DOCSLIB.ORG

Download It Using the Following Command

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Download It Using the Following Command UC San Diego UC San Diego Electronic Theses and Dissertations Title New methods for inferring, assessing, and using phylogenetic trees from genomic and microbiome data Permalink https://escholarship.org/uc/item/8nc7x677 Author Sayyari, Erfan Publication Date 2019 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SAN DIEGO New methods for inferring, assessing, and using phylogenetic trees from genomic and microbiome data A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Electrical Engineering (Signal and Image Processing) by Erfan Sayyari Committee in charge: Professor Siavash Mirarab, Chair Professor Vineet Bafna Professor Alon Orlitsky Professor Greg Rouse Professor Behrouz Touri 2019 Copyright Erfan Sayyari, 2019 All rights reserved. The dissertation of Erfan Sayyari is approved, and it is ac- ceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2019 iii DEDICATION I dedicate my dissertation to my beloved mother and father. iv EPIGRAPH Nothing in Biology Makes Sense Except in the Light of Evolution. —Theodosius Dobzhansky v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . v Table of Contents . vi List of Figures . x List of Tables . xiv Acknowledgements . xv Vita . xviii Abstract of the Dissertation . xx Chapter 1 Introduction . 1 Chapter 2 Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction . 8 2.1 Background . 9 2.2 Methods . 11 2.2.1 General theoretical results . 12 2.2.2 Tree inference algorithms . 19 2.2.3 DISTIQUE (theory) . 22 2.2.4 DISTIQUE (algorithmic design) . 23 2.2.5 Computing pseudo-counts for allpairs-max . 24 2.2.6 Difficulties with long branches and need for majority con- sensus . 25 2.2.7 Experimental setup . 33 2.3 Results . 36 2.3.1 Comparison between DISTIQUE variants . 36 2.3.2 DISTIQUE versus other methods . 43 2.3.3 Biological results . 47 2.4 Discussion . 49 2.5 Conclusions . 51 2.6 Acknowledgements . 51 vi Chapter 3 Fast coalescent-based computation of local branch support from quartet frequencies . 56 3.1 Introduction . 57 3.2 New Approaches . 60 3.2.1 Calculation of local posterior probability . 61 3.2.2 Calculation of branch length . 69 3.2.3 Calculation of quartet support . 72 3.2.4 Other considerations . 73 3.3 Materials and Methods . 73 3.3.1 Datasets . 73 3.3.2 Evaluation procedure . 78 3.4 Results . 79 3.4.1 A-200 dataset . 79 3.4.2 Avian . 89 3.4.3 Posterior and MLBS . 90 3.4.4 Biological datasets . 95 3.5 Discussions . 105 3.5.1 Gene tree estimation error . 106 3.5.2 High support despite high discordance . 108 3.5.3 Limitations and future work . 109 3.6 Acknowledgements . 109 Chapter 4 Testing for polytomies in phylogenetic species trees using quartet fre- quencies . 110 4.1 Introduction . 111 4.2 Materials and Methods . 115 4.2.1 Background . 115 4.2.2 A statistical test of polytomy . 115 4.2.3 Evaluations . 119 4.3 Results . 123 4.3.1 Simulated datasets . 123 4.3.2 Biological dataset . 126 4.4 Discussion . 132 4.4.1 Power . 132 4.4.2 Divergence from the MSC model and connections to localPP135 4.4.3 The effective number of gene trees . 