DOCSLIB.ORG

University of Florida Thesis Or Dissertation Formatting Template

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Florida Thesis Or Dissertation Formatting Template THE OCCURRENCE OF ENTOMOPATHOGENIC NEMATODES AND THEIR NATURAL ENEMIES IN GREEK CITRUS ORCHARDS By ALEXANDROS DRITSOULAS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2020 © 2020 Alexandros Dritsoulas To my wife, Stella and Greece ACKNOWLEDGMENTS I would like to begin by wholeheartedly thanking my advisor Dr. Larry W. Duncan for his unceasing support of my doctoral research. I would like to express my gratitude and appreciation to him for his immense enthusiasm and motivation during my studies. His insightful guidance has helped me navigate the most challenging part of my life thus far. I am a better person for having known him. I would also like to acknowledge Dr. Tesfamariam Mengistu for his advice, assistance, and consideration for me particularly during my first two years as a Ph.D. student. I am also indebted to the rest of my dissertation committee: Dr. Peter DiGennaro, Dr. Felipe Soto-Adames, Dr. Lukasz Stelinski, and Dr. Nian Wang for their perceptive comments and for encouraging me to widen the scope of my research. My fellow graduate students and lab mates have been an integral part of my grad-student life and I would like to thank them for their friendship, compassion, and camaraderie. Their inspiring words will accompany me throughout my career and life. Last but not least, I would like to express my immense appreciation to my parents for standing by me, and my wife for all the sacrifices she made and her willingness to follow me on the path I have chosen. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................7 LIST OF FIGURES .........................................................................................................................8 ABSTRACT ...................................................................................................................................10 CHAPTER 1 GENERAL INTRODUCTION ..............................................................................................12 Review of Literature ...............................................................................................................14 Entomopathogenic Nematode Ecology ...........................................................................14 Entomopathogenic Nematode Phylogeny .......................................................................16 Soil Microarthropods .......................................................................................................18 Molecular approach and characterization of the target population .................................24 Conserving Services of Entomopathogenic Nematodes: An Example ...........................28 2 TOWARD MAXIMIZING TAXONOMIC COVERAGE IN METAGENOMIC STUDIES OF ENVIRONMENTAL SAMPLES ...................................................................31 Introduction .............................................................................................................................32 Materials and Methods ...........................................................................................................35 Sucrose Centrifugation and Flotation-Berlese-Flotation Comparison ............................35 Sucrose Centrifugation, Berlese funnels and Heptane Flotation Comparison. ...............36 Results.....................................................................................................................................37 Sucrose Centrifugation and Flotation-Berlese-Flotation Fomparison .............................37 Sucrose Centrifugation, Berlese Funnels and Heptane Flotation Comparison. ..............37 Discussion ...............................................................................................................................38 3 COMPARING HIGH THROUGHPUT SEQUENCING AND REAL TIME QPCR FOR CHARACTERIZING ENTOMOPATHOGENIC NEMATODE BIOGEOGRAPHY .................................................................................................................47 Introduction .............................................................................................................................48 Materials and Method .............................................................................................................50 Samples Collection ..........................................................................................................50 Library Preparation ..........................................................................................................51 Bioinformatics .................................................................................................................52 Statistical Analysis ..........................................................................................................53 Phylogenetic Tree ............................................................................................................54 Results.....................................................................................................................................55 Discussion ...............................................................................................................................57 5 4 NATURAL OCCURRENCE OF ENTOMOPATHOGENIC NEMATODES AND THEIR NATURAL ENEMIES IN GREEK CITRUS ORCHARDS.....................................70 Introduction .............................................................................................................................71 Materials and methods ............................................................................................................73 Sampling ..........................................................................................................................73 Soil analysis .....................................................................................................................74 DNA extraction ...............................................................................................................74 