DOCSLIB.ORG

Proefschrift Marieke Van Erp 300610

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Proefschrift Marieke Van Erp 300610 Tilburg University Accessing natural history van Erp, M.G.J. Publication date: 2010 Document Version Publisher's PDF, also known as Version of record Link to publication in Tilburg University Research Portal Citation for published version (APA): van Erp, M. G. J. (2010). Accessing natural history: Discoveries in data cleaning, structuring, and retrieval. TICC Dissertation Series 13. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 26. sep. 2021 Accessing Natural History Discoveries in Data Cleaning, Structuring, and Retrieval proefschrift ter verkrijging van de graad van doctor aan de Universiteit van Tilburg, op gezag van de rector magnificus, prof. dr. Ph. Eijlander, in het openbaar te verdedigen ten overstaan van een door het college voor promoties aangewezen commissie in de aula van de Universiteit op woensdag 30 juni 2010 om 14:15 uur door Maria Godefrida Jacoba van Erp geboren op 18 november 1982 te Breda ii Promotor: Prof. dr. A. P. J. van den Bosch Copromotor: Dr. P. K. Lendvai Promotiecommissie: Prof. dr. H. J. van den Herik Prof. dr. W. M. P. Daelemans Dr. R. W. R. J. Dekker Dr. E. Hovy The research reported in this thesis was funded by the Netherlands Organization for Scientific Research (NWO) in the project Mining for Information in Texts from the Cul- tural Heritage (MITCH), grant number 640.002.403. The MITCH project is part of the Continuous Access to Cultural Heritage Research (CATCH) Programme. SIKS Dissertation Series No. 2010-30 The research reported in this thesis was carried out under the auspices of SIKS, the Dutch Research School for Information and Knowledge Systems. TiCC Dissertation Series no. 13. ISBN 978-90-8559-027-9 c Marieke van Erp 2010 Cover photo c NCB Naturalis All rights reserved. No part of this publication may be reproduced in any form by any electronic or mechanical means (including photocopying, recording or information storage and retrieval) without permission from the author, except for reading and browsing via the World Wide Web. Users are not permitted to mount this file on any network servers. Voor opa Preface In the spring of 2005, while I was finishing up my Master's degree at Tilburg University, I knew I wasn't quite done with academia and wanted to pursue a Ph.D. Unexpectedly (to me at least) I landed a Ph.D. position at Tilburg Uni- versity in collaboration with the National Museum of Natural History Naturalis in Leiden. So, in the autumn of 2005, I moved to Leiden: to new adventures, and a fair amount of time on the train to Tilburg for the weekly meetings with my supervisor and promotor Antal van den Bosch and to hang out and learn from the members of the ILK group. I am very grateful to Antal for giving me the chance to do this project and start exploring the wondrous world of interdisciplinary re- search in such a `gezellige' environment and to the ILK members for making it such a fabulous place. At my other office, Naturalis, I want to thank the researchers and database managers for educating me and my fellow MITCH colleagues about the basics of natural history research and showing us around in their databases, in particular Pim Arntzen, Eric van Nieukerken and Dirk Houtgraaf during the early days of MITCH, and later on Marian van der Meij and Ren´eDekker. Somewhere halfway during my project, Antal and I realised that my work was moving away from core ILK business towards knowledge representation and ontologies. Antal thought this would be an excellent opportunity to gain know- ledge elsewhere and see how another research group runs from the inside. He also knew a perfect mentor to help me explore these topics: dr. Eduard Hovy at the vi Information Sciences Institute in Marina del Rey, California, USA. Again I was given an amazing opportunity, as Ed was willing to have me at ISI for a couple of months. So in September 2007, I moved to sunny California. This (ultimately) 7-month stint meant a huge turnaround for my research (and my private life, but more on that later) as ISI's bustling community provided me with new inspiration and research directions, as well as giving me an incredibly good time exploring Los Angeles