137 4.4.4 Interpretation . 140 4.5 Conclusions . 141 4.6 Acknowledgements . 141 vii Chapter 5 Fragmentary gene sequences negatively impact gene tree and species tree reconstruction . 142 5.1 Introduction . 143 5.2 Results . 147 5.2.1 Simulation Results . 147 5.2.2 Empirical Results . 151 5.3 Discussion . 157 5.3.1 Impacts of fragments . 157 5.3.2 Methodological limitations . 162 5.4 Materials and Methods . 163 5.4.1 Analysis pipeline for insect dataset . 163 5.4.2 Simulation procedure . 184 5.4.3 Statistical tests . 186 5.5 Acknowledgements . 186 Chapter 6 DiscoVista: interpretable visualizations of gene tree discordance . 187 6.1 Introduction . 187 6.2 Results . 190 6.3 Acknowledgements . 206 Chapter 7 TADA . 207 7.1 Introduction . 208 7.2 The TADA method . 210 7.2.1 Background and Notations . 210 7.2.2 Generative model used in TADA . 211 7.2.3 Data augmentation procedure . 215 7.2.4 Balancing . 220 7.3 Experimental setup . 222 7.3.1 Datasets . 222 7.3.2 Experiments . 223 7.3.3 Evaluation procedure. 224 7.3.4 Method details . 224 7.4 Results . 228 7.4.1 E1: complete datasets . 228 7.4.2 E2: unbalanced class labels . 230 7.4.3 E3: biased class labels . 234 7.5 Discussions and conclusions . 234 7.5.1 Using a Beta-Binomial distribution with two parameters 237 7.6 Acknowledgements . 243 Appendix A Anchored distances for quartet-based estimation of phylogenetic trees and applications to coalescent-based analyses . 244 A.1 Commands and version numbers . 244 viii Appendix B Supplementary Material for “Fast coalescent-based computation of local branch support from quartet frequencies” . 246 B.1 Commands and version numbers . 247 B.1.1 ASTRAL . 247 B.1.2 MP-EST . 247 Appendix C Supplementary Material for “DiscoVista: interpretable visualizations of gene tree discordance” . 248 C.1 Structure of parameter files . 248 C.2 Installation, Commands, and Usage . 249 Bibliography . 251 ix LIST OF FIGURES Figure 2.1: Possible ways of adding anchors to a quartet. 14 Figure 2.2: An example where long branches can cause problems. See section 2.3 for descriptions. 24 Figure 2.3: Accuracy of different implementations of DISTIQUE for the Mammalian dataset. 37 Figure 2.4: Accuracy of different implementations of DISTIQUE for the Avian dataset. 38 Figure 2.5: Impact of number of rounds of anchor sampling on accuracy. 40 Figure 2.6: Impact of number of rounds of anchor sampling on accuracy. 41 Figure 2.7: Impact of distance method on accuracy. 42 Figure 2.8: DISTIQUE versus other methods on (A) simPhy-size and (B) simPhy- ILS datasets using estimated gene trees. Boxes: (A) number of genes and (B) levels of ILS. 44 Figure 2.9: Running time comparisons on the simPhy-size datasets with 1000 genes. 46 Figure 2.10: Running times of DISTIQUE versus other methods for the simPhy-size dataset. 46 Figure 2.11: The accuracy of methods on Avian (A) and Mammalian (B) datasets using estimated gene trees. Left: number of genes is fixed (1000 for avian, 200 for mammalian) and ILS levels change. 48 Figure 2.12: Species trees generated using DISTIQUE on Avian biological dataset [214]. 49 Figure 2.13: Species trees generated using ASTRID (NJst) and ASTRAL on Avian biological dataset [214]..