Library preparation ..........................................................................................................74 Bioinformatics .................................................................................................................76 Real time PCR testing, cultures of EPN and standard curve preparation .......................77 Gene copies by individuals’ volume and data correction. ...............................................78 Phylogenetic analysis ......................................................................................................78 Statistical Analysis ..........................................................................................................79 Results.....................................................................................................................................79 Discussion ...............................................................................................................................82 5 CONCLUSION.....................................................................................................................101 LIST OF REFERENCES ............................................................................................................104 BIOGRAPHICAL SKETCH .......................................................................................................118 6 LIST OF TABLES Table page 3-1 Detection frequency of entomopathogenic nematodes (EPNs) and species previously reported to EPN competitors ..............................................................................................62 3-2 Non-parametric Spearman's correlations between the species’ measurements from metabarcoding and qPCR ..................................................................................................62 3-3 Significant variables from stepwise multiple regression of two nematode species measured by high throughput sequencing or qPCR ...........................................................63 3-4 Significance of the Canonical Correspondence Analysis model, axes, and variables. ......63 3-5 S. feltiae ASVs table illustrating “head-tail” structure associated with the presence of within the species variation. ...............................................................................................64 4-1 Amplicon sequence variant (ASV) table illustrating “head-tail” structures associated with intraspecific variation ................................................................................................88 4-2 Non-parametric (Spearman's) correlations between number of metabarcoding reads and the Ct values derived from qPCR measurements of the nine EPN species ................89 4-3 Significance of the Canonical Correspondence Analysis variables. ..................................90 4-4 Significant variables from stepwise multiple regression of nine nematode species measured by high throughput sequencing..........................................................................91 7 LIST OF FIGURES Figure page 2-1 Process flow diagrams for four extraction methods ..........................................................41 2-2 Efficiency of sucrose centrifugation (SC) compared to that
Load more

Recommended publications
  • Going Deeper Into High and Low Phylogenetic Relationships of Protura
    G C A T T A C G G C A T genes Article Going Deeper into High and Low Phylogenetic Relationships of Protura 1, , 2,3, 3 1 1 Antonio Carapelli * y , Yun Bu y, Wan-Jun Chen , Francesco Nardi , Chiara Leo , Francesco Frati 1 and Yun-Xia Luan 3,4,* 1 Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; [email protected] (F.N.); [email protected] (C.L.); [email protected] (F.F.) 2 Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai 200041, China; [email protected] 3 Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; [email protected] 4 Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China * Correspondence: [email protected] (A.C.); [email protected] (Y.-X.L.); Tel.: +39-0577-234410 (A.C.); +86-18918100826 (Y.-X.L.) These authors contributed equally to this work. y Received: 16 March 2019; Accepted: 5 April 2019; Published: 10 April 2019 Abstract: Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification.
    [Show full text]
  • 1 Reproductive Efficiency of Entomopathogenic Nematodes As Scavengers. Are They Able to 1 Fight for Insect's Cadavers?
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Sapientia 1 Reproductive efficiency of entomopathogenic nematodes as scavengers. Are they able to 2 fight for insect’s cadavers? 3 4 Rubén Blanco-Péreza,b, Francisco Bueno-Palleroa,b, Luis Netob, Raquel Campos-Herreraa,b,* 5 6 a MeditBio, Centre for Mediterranean Bioresources and Food, Universidade do Algarve, Campus 7 de Gambelas, 8005, Faro (Portugal) 8 b Universidade do Algarve, Campus de Gambelas, 8005, Faro (Portugal) 9 10 *Corresponding author 11 Email: [email protected] 12 1 13 Abstract 14 15 Entomopathogenic nematodes (EPNs) and their bacterial partners are well-studied insect 16 pathogens, and their persistence in soils is one of the key parameters for successful use as 17 biological control agents in agroecosystems. Free-living bacteriophagous nematodes (FLBNs) in 18 the genus Oscheius, often found in soils, can interfere in EPN reproduction when exposed to live 19 insect larvae. Both groups of nematodes can act as facultative scavengers as a survival strategy. 20 Our hypothesis was that EPNs will reproduce in insect cadavers under FLBN presence, but their 21 reproductive capacity will be severely limited when competing with other scavengers for the same 22 niche. We explored the outcome of EPN - Oscheius interaction by using freeze-killed larvae of 23 Galleria mellonella. The differential reproduction ability of two EPN species (Steinernema 24 kraussei and Heterorhabditis megidis), single applied or combined with two FLBNs (Oscheius 25 onirici or Oscheius tipulae), was evaluated under two different infective juvenile (IJ) pressure: 26 low (3 IJs/host) and high (20 IJs/host).