bars and clubs, yoga, the beach, and American traditions. Thank you Ed, for giving me this opportunity, guidance, and for finding the time to be on my thesis committee. I also wish to thank the other members of my thesis committee for their advice and comments on my text: prof. dr. Jaap van den Herik, prof. dr. Walter Daelemans, and dr. Ren´eDekker. Work hard, play hard. Luckily, my friends and family provided enough dis- tractions from deadlines and the frustrations of working with computers in the form of concerts, surf trips, dance lessons, guitar sessions, dinner parties, trips to North End, and British comedy. Special thanks to Judith and Arthur for keeping me awake far past my bedtime in Leiden and to Steve for being a great program- mer and friend. Without you this thesis would have looked very differently and my guitar skills would have been even worse than they are now. I would never have gotten anywhere near a Ph.D. if it weren't for my family. I have amazing parents who raised me to be curious and open to the world, and who have supported me with every step. It was also a true joy to grow up with my brothers Frank and Hans, and my sister Sara. I hope that you all forgive me for moving away from Etten-Leur, but there's always space for you to crash in Amsterdam. Fresh inspiration for my research wasn't the only thing I found in LA. I also found Paul, my soon-to-be husband. Thank you for your advice, distraction, bread-crusted Ahi tuna, coffee breaks, trips to exciting places far and near, music, smiles, and love. On to new adventures! Marieke van Erp Amsterdam, 11 May 2010 Contents Prefacev Contents vii 1 Introduction1 1.1 Research Motivation..........................2 1.2 Problem Statement and Research Questions.............4 1.3 Research Methodology.........................7 1.4 Thesis Outline.............................7 2 Background and Resources9 2.1 Natural History.............................9 2.1.1 Biogeography.......................... 11 2.1.2 Systematics........................... 11 2.1.3 Biodiversity Informatics.................... 14 2.2 The Naturalis Reptiles and Amphibians Data Sets......... 16 2.2.1 The R&A Database...................... 16 2.2.2 Field Logbooks and Registers................. 17 2.3 Additional Resources.......................... 19 2.3.1 GeoNames............................ 19 2.3.2 Taxonomic Resources..................... 22 viii CONTENTS 2.4 Discussion................................ 24 3 Preparatory Work 25 3.1 Automatic R&A Database Population................ 26 3.1.1 Overlap between Field Logbooks and Registers and R&A Database............................ 27 3.1.2 Annotated Training and Test Data.............. 29 3.1.3 Experiments and Results................... 29 3.2 A Manually Constructed Ontology.................. 31 3.2.1 Ontology Basics........................ 31 3.2.2 Resources Involved....................... 33 3.2.3 Ontology Building Principles................. 35 3.2.4 Ontology Construction Methodology............. 36 3.2.5 Description of the Ontology.................. 37 3.3 Chapter Summary........................... 41 4 Data Cleaning 45 4.1 The Essence of Data Cleaning..................... 46 4.2 The Importance of Automatic Data Cleaning............ 48 4.2.1 Data Cleaning Steps...................... 49 4.2.2 Types of Errors......................... 50 4.2.3 R&A Database Error Analysis................ 52 4.3 Normalisation.............................. 53 4.4 Data-driven Data Cleaning...................... 54 4.4.1 Timpute ............................ 55 4.4.2 Experiments and Results................... 57 4.5 Ontology-driven Data Cleaning.................... 63 4.5.1 Related Work.......................... 64 4.5.2 Validato ............................ 64 4.5.3 Experiments and Results................... 65 4.6 Discussion and Conclusions...................... 74 5 Automatic Data Structuring 79 5.1 Automatic Ontology Construction.................. 80 5.2 Twibio ................................. 83 5.2.1 Wikipedia............................ 84 CONTENTS ix 5.2.2 Related Work.......................... 86 5.2.3 Data Preparation........................ 87 5.2.4 Twibio System Setup..................... 89 5.2.5 Evaluation Methodology.................... 91 5.2.6 Twibio Results ........................ 92 5.3 Ontology Comparison......................... 95 5.3.1 Manual Ontology Comparison................. 95 5.3.2 Automatic Ontology Comparison............... 97 5.3.3 Manual vs. Twibio Ontology................. 99 5.4 Discussion and Conclusions...................... 99 6 Data Retrieval 101 6.1 Information Retrieval......................... 102 6.2 The Naturalis