Load more

Recommended publications
  • Millichope Park and Estate Invertebrate Survey 2020
    Millichope Park and Estate Invertebrate survey 2020 (Coleoptera, Diptera and Aculeate Hymenoptera) Nigel Jones & Dr. Caroline Uff Shropshire Entomology Services CONTENTS Summary 3 Introduction ……………………………………………………….. 3 Methodology …………………………………………………….. 4 Results ………………………………………………………………. 5 Coleoptera – Beeetles 5 Method ……………………………………………………………. 6 Results ……………………………………………………………. 6 Analysis of saproxylic Coleoptera ……………………. 7 Conclusion ………………………………………………………. 8 Diptera and aculeate Hymenoptera – true flies, bees, wasps ants 8 Diptera 8 Method …………………………………………………………… 9 Results ……………………………………………………………. 9 Aculeate Hymenoptera 9 Method …………………………………………………………… 9 Results …………………………………………………………….. 9 Analysis of Diptera and aculeate Hymenoptera … 10 Conclusion Diptera and aculeate Hymenoptera .. 11 Other species ……………………………………………………. 12 Wetland fauna ………………………………………………….. 12 Table 2 Key Coleoptera species ………………………… 13 Table 3 Key Diptera species ……………………………… 18 Table 4 Key aculeate Hymenoptera species ……… 21 Bibliography and references 22 Appendix 1 Conservation designations …………….. 24 Appendix 2 ………………………………………………………… 25 2 SUMMARY During 2020, 811 invertebrate species (mainly beetles, true-flies, bees, wasps and ants) were recorded from Millichope Park and a small area of adjoining arable estate. The park’s saproxylic beetle fauna, associated with dead wood and veteran trees, can be considered as nationally important. True flies associated with decaying wood add further significant species to the site’s saproxylic fauna. There is also a strong
    [Show full text]
  • Acmasphere Issue 62
    acma investigations Broadcasting investigations, October to December 2010 � This summary is of ACMA broadcasting investigations completed in the three months from 1 October to 31 December 2010. There is also, with the cooperation of Free TV Australia and Commercial Radio Australia (CRA), a three-month report of the number and substance of complaints made directly to the commercial broadcasters. The broadcasting Complaints about possible breaches Most investigation reports (with the complaints process of program standards (children’s exception of community non-breach Primary responsibility for the resolution television, Australian content, captioning investigation reports) are published of broadcasting code-related and disclosure), provisions of the BSA on the ACMA website at complaints rests with the licensees. and licence conditions may be made www.acma.gov.au (go to About The Broadcasting Services Act 1992 directly to the ACMA. Complainants ACMA: Publications & research > (the BSA) lays down a general procedure are not obliged to contact a licensee Publications > Broadcasting publications for complaints-handling whereby a first in these instances. > Broadcasting investigations reports). complainant is required to approach a licensee first, who in turn is obliged The ACMA may find that a licensee to respond. has breached a broadcasting code of practice or a licensee may admit However, if a complainant does not to a breach of a code. Breaches of receive a response within 60 days, the codes are not breaches of the or considers the response received BSA, although the ACMA may make to be inadequate, the matter may then compliance with a code a condition be referred to the ACMA for investigation.
    [Show full text]
  • CR-126149) an EMPIRICAL METHOD for D172-22859 - DETERMINING the LUNAR GRAVITY FIELD Ph.D
    — 1 (NASA-CR-126149) AN EMPIRICAL METHOD FOR D172-22859 - DETERMINING THE LUNAR GRAVITY FIELD Ph.D. Thesis - George Washington Univ. A.J. Ferrari (Bencomm, Inc.) Sep, 1971 158 p CSCL 03B G3/30 24617 ,..4 .- 1.,t,-;.-:', rt' ''''...- - '. ' ' ',,c , - (y,,,,- At.,. ','c -...,: <,,...,,,,,..,. ,„.,... c‘,,,,, ,,,, :.--s-f PPR 1012 %--..,i, I ,c\f71 , ,•., r,..) ,,,::.:,,..,,,,f.:11:11iiI ti.:. ic'":.,: ;,f,. ti!at ',.1,,,t.. kFI Cilifil,..r. c"--: --', I :VI ::::::C: , 3 AN EMPIRICAL METHOD FOR DETERMINING THE LUNAR GRAVITY FIELD By ALFRED JOHN FERRARI B.E.E. Manhattan College 1963 M.S. The George Washington University 1967 A Dissertation Submitted To The Faculty Of The School of Engineering and Applied Science Of The George Washington University In partial satisfaction of the requirements for the degree of Doctor of Science. September 1971 BIOGRAPHY ALFRED JOHN FERRARI Alfred J. Ferrari was born in , the son of Margaret Ferrari and Johr C. Ferrari. He attended Loyola High School in New York City and, upon graduation in 1959, he enrolled in Manhattan College, Riverdale, New York. In June of 1963 he received a Bachelor of Electrical Engineering degree. After graduation he entered the United States Air Force and was assigned to the National Security Agency in Washington, D. C. where his work dealt with electronic systems analysis. In September 1964 he entered the George Washington University, Washington, D. C. and received a Master of Science degree in June 1967. In June 1967 he began studies at the George Washington University in a Doctor of Science program. In September 1967, upon completion of military duty, he accepted employment at Bellcomm, Inc., Washington, D.