    [Show full text]
  • Towards Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius Tipulae to Identify Mutations Affecting Vulva Development
    Genetics: Early Online, published on June 19, 2017 as 10.1534/genetics.117.203521 Towards universal forward genetics: using a draft genome sequence of the nematode Oscheius tipulae to identify mutations affecting vulva development 5 Fabrice Besnard*1,2,3, Georgios Koutsovoulos†1,4, Sana Dieudonné*, Mark Blaxter†,5 and Marie-Anne Félix*2,5 10 * Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure, 75005 Paris, France † Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK 1 Co-first authors. 2 Co-corresponding authors: [email protected], [email protected] 3 Current Address: Laboratoire de Reproduction de développement des plantes, Lyon, France; 15 4 Current Address: INRA, Université Côte d’Azur, CNRS, ISA, France 5 Co-last authors Besnard F., Koutsovoulos G. et al. Oscheius Mapping-by-sequencing 1/48 Copyright 2017. Running title: Oscheius Mapping-by-sequencing Key words : Oscheius tipulae, genome assembly, mapping-by sequencing, vulva development, mig-13 Co-corresponding authors: Fabrice Besnard Address: Laboratoire Reproduction et Développement des Plantes (RDP) 20 Ecole Normale Supérieure de Lyon (ENS-Lyon) 46, allée d'Italie, 69364 LYON Cedex 07. Tel: +33-4-72-72-86-05 mail: [email protected] Marie-Anne Félix Address: Institute of Biology of the Ecole Normale Supérieure (IBENS) 25 46 rue d'Ulm, 75230 Paris cedex 05, France Tel: +33-1-44-32-39-44 mail: [email protected] Besnard F., Koutsovoulos G. et al. Oscheius Mapping-by-sequencing 2/48 Abstract Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species.
    [Show full text]
  • For the Love of Insects
    For the Love of Insects “In terms of biomass and their interactions with other terrestrial organisms, insects are the most important group of terrestrial animals.” --Grimaldi and Engel, 2005 Outline • The Most Successful Animals on Earth: a Brief (Entomological) Journey through Time • Insect Physiology and Development • Common Insects and their Identification Whence and Whither: Insect Origins and Evolution Before diversity, there was evolution… A ~500 million year journey… Silurian • Insect Flight: 400 mya • Modern insect orders: 250 mya • Primitive mammals: 120 mya • Modern mammals: 60 mya The Jointed Animals Phylum: Arthropoda • 75% of all species on earth are arthropods • Internal/External specialization of body parts = tagmosis • Hardened exoskeleton • Articulated body plates • Paired, jointed appendages sciencenewsjournal.com Tagmosis: highly specialized body segments found in all arthropods; insects: head, thorax, abdomen; spiders: cephalothorax and opisthosoma Epiclass HEXAPODA: Late Silurian/Early Devonian Class Entognatha Order Diplura Ellipura Order Protura Order Collembola Class Insecta (= Ectognatha) Hexapoda • 6 legs; 11 abdominal segments (or fewer) taxondiversity.fieldofscience.com • Entognatha: Protura, Diplura, and Collembola • Ectognatha: Insects The First Insects: Apterygota Archaeognatha: The Jumping Bristletails • ~500 spp. worldwide; wide range of habitats; • 4 Families (2 extinct) which occur mostly in rocky habitats • Mostly detritovores, but scavenge dead arthropods or eat exuviae; • Indirect mating behavior;
    [Show full text]
  • Research/Investigación Addition of a New Insect Parasitic Nematode, Oscheius Tipulae, to Iranian Fauna