Load more

Recommended publications
  • Stream Frogs, Mannophryne Trinitatis (Dendrobatidae): an Example of Anti-Predator Behaviour
    HERPETOLOGICAL JOURNAL, Vol. 11, pp. 91-100 (2001) SELECTION OF TAD POLE DEPOSITION SITES BY MALE TRINIDADIAN STREAM FROGS, MANNOPHRYNE TRINITATIS (DENDROBATIDAE): AN EXAMPLE OF ANTI-PREDATOR BEHAVIOUR J. R. DOWNIE, S. R. LIVINGSTONE AND J. R. CORMACK Division of Environmental and Evolutionary Biology, Institute of Biomedical & Life Sciences, University of Glasgow, Scotland, UK Trinidad's only dendrobatid frog, Mannophryne (=Colostethus) trinitatis, lives by the small streams draining the slopes of the Northern Range mountains and at Tamana Hill in the Central Range. Adults are often very abundant, but tadpoles are found patchily in the streams. In the absence of two potential predators - the fish Rivulus hartii and shrimps of the genus Macrobrachium - tadpoles are abundant in pools. Where the predators are present, tadpoles are uncommon or absent. Tadpoles may also be found in small, isolated bodies of water at some distance from streams. Males carrying tadpoles retained them for 3-4 days, in the absence of suitable pools. When presented with a choice of pools, males preferred to deposit their tadpoles in pools lacking predators. There were differences in behaviour between males fromthe northern and southern slopes of the Northern Range. For example, north coast males deposited tadpoles in pools containing other conspecific tadpoles in preference to empty pools, whereas males from southern slopes made the opposite choice. When presented only with pools containing predators (i.e. shrimps or fish), north coast males shed their tadpoles in damp leaf litter rather than in the pools, while males from the southern slopes deposited tadpoles in pools with shrimps - predators uncommon in the southern slopes streams.
    [Show full text]
  • Catalogue of the Amphibians of Venezuela: Illustrated and Annotated Species List, Distribution, and Conservation 1,2César L
    Mannophryne vulcano, Male carrying tadpoles. El Ávila (Parque Nacional Guairarepano), Distrito Federal. Photo: Jose Vieira. We want to dedicate this work to some outstanding individuals who encouraged us, directly or indirectly, and are no longer with us. They were colleagues and close friends, and their friendship will remain for years to come. César Molina Rodríguez (1960–2015) Erik Arrieta Márquez (1978–2008) Jose Ayarzagüena Sanz (1952–2011) Saúl Gutiérrez Eljuri (1960–2012) Juan Rivero (1923–2014) Luis Scott (1948–2011) Marco Natera Mumaw (1972–2010) Official journal website: Amphibian & Reptile Conservation amphibian-reptile-conservation.org 13(1) [Special Section]: 1–198 (e180). Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation 1,2César L. Barrio-Amorós, 3,4Fernando J. M. Rojas-Runjaic, and 5J. Celsa Señaris 1Fundación AndígenA, Apartado Postal 210, Mérida, VENEZUELA 2Current address: Doc Frog Expeditions, Uvita de Osa, COSTA RICA 3Fundación La Salle de Ciencias Naturales, Museo de Historia Natural La Salle, Apartado Postal 1930, Caracas 1010-A, VENEZUELA 4Current address: Pontifícia Universidade Católica do Río Grande do Sul (PUCRS), Laboratório de Sistemática de Vertebrados, Av. Ipiranga 6681, Porto Alegre, RS 90619–900, BRAZIL 5Instituto Venezolano de Investigaciones Científicas, Altos de Pipe, apartado 20632, Caracas 1020, VENEZUELA Abstract.—Presented is an annotated checklist of the amphibians of Venezuela, current as of December 2018. The last comprehensive list (Barrio-Amorós 2009c) included a total of 333 species, while the current catalogue lists 387 species (370 anurans, 10 caecilians, and seven salamanders), including 28 species not yet described or properly identified. Fifty species and four genera are added to the previous list, 25 species are deleted, and 47 experienced nomenclatural changes.