    [Show full text]
  • Final Report 1
    Sand pit for Biodiversity at Cep II quarry Researcher: Klára Řehounková Research group: Petr Bogusch, David Boukal, Milan Boukal, Lukáš Čížek, František Grycz, Petr Hesoun, Kamila Lencová, Anna Lepšová, Jan Máca, Pavel Marhoul, Klára Řehounková, Jiří Řehounek, Lenka Schmidtmayerová, Robert Tropek Březen – září 2012 Abstract We compared the effect of restoration status (technical reclamation, spontaneous succession, disturbed succession) on the communities of vascular plants and assemblages of arthropods in CEP II sand pit (T řebo ňsko region, SW part of the Czech Republic) to evaluate their biodiversity and conservation potential. We also studied the experimental restoration of psammophytic grasslands to compare the impact of two near-natural restoration methods (spontaneous and assisted succession) to establishment of target species. The sand pit comprises stages of 2 to 30 years since site abandonment with moisture gradient from wet to dry habitats. In all studied groups, i.e. vascular pants and arthropods, open spontaneously revegetated sites continuously disturbed by intensive recreation activities hosted the largest proportion of target and endangered species which occurred less in the more closed spontaneously revegetated sites and which were nearly absent in technically reclaimed sites. Out results provide clear evidence that the mosaics of spontaneously established forests habitats and open sand habitats are the most valuable stands from the conservation point of view. It has been documented that no expensive technical reclamations are needed to restore post-mining sites which can serve as secondary habitats for many endangered and declining species. The experimental restoration of rare and endangered plant communities seems to be efficient and promising method for a future large-scale restoration projects in abandoned sand pits.
    [Show full text]
  • Development of Native Bees As Pollinators of Vegetable Seed Crops
    Development of native bees as pollinators of vegetable seed crops Dr Katja Hogendoorn The University of Adelaide Project Number: VG08179 VG08179 This report is published by Horticulture Australia Ltd to pass on information concerning horticultural research and development undertaken for the vegetables industry. The research contained in this report was funded by Horticulture Australia Ltd with the financial support of Rijk Zwaan Australia Pty Ltd. All expressions of opinion are not to be regarded as expressing the opinion of Horticulture Australia Ltd or any authority of the Australian Government. The Company and the Australian Government accept no responsibility for any of the opinions or the accuracy of the information contained in this report and readers should rely upon their own enquiries in making decisions concerning their own interests. ISBN 0 7341 2699 9 Published and distributed by: Horticulture Australia Ltd Level 7 179 Elizabeth Street Sydney NSW 2000 Telephone: (02) 8295 2300 Fax: (02) 8295 2399 © Copyright 2011 Horticulture Australia Limited Final Report: VG08179 Development of native bees as pollinators of vegetable seed crops 1 July 2009 – 9 September 2011 Katja Hogendoorn Mike Keller The University of Adelaide HAL Project VG08179 Development of native bees as pollinators of vegetable seed crops 1 July 2009 – 9 September 2011 Project leader: Katja Hogendoorn The University of Adelaide Waite Campus Adelaide SA 5005 e-mail: [email protected] Phone: 08 – 8303 6555 Fax: 08 – 8303 7109 Other key collaborators: Assoc. Prof. Mike Keller, The University of Adelaide Mr Arie Baelde, Rijk Zwaan Australia Ms Lea Hannah, Rijk Zwaan Australia Ir. Ronald Driessen< Rijk Zwaan This report details the research and extension delivery undertaken in the above project aimed at identification of the native bees that contribute to the pollination of hybrid carrot and leek, and at the development of methods to enhance the presence of these bees on the crops and at enabling their use inside greenhouses.