    RESEARCH/INVESTIGACIÓN ADDITION OF A NEW INSECT PARASITIC NEMATODE, OSCHEIUS TIPULAE, TO IRANIAN FAUNA J. Karimi1*, N. Rezaei1, and E. Shokoohi2 1Biocontrol and Insect Pathology Lab., Department of Plant Protection, Ferdowsi University of Mashhad, PO Box 91775-1163, Mashhad, Iran; 2Unit for Environmental Sciences and Management, Potchefstroom, North West University, South Africa; *Corresponding author: [email protected] ABSTRACT Karimi, J., N. Rezaei, and E. Shokoohi. 2018. Addition of a new insect parasitic nematode, Oscheius tipulae, to Iranian fauna. Nematropica 48:00-00. On behalf of an ongoing project on diversity of insect pathogenic and insect parasitic nematodes of Iran, a new species was collected and characterized. This species was collected in soil from the Mashhad, Arak, and Mahalat regions of Iran through 2011-2012 using Galleria larvae baits. Based on morphologic and morphometric traits as well as SEM images, the species tentatively has been identified as Oscheius tipulae. Phylogenetic analysis based on ITS and 18S rDNA genes confirmed the species delimitation. This is the first record of this species from Iran. Key words: 18S rDNA, insect parasitic nematode, Iran, ITS, Oscheius tipulae, SEM RESUMEN Karimi, J., N. Rezaei, y E. Shokoohi. 2018. Adición de un nuevo nematodo parásito de insectos, Oscheius tipulae, a la fauna Irán. Nematropica 48:00-00. En nombre de un proyecto en curso sobre diversidad de patógenos de insectos y nematodos parásitos de insectos de Irán, se recolectó y caracterizó una nueva especie. Esta especie fue recolectada en suelo de las regiones de Mashhad, Arak y Mahalat de Irán durante el período 2011-2012 utilizando cebos Galleria.
    [Show full text]
  • Systematic and Biogeographical Study of Protura (Hexapoda) in Russian Far East: New Data on High Endemism of the Group
    A peer-reviewed open-access journal ZooKeys 424:Systematic 19–57 (2014) and biogeographical study of Protura (Hexapoda) in Russian Far East... 19 doi: 10.3897/zookeys.424.7388 RESEARCH ARTICLE www.zookeys.org Launched to accelerate biodiversity research Systematic and biogeographical study of Protura (Hexapoda) in Russian Far East: new data on high endemism of the group Yun Bu1, Mikhail B. Potapov2, Wen Ying Yin1 1 Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China 2 Moscow State Pedagogical University, Kibalchich str., 6, korp. 5, Moscow, 129278 Russia Corresponding author: Yun Bu ([email protected]) Academic editor: L. Deharveng | Received 4 March 2014 | Accepted 4 June 2014 | Published 8 July 2014 http://zoobank.org/38EAC4B7-8834-4054-B9AC-9747AC476543 Citation: Bu Y, Potapov MB, Yin WY (2014) Systematic and biogeographical study of Protura (Hexapoda) in Russian Far East: new data on high endemism of the group. ZooKeys 424: 19–57. doi: 10.3897/zookeys.424.7388 Abstract Proturan collections from Magadan Oblast, Khabarovsk Krai, Primorsky Krai, and Sakhalin Oblast are re- ported here. Twenty-five species are found of which 13 species are new records for Russian Far East which enrich the knowledge of Protura known for this area. Three new species Baculentulus krabbensis sp. n., Fjellbergella lazovskiensis sp. n. and Yichunentulus alpatovi sp. n. are illustrated and described. The new materials of Imadateiella sharovi (Martynova, 1977) are studied and described in details. Two new combi- nations, Yichunentulus borealis (Nakamura, 2004), comb. n. and Fjellbergella jilinensis (Wu & Yin, 2007), comb.