    [Show full text]
  • Gardner, Michael George. Breakdown of Phylogenetic Signal: a Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species
    PUBLISHED VERSION Meglécz, Emese; Nève, Gabriel; Biffin, Edward Sturt; Gardner, Michael George. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model Eukaryote species. PLoS ONE, 2012; 7(7):e40861 Copyright: © 2012 Meglécz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. PERMISSIONS http://www.plosone.org/static/policies.action#copyright 3. Copyright and License Policies Open access agreement. Upon submission of an article, its authors are asked to indicate their agreement to abide by an open access Creative Commons license (CC-BY). Under the terms of this license, authors retain ownership of the copyright of their articles. However, the license permits any user to download, print out, extract, reuse, archive, and distribute the article, so long as appropriate credit is given to the authors and source of the work. The license ensures that the authors' article will be available as widely as possible and that the article can be included in any scientific archive. Open access agreement: US government authors. Papers authored by one or more US government employees are not copyrighted, but are licensed under a Creative Commons public domain license (CC0), which allows unlimited distribution and reuse of the article for any lawful purpose. Authors should read about CC-BY or CC0 before submitting papers. Archiving in PubMed Central. Upon publication, PLoS also deposits all articles in PubMed Central. This complies with the policies of funding agencies, such as the NIH in the USA, the Wellcome Trust, and the Research Councils in the UK, and the Deutsche Forschungsgemeinschaft in Germany, which request or require deposition of the published articles that they fund into publicly available databases.
    [Show full text]
  • An Annotated Type Catalogue of the Dragon Lizards (Reptilia: Squamata: Agamidae) in the Collection of the Western Australian Museum Ryan J
    RECORDS OF THE WESTERN AUSTRALIAN MUSEUM 34 115–132 (2019) DOI: 10.18195/issn.0312-3162.34(2).2019.115-132 An annotated type catalogue of the dragon lizards (Reptilia: Squamata: Agamidae) in the collection of the Western Australian Museum Ryan J. Ellis Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia. Biologic Environmental Survey, 24–26 Wickham St, East Perth, Western Australia 6004, Australia. Email: [email protected] ABSTRACT – The Western Australian Museum holds a vast collection of specimens representing a large portion of the 106 currently recognised taxa of dragon lizards (family Agamidae) known to occur across Australia. While the museum’s collection is dominated by Western Australian species, it also contains a selection of specimens from localities in other Australian states and a small selection from outside of Australia. Currently the museum’s collection contains 18,914 agamid specimens representing 89 of the 106 currently recognised taxa from across Australia and 27 from outside of Australia. This includes 824 type specimens representing 45 currently recognised taxa and three synonymised taxa, comprising 43 holotypes, three syntypes and 779 paratypes. Of the paratypes, a total of 43 specimens have been gifted to other collections, disposed or could not be located and are considered lost. An annotated catalogue is provided for all agamid type material currently and previously maintained in the herpetological collection of the Western Australian Museum. KEYWORDS: type specimens, holotype, syntype, paratype, dragon lizard, nomenclature. INTRODUCTION Australia was named by John Edward Gray in 1825, The Agamidae, commonly referred to as dragon Clamydosaurus kingii Gray, 1825 [now Chlamydosaurus lizards, comprises over 480 taxa worldwide, occurring kingii (Gray, 1825)].