    [Show full text]
  • The Female Cephalothorax of Xenos Vesparum Rossi, 1793 (Strepsiptera: Xenidae) 327-347 75 (2): 327 – 347 8.9.2017
    ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Arthropod Systematics and Phylogeny Jahr/Year: 2017 Band/Volume: 75 Autor(en)/Author(s): Richter Adrian, Wipfler Benjamin, Beutel Rolf Georg, Pohl Hans Artikel/Article: The female cephalothorax of Xenos vesparum Rossi, 1793 (Strepsiptera: Xenidae) 327-347 75 (2): 327 – 347 8.9.2017 © Senckenberg Gesellschaft für Naturforschung, 2017. The female cephalothorax of Xenos vesparum Rossi, 1793 (Strepsiptera: Xenidae) Adrian Richter, Benjamin Wipfler, Rolf G. Beutel & Hans Pohl* Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbert- straße 1, 07743 Jena, Germany; Hans Pohl * [[email protected]] — * Corresponding author Accepted 16.v.2017. Published online at www.senckenberg.de/arthropod-systematics on 30.viii.2017. Editors in charge: Christian Schmidt & Klaus-Dieter Klass Abstract The female cephalothorax of Xenos vesparum (Strepsiptera, Xenidae) is described and documented in detail. The female is enclosed by exuvia of the secondary and tertiary larval stages and forms a functional unit with them. Only the cephalothorax is protruding from the host’s abdomen. The cephalothorax comprises the head and thorax, and the anterior half of the first abdominal segment. Adult females and the exuvia of the secondary larva display mandibles, vestigial antennae, a labral field, and a mouth opening. Vestiges of maxillae are also recognizable on the exuvia but almost completely reduced in the adult female. A birth opening is located between the head and prosternum of the exuvia of the secondary larva. A pair of spiracles is present in the posterolateral region of the cephalothorax.
    [Show full text]
  • The Linsenmaier Chrysididae Collection Housed in the Natur-Museum Luzern (Switzerland) and the Main Results of the Related GBIF Hymenoptera Project (Insecta)
    Zootaxa 3986 (5): 501–548 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2015 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3986.5.1 http://zoobank.org/urn:lsid:zoobank.org:pub:0BC8E78B-2CB2-4DBD-B036-5BE1AEC4426F The Linsenmaier Chrysididae collection housed in the Natur-Museum Luzern (Switzerland) and the main results of the related GBIF Hymenoptera Project (Insecta) PAOLO ROSA1, 2, 4, MARCO VALERIO BERNASCONI1 & DENISE WYNIGER1, 3 1Natur-Museum Luzern, Kasernenplatz 6, CH-6003 Luzern, Switzerland 2Private address: Via Belvedere 8/d I-20881 Bernareggio (MB), Italy 3present address: Naturhistorisches Museum Basel, Augustinergasse 2, CH-4001 Basel, Switzerland 4Corresponding author. E-mail: [email protected] Table of contents Abstract . 501 Introduction . 502 Linsenmaier's Patrimony . 502 Historical overview . 503 The Linsenmaier Chrysididae collection . 506 Material and methods . 507 GBIF project . 507 The reorganization of the Linsenmaier collection . 508 Manuscripts . 513 Observations on some specimens and labels found in the collection . 515 Type material . 519 New synonymies . 524 Conclusions . 525 Acknowledgements . 525 References . 525 APPENDIX A . 531 Species-group names described by Walter Linsenmaier. 531 Replacement names given by Linsenmaier . 543 Unnecessary replacement names given by Linsenmaier . 543 Genus-group names described by Linsenmaier . 544 Replacement names in the genus-group names . 544 APPENDIX B . 544 List of the types housed in Linsenmaier's
    [Show full text]
  • Heteroptera: Gerromorpha) in Central Europe