    [Show full text]
  • Developmental Plasticity, Ecology, and Evolutionary Radiation of Nematodes of Diplogastridae
    Developmental Plasticity, Ecology, and Evolutionary Radiation of Nematodes of Diplogastridae Dissertation der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Vladislav Susoy aus Berezniki, Russland Tübingen 2015 Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen. Tag der mündlichen Qualifikation: 5 November 2015 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Ralf J. Sommer 2. Berichterstatter: Prof. Dr. Heinz-R. Köhler 3. Berichterstatter: Prof. Dr. Hinrich Schulenburg Acknowledgements I am deeply appreciative of the many people who have supported my work. First and foremost, I would like to thank my advisors, Professor Ralf J. Sommer and Dr. Matthias Herrmann for giving me the opportunity to pursue various research projects as well as for their insightful scientific advice, support, and encouragement. I am also very grateful to Matthias for introducing me to nematology and for doing an excellent job of organizing fieldwork in Germany, Arizona and on La Réunion. I would like to thank the members of my examination committee: Professor Heinz-R. Köhler and Professor Hinrich Schulenburg for evaluating this dissertation and Dr. Felicity Jones, Professor Karl Forchhammer, and Professor Rolf Reuter for being my examiners. I consider myself fortunate for having had Dr. Erik J. Ragsdale as a colleague for several years, and more than that to count him as a friend. We have had exciting collaborations and great discussions and I would like to thank you, Erik, for your attention, inspiration, and thoughtful feedback. I also want to thank Erik and Orlando de Lange for reading over drafts of this dissertation and spelling out some nuances of English writing.
    [Show full text]
  • Role of Arthropods in Maintaining Soil Fertility
    Agriculture 2013, 3, 629-659; doi:10.3390/agriculture3040629 OPEN ACCESS agriculture ISSN 2077-0472 www.mdpi.com/journal/agriculture Review Role of Arthropods in Maintaining Soil Fertility Thomas W. Culliney Plant Epidemiology and Risk Analysis Laboratory, Plant Protection and Quarantine, Center for Plant Health Science and Technology, USDA-APHIS, 1730 Varsity Drive, Suite 300, Raleigh, NC 27606, USA; E-Mail: [email protected]; Tel.: +1-919-855-7506; Fax: +1-919-855-7595 Received: 6 August 2013; in revised form: 31 August 2013 / Accepted: 3 September 2013 / Published: 25 September 2013 Abstract: In terms of species richness, arthropods may represent as much as 85% of the soil fauna. They comprise a large proportion of the meso- and macrofauna of the soil. Within the litter/soil system, five groups are chiefly represented: Isopoda, Myriapoda, Insecta, Acari, and Collembola, the latter two being by far the most abundant and diverse. Arthropods function on two of the three broad levels of organization of the soil food web: they are plant litter transformers or ecosystem engineers. Litter transformers fragment, or comminute, and humidify ingested plant debris, which is deposited in feces for further decomposition by micro-organisms, and foster the growth and dispersal of microbial populations. Large quantities of annual litter input may be processed (e.g., up to 60% by termites). The comminuted plant matter in feces presents an increased surface area to attack by micro-organisms, which, through the process of mineralization, convert its organic nutrients into simpler, inorganic compounds available to plants. Ecosystem engineers alter soil structure, mineral and organic matter composition, and hydrology.
