Ave., 219 Hodson Hall, St. Paul, Minnesota 55108 USA Abstract. Systematics, or taxonomy, is the study of the diversity of life on Earth. Its goals are to discover and describe new biological diversity and to understand its evolutionary and biogeographic origins and relationships. Here we review the contributions to the field of systematics and taxonomy published over the last 25 y in J-NABS and its predecessor Freshwater Invertebrate Biology (FIB). We examined a total of 64 studies that we considered to be largely taxonomic in nature. We classified these studies into 2 major categories: morphological (e.g., descriptive taxonomy, taxonomic revisions) and molecular (e.g., deoxyribonucleic acid [DNA] barcoding, population genetics). We examined studies in 5-y increments for J-NABS. We also studied the period 1982 to 1985, during which FIB was published. On average, 12 taxonomic studies were published within each 5-y period. Molecular studies first appeared in 1986 and have slowly increased, reaching their greatest number within the last 5 y. Studies also were classified by their individual attributes. Morphological studies were, by far, the most common, but studies also included molecular data, biological information, distributional data, keys, and biogeographical analyses. -
Arthropod Phylogeny Revisited, with a Focus on Crustacean Relationships
Arthropod Structure & Development 39 (2010) 88–110 Contents lists available at ScienceDirect Arthropod Structure & Development journal homepage: www.elsevier.com/locate/asd Arthropod phylogeny revisited, with a focus on crustacean relationships Stefan Koenemann a,*, Ronald A. Jenner b,**, Mario Hoenemann a, Torben Stemme a, Bjo¨rn M. von Reumont c,*** a Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine Hannover, Bu¨nteweg 17d, D-30559 Hannover, Germany b Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK c Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany article info abstract Article history: Higher-level arthropod phylogenetics is an intensely active field of research, not least as a result of the Received 10 June 2009 hegemony of molecular data. However, not all areas of arthropod phylogenetics have so far received Accepted 14 October 2009 equal attention. The application of molecular data to infer a comprehensive phylogeny of Crustacea is still in its infancy, and several emerging results are conspicuously at odds with morphology-based studies. Keywords: In this study, we present a series of molecular phylogenetic analyses of 88 arthropods, including 18S rDNA 57 crustaceans, representing all the major lineages, with Onychophora and Tardigrada as outgroups. Our 16S rDNA analyses are based on published and new sequences for two mitochondrial markers, 16S rDNA and Cytochrome c oxidase subunit I Structural alignment cytochrome c oxidase subunit I (COI), and the nuclear ribosomal gene 18S rDNA. We designed our Multiple alignment optimization phylogenetic analyses to assess the effects of different strategies of sequence alignment, alignment Sensitivity analysis masking, nucleotide coding, and model settings. -
From Writing to Reading the Encyclopedia of Life Rstb.Royalsocietypublishing.Org Paul D
Downloaded from http://rstb.royalsocietypublishing.org/ on October 9, 2016 From writing to reading the encyclopedia of life rstb.royalsocietypublishing.org Paul D. N. Hebert1, Peter M. Hollingsworth2 and Mehrdad Hajibabaei1 1Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1 2Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK Introduction PDNH, 0000-0002-3081-6700; PMH, 0000-0003-0602-0654; MH, 0000-0002-8859-7977 Cite this article: Hebert PDN, Hollingsworth Prologue ‘As the study of natural science advances, the language of scientific PM, Hajibabaei M. 2016 From writing to description may be greatly simplified and abridged. This has already been reading the encyclopedia of life. Phil. done by Linneaus and may be carried still further by other invention. The Trans. R. Soc. B 371: 20150321. descriptions of natural orders and genera may be reduced to short defi- http://dx.doi.org/10.1098/rstb.2015.0321 nitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to con- ceive with what facility, and in how short a time, a knowledge of all the Accepted: 24 May 2016 objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially One contribution of 16 to a theme issue ‘From devoted to it, may at length be universally possessed in every civilized DNA barcodes to biomes’. country and in every rank of life’. J. C. Louden 1829. Magazine of natural history, vol. -
Biosyst.EU 2013 Global Systematics! 18-22 February 2013
U E . T S Y S O I B V I E N N A BioSyst EU BioSyst.EU 2013 Global systematics! 18-22 February 2013 Abstract volume Sponsored by Official Carrier BioSyst.EU 2013 Global systematics! 18–22 February 2013 2nd BioSyst.EU joint meeting 14th Annual Meeting of the Society for Biological Systematics (Gesellschaft für Biologische Systematik, GfBS) 7th Annual Meeting of the Network of Biological Systematics Austria (NOBIS Austria) Abstract-Volume Andreas Kroh, Björn Berning, Elisabeth Haring, Mathias Harzhauser, Helmut Sattmann, Julia Walochnik, Dominique Zimmermann & Martin Zuschin (Eds.) NOBIS Austria Vienna, 2013 BioSyst.EU 2013 ● Global systematics! ● 18–22 February 2013, Vienna, Austria Impressum/Imprint Eigentümer, Herausgeber und Verleger: © 2013 NOBIS Austria. Alle Rechte vorbehalten. Für den Inhalt der Beiträge sind die Autoren verantwortlich. Redaktion: Andreas Kroh Naturhistorisches Museum Wien Burgring 7, 1010 Wien, Österreich (Austria) Tel.: +43 (1) 521 77 / 576 Fax: +43 (1) 521 77 / 459 e-mail: [email protected] Umschlagentwurf: Mathias Harzhauser & Andreas Kroh Layout: Andreas Kroh Druck: Grasl Druck & Neue Medien GmbH, Bad Vöslau Disclaimer: Following the recommendation of the various nomenclatorial codes this work is not issued for the purpose of public and permanent scientific record, or for purposes of nomenclature and as such is not published within the meaning of the various codes. Any nomenclatural act contained herein (e.g. new combinations, new names), do thus not enter biological nomenclature or pre-empt intended publication in another work. 2 BioSyst.EU 2013 ● Global systematics! ● 18–22 February 2013, Vienna, Austria Contents Organising Committee ................................................................................... 4 Advisory Board ............................................................................................... 4 Preface ............................................................................................................