    Shortened web version University of South Bohemia in České Budějovice Faculty of Science Ecology of Veliidae and Mesoveliidae (Heteroptera: Gerromorpha) in Central Europe RNDr. Tomáš Ditrich Ph.D. Thesis Supervisor: Prof. RNDr. Miroslav Papáček, CSc. University of South Bohemia, Faculty of Education České Budějovice 2010 Shortened web version Ditrich, T., 2010: Ecology of Veliidae and Mesoveliidae (Heteroptera: Gerromorpha) in Central Europe. Ph.D. Thesis, in English. – 85 p., Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic. Annotation Ecology of Veliidae and Mesoveliidae (Hemiptera: Heteroptera: Gerromorpha) was studied in selected European species. The research of these non-gerrid semiaquatic bugs was especially focused on voltinism, overwintering with physiological consequences and wing polymorphism with dispersal pattern. Hypotheses based on data from field surveys were tested by laboratory, mesocosm and field experiments. New data on life history traits and their ecophysiological consequences are discussed in seven original research papers (four papers published in peer-reviewed journals, one paper accepted to publication, one submitted paper and one communication in a conference proceedings), creating core of this thesis. Keywords Insects, semiaquatic bugs, life history, overwintering, voltinism, dispersion, wing polymorphism. Financial support This thesis was mainly supported by grant of The Ministry of Education, Youth and Sports of the Czech Republic No. MSM 6007665801, partially by grant of the Grant Agency of the University of South Bohemia No. GAJU 6/2007/P-PřF, by The Research Council of Norway: The YGGDRASIL mobility program No. 195759/V11 and by Czech Science Foundation grant No. 206/07/0269. Shortened web version Declaration I hereby declare that I worked out this Ph.D.
    [Show full text]
  • The Semiaquatic Hemiptera of Minnesota (Hemiptera: Heteroptera) Donald V
    The Semiaquatic Hemiptera of Minnesota (Hemiptera: Heteroptera) Donald V. Bennett Edwin F. Cook Technical Bulletin 332-1981 Agricultural Experiment Station University of Minnesota St. Paul, Minnesota 55108 CONTENTS PAGE Introduction ...................................3 Key to Adults of Nearctic Families of Semiaquatic Hemiptera ................... 6 Family Saldidae-Shore Bugs ............... 7 Family Mesoveliidae-Water Treaders .......18 Family Hebridae-Velvet Water Bugs .......20 Family Hydrometridae-Marsh Treaders, Water Measurers ...22 Family Veliidae-Small Water striders, Rime bugs ................24 Family Gerridae-Water striders, Pond skaters, Wherry men .....29 Family Ochteridae-Velvety Shore Bugs ....35 Family Gelastocoridae-Toad Bugs ..........36 Literature Cited ..............................37 Figures ......................................44 Maps .........................................55 Index to Scientific Names ....................59 Acknowledgement Sincere appreciation is expressed to the following individuals: R. T. Schuh, for being extremely helpful in reviewing the section on Saldidae, lending specimens, and allowing use of his illustrations of Saldidae; C. L. Smith for reading the section on Veliidae, checking identifications, and advising on problems in the taxon­ omy ofthe Veliidae; D. M. Calabrese, for reviewing the section on the Gerridae and making helpful sugges­ tions; J. T. Polhemus, for advising on taxonomic prob­ lems and checking identifications for several families; C. W. Schaefer, for providing advice and editorial com­ ment; Y. A. Popov, for sending a copy ofhis book on the Nepomorpha; and M. C. Parsons, for supplying its English translation. The University of Minnesota, including the Agricultural Experi­ ment Station, is committed to the policy that all persons shall have equal access to its programs, facilities, and employment without regard to race, creed, color, sex, national origin, or handicap. The information given in this publication is for educational purposes only.