    [Show full text]
  • Mannophryne Olmonae) Catherine G
    The College of Wooster Libraries Open Works Senior Independent Study Theses 2014 A Not-So-Silent Spring: The mpI acts of Traffic Noise on Call Features of The loB ody Bay Poison Frog (Mannophryne olmonae) Catherine G. Clemmens The College of Wooster, [email protected] Follow this and additional works at: https://openworks.wooster.edu/independentstudy Part of the Other Environmental Sciences Commons Recommended Citation Clemmens, Catherine G., "A Not-So-Silent Spring: The mpI acts of Traffico N ise on Call Features of The loodyB Bay Poison Frog (Mannophryne olmonae)" (2014). Senior Independent Study Theses. Paper 5783. https://openworks.wooster.edu/independentstudy/5783 This Senior Independent Study Thesis Exemplar is brought to you by Open Works, a service of The oC llege of Wooster Libraries. It has been accepted for inclusion in Senior Independent Study Theses by an authorized administrator of Open Works. For more information, please contact [email protected]. © Copyright 2014 Catherine G. Clemmens A NOT-SO-SILENT SPRING: THE IMPACTS OF TRAFFIC NOISE ON CALL FEATURES OF THE BLOODY BAY POISON FROG (MANNOPHRYNE OLMONAE) DEPARTMENT OF BIOLOGY INDEPENDENT STUDY THESIS Catherine Grace Clemmens Adviser: Richard Lehtinen Submitted in Partial Fulfillment of the Requirement for Independent Study Thesis in Biology at the COLLEGE OF WOOSTER 2014 TABLE OF CONTENTS I. ABSTRACT II. INTRODUCTION…………………………………………...............…...........1 a. Behavioral Effects of Anthropogenic Noise……………………….........2 b. Effects of Anthropogenic Noise on Frog Vocalization………………....6 c. Why Should We Care? The Importance of Calling for Frogs..................8 d. Color as a Mode of Communication……………………………….…..11 e. Biology of the Bloody Bay Poison Frog (Mannophryne olmonae)…...13 III.
    [Show full text]
  • Reptiles of the Wet Tropics
    Reptiles of the Wet Tropics The concentration of endemic reptiles in the Wet Tropics is greater than in any other area of Australia. About 162 species of reptiles live in this region and 24 of these species live exclusively in the rainforest. Eighteen of them are found nowhere else in the world. Many lizards are closely related to species in New Guinea and South-East Asia. The ancestors of two of the resident geckos are thought to date back millions of years to the ancient super continent of Gondwana. PRICKLY FOREST SKINK - Gnypetoscincus queenlandiae Length to 17cm. This skink is distinguished by its very prickly back scales. It is very hard to see, as it is nocturnal and hides under rotting logs and is extremely heat sensitive. Located in the rainforest in the Wet Tropics only, from near Cooktown to west of Cardwell. RAINFOREST SKINK - Eulamprus tigrinus Length to 16cm. The body has irregular, broken black bars. They give birth to live young and feed on invertebrates. Predominantly arboreal, they bask in patches of sunlight in the rainforest and shelter in tree hollows at night. Apparently capable of producing a sharp squeak when handled or when fighting. It is rare and found only in rainforests from south of Cooktown to west of Cardwell. NORTHERN RED-THROATED SKINK - Carlia rubrigularis Length to 14cm. The sides of the neck are richly flushed with red in breeding males. Lays 1-2 eggs per clutch, sometimes communally. Forages for insects in leaf litter, fallen logs and tree buttresses. May also prey on small skinks and own species.