    [Show full text]
  • The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea Augens, a Key Reference Hexapod for Studying the Emergence of Insect Innovations
    bioRxiv preprint doi: https://doi.org/10.1101/585695; this version posted June 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations Mosè Manni1*, Felipe A. Simao1, Hugh M. Robertson2, Marco A. Gabaglio1, Robert M. Waterhouse3, Bernhard Misof4, Oliver Niehuis5, Nikolaus U. Szucsich6, Evgeny M. Zdobnov1* 1Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland. 2Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. 3Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland. 4Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany. 5Department of Evolutionary Biology and Ecology, Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany. 6Natural History Museum Vienna, 3rd Zoological Dept., Vienna, Austria. *Authors for Correspondence: Evgeny M. Zdobnov, email: [email protected] Mosè Manni, email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/585695; this version posted June 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • Life in the Leaf Litter Layer
    CONTENTS Introduction..........................................................1 The City Woodland: Nature Next Door....................1 Life in the Leaf Litter Layer ....................................5 Some of the Animals You Might Find in Your City Woodlands .........................................7 Slugs and Snails ....................................................7 Roundworms ........................................................7 Worms .................................................................7 Water Bears..........................................................9 Animals with Jointed Legs (Arthropoda) .................9 Sowbugs.......................................................10 Spiders, Harvestmen, Pseudoscorpions, Mites .................................10 Acknowledgements: Millipedes, Centipedes, and Symphylans .........12 Thanks to our many helpful reviewers: Regina Alvarez (Central Park Conservancy) Proturans, Double-Tails, and Springtails ..........14 Dennis Burton (Schuylkill Center, Philadelphia) Margaret Carreiro (University of Louisville) Insects..........................................................15 Robert DeCandido (Linnaean Society of New York) ......................................... David Grimaldi (American Museum of Natural History) Conserving Leaf Litter 20 Richard Kruzansky (Central Park Conservancy) Human Impact on Leaf Litter Invertebrates......20 Mariet Morgan (American Museum of Natural History) Richard Pouyat (USDA Forest Service) Park Managers to the Rescue .........................22
    [Show full text]
  • A History of Insect Phylogenetics Rsif.Royalsocietypublishing.Org Karl M
    Progress, pitfalls and parallel universes: a history of insect phylogenetics rsif.royalsocietypublishing.org Karl M. Kjer1, Chris Simon2, Margarita Yavorskaya3 and Rolf G. Beutel3 1Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA Review 2Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA Cite this article: Kjer KM, Simon C, 3Institut fu¨r Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany Yavorskaya M, Beutel RG. 2016 Progress, KMK, 0000-0001-7370-9617 pitfalls and parallel universes: a history of insect phylogenetics. J. R. Soc. Interface 13: The phylogeny of insects has been both extensively studied and vigorously 20160363. debated for over a century. A relatively accurate deep phylogeny had been pro- duced by 1904. It was not substantially improved in topology until recently http://dx.doi.org/10.1098/rsif.2016.0363 when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecu- lar phylogenetic studies (1985–2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Received: 9 May 2016 Adding to the lack of consensus, this period was characterized by a polariz- Accepted: 19 July 2016 ation of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably Subject Category: erroneous. The size of datasets has been growing exponentially since the mid- 1980s accompanied by a wave of confidence that all relationships will soon be Review known.
    [Show full text]
  • Influence of Climatic Variables and Biological Control Agents
    INFLUENCE OF CLIMATIC VARIABLES AND BIOLOGICAL CONTROL AGENTS (NEMATODES) ON THE DISTRIBUTION AND SURVIVAL OF THE COFFEE BERRY BORER, HYPOTHENEMUS HAMPEI, IN PUERTO RICO By José Miguel García Peña A dissertation submitted to the DEPARTMENT OF BIOLOGY FACULTY OF NATURAL SCIENCES UNIVERSITY OF PUERTO RICO RÍO PIEDRAS CAMPUS In partial fulfillment of the requirements for the degree of DOCTOR IN PHILOSOPHY December 2019 San Juan, Puerto Rico © José Miguel García Peña All rights reserved ii This dissertation has been accepted by faculty of the: DEPARTMENT OF BIOLOGY FACULTY OF NATURAL SCIENCES UNIVERSITY OF PUERTO RICO RÍO PIEDRAS CAMPUS In partial fulfillment of the requirements for the degree of DOCTOR IN PHILOSOPHY Dissertation Committee: _________________________________________ José Carlos Verle Rodríguez, Ph.D., Advisor __________________________________________ William Gould, Ph.D. __________________________________________ Paul Bayman, Ph.D. __________________________________________ Alberto M. Sabat, Ph.D. __________________________________________ Miguel Acevedo, Ph.D. iii TABLE OF CONTENS LIST OF TABLES ................................................................................................................................vi LIST OF FIGURES ............................................................................................................................. vii ABSTRACT ...................................................................................................................................... viii DEDICATION
    [Show full text]