    [Show full text]
  • The Transcriptomic and Genomic Architecture of Acrididae Grasshoppers
    The Transcriptomic and Genomic Architecture of Acrididae Grasshoppers Dissertation To Fulfil the Requirements for the Degree of “Doctor of Philosophy” (PhD) Submitted to the Council of the Faculty of Biological Sciences of the Friedrich Schiller University Jena by Bachelor of Science, Master of Science, Abhijeet Shah born on 7th November 1984, Hyderabad, India 1 Academic reviewers: 1. Prof. Holger Schielzeth, Friedrich Schiller University Jena 2. Prof. Manja Marz, Friedrich Schiller University Jena 3. Prof. Rolf Beutel, Friedrich Schiller University Jena 4. Prof. Frieder Mayer, Museum für Naturkunde Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin 5. Prof. Steve Hoffmann, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena 6. Prof. Aletta Bonn, Friedrich Schiller University Jena Date of oral defense: 24.02.2020 2 Table of Contents Abstract ........................................................................................................................... 5 Zusammenfassung............................................................................................................ 7 Introduction ..................................................................................................................... 9 Genetic polymorphism ............................................................................................................. 9 Lewontin’s paradox ....................................................................................................................................... 9 The evolution
    [Show full text]
  • Mousebirds Tle Focus Has Been Placed Upon Them
    at all, in private aviculture, and only a few zoos have them in their col1ec­ tions. According to the ISIS report of September 1998, Red-hacks are not to be found in any USA collections. This is unfortunate as all six species have been imported in the past although lit­ Mousebirds tle focus has been placed upon them. Hopeful1y this will change in the for the New Millennium upcoming years. Speckled Mousebirds by Kateri J. Davis, Sacramento, CA Speckled Mousebirds Colius striatus, also known as Bar-breasted or Striated, are the most common mousebirds in crops and frequent village gardens. USA private and zoological aviculture he word is slowly spreading; They are considered a pest bird by today. There are 17 subspecies, differ­ mousebirds make great many Africans and destroyed as such. ing mainly in color of the legs, eyes, T aviary birds and, surprising­ Luckily, so far none of the mousebird throat, and cheek patches or ear ly, great household pets. Although still species are endangered or listed on coverts. They have reddish brown body generally unknown, they are the up­ CITES even though some of them have plumage with dark barrings and a very and-coming pet bird of the new mil­ naturally small ranges. wide, long, stiff tail. Their feathering is lennium. They share many ofthe qual­ Mousebirds are not closely related to soft and easily damaged. They have a ities ofsmall pet parrots, but lack many any other bird species, although they soft chattering cal1 and are the most of their vices, which helps explain share traits with parrots.
    [Show full text]
  • Odonata: Zygoptera) Focusing on Functional Aspects of the Mouthparts Sebastian Büsse1* , Thomas Hörnschemeyer2 and Stanislav N
    Büsse et al. Frontiers in Zoology (2017) 14:25 DOI 10.1186/s12983-017-0209-x RESEARCH Open Access The head morphology of Pyrrhosoma nymphula larvae (Odonata: Zygoptera) focusing on functional aspects of the mouthparts Sebastian Büsse1* , Thomas Hörnschemeyer2 and Stanislav N. Gorb1 Abstract Background: The understanding of concerted movements and its underlying biomechanics is often complex and elusive. Functional principles and hypothetical functions of these complex movements can provide a solid basis for biomechanical experiments and modelling. Here a description of the cephalic anatomy of Pyrrhosoma nymphula (Zygoptera, Coenagrionidae) focusing on functional aspects of the mouthparts using micro computed tomography (μCT) is presented. Results: We compared six different instars of the damselfly P. nymphula as well as one instar of the dragonfly Aeshna cyanea and Epiophlebia superstes each. In total 42 head muscles were described with only minor differences of the attachment points between the examined species and the absence of antennal muscle M. scapopedicellaris medialis (0an7) in Epiophlebia as a probable apomorphy of this group. Furthermore, the ontogenetic differences between the six larval instars are minor; the only considerable finding is the change of M. submentopraementalis (0la8), which is dichotomous in the early instars (I1,I2 and I3) with a second point of origin at the postero-lateral base of the submentum. This dichotomy is not present in any of the older instars studied (I6, middle-late and pen-ultimate). Conclusion: However, the main focus of the study herein, is to use these detailed morphological descriptions as basis for hypothetic functional models of the odonatan mouthparts. We present blueprint like description of the mouthparts and their musculature, highlighting the caused direction of motion for every single muscle.
    [Show full text]