    [Show full text]
  • The Reptile Collection of the Museu De Zoologia, Pecies
    Check List 9(2): 257–262, 2013 © 2013 Check List and Authors Chec List ISSN 1809-127X (available at www.checklist.org.br) Journal of species lists and distribution The Reptile Collection of the Museu de Zoologia, PECIES S Universidade Federal da Bahia, Brazil OF Breno Hamdan 1,2*, Daniela Pinto Coelho 1 1, Eduardo José dos Reis Dias3 ISTS 1 L and Rejâne Maria Lira-da-Silva , Annelise Batista D’Angiolella 40170-115, Salvador, BA, Brazil. 1 Universidade Federal da Bahia, Instituto de Biologia, Departamento de Zoologia, Núcleo Regional de Ofiologia e Animais Peçonhentos. CEP Sala A0-92 (subsolo), Laboratório de Répteis, Ilha do Fundão, Av. Carlos Chagas Filho, N° 373. CEP 21941-902. Rio de Janeiro, RJ, Brazil. 2 Programa de Pós-Graduação em Zoologia, Museu Nacional/UFRJ. Universidade Federal do Rio de Janeiro Centro de Ciências da Saúde, Bloco A, Carvalho. CEP 49500-000. Itabaian, SE, Brazil. * 3 CorrUniversidadeesponding Federal author. de E-mail: Sergipe, [email protected] Departamento de Biociências, Laboratório de Biologia e Ecologia de Vertebrados (LABEV), Campus Alberto de Abstract: to its history. The Reptile Collection of the Museu de Zoologia from Universidade Federal da Bahia (CRMZUFBA) has 5,206 specimens and Brazilian 185 species scientific (13 collections endemic to represent Brazil and an 9important threatened) sample with of one the quarter country’s of biodiversitythe known reptile and are species a testament listed in Brazil, from over 175 municipalities. Although the CRMZUFBA houses species from all Brazilian biomes there is a strong regional presence. Knowledge of the species housed in smaller collections could avoid unrepresentative species descriptions and provide information concerning intraspecific variation, ecological features and geographic coverage.
    [Show full text]
  • Literature Cited in Lizards Natural History Database
    Literature Cited in Lizards Natural History database Abdala, C. S., A. S. Quinteros, and R. E. Espinoza. 2008. Two new species of Liolaemus (Iguania: Liolaemidae) from the puna of northwestern Argentina. Herpetologica 64:458-471. Abdala, C. S., D. Baldo, R. A. Juárez, and R. E. Espinoza. 2016. The first parthenogenetic pleurodont Iguanian: a new all-female Liolaemus (Squamata: Liolaemidae) from western Argentina. Copeia 104:487-497. Abdala, C. S., J. C. Acosta, M. R. Cabrera, H. J. Villaviciencio, and J. Marinero. 2009. A new Andean Liolaemus of the L. montanus series (Squamata: Iguania: Liolaemidae) from western Argentina. South American Journal of Herpetology 4:91-102. Abdala, C. S., J. L. Acosta, J. C. Acosta, B. B. Alvarez, F. Arias, L. J. Avila, . S. M. Zalba. 2012. Categorización del estado de conservación de las lagartijas y anfisbenas de la República Argentina. Cuadernos de Herpetologia 26 (Suppl. 1):215-248. Abell, A. J. 1999. Male-female spacing patterns in the lizard, Sceloporus virgatus. Amphibia-Reptilia 20:185-194. Abts, M. L. 1987. Environment and variation in life history traits of the Chuckwalla, Sauromalus obesus. Ecological Monographs 57:215-232. Achaval, F., and A. Olmos. 2003. Anfibios y reptiles del Uruguay. Montevideo, Uruguay: Facultad de Ciencias. Achaval, F., and A. Olmos. 2007. Anfibio y reptiles del Uruguay, 3rd edn. Montevideo, Uruguay: Serie Fauna 1. Ackermann, T. 2006. Schreibers Glatkopfleguan Leiocephalus schreibersii. Munich, Germany: Natur und Tier. Ackley, J. W., P. J. Muelleman, R. E. Carter, R. W. Henderson, and R. Powell. 2009. A rapid assessment of herpetofaunal diversity in variously altered habitats on Dominica.
    [Show full text]
  • Anura: Aromobatidae)
    bioRxiv preprint doi: https://doi.org/10.1101/771287; this version posted September 16, 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 4.0 International license. 1 Sexual dichromatism in the neotropical genus Mannophryne (Anura: Aromobatidae) 2 Mark S. Greener1*, Emily Hutton2, Christopher J. Pollock3, Annabeth Wilson2, Chun Yin Lam2, Mohsen 3 Nokhbatolfoghahai 2, Michael J. Jowers4, and J. Roger Downie2 4 1Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent 5 University, B-9820 Merelbeke, Belgium. 6 2 School of Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK. 7 3 School of Biology, Faculty of Biological sciences, University of Leeds, Leeds LS2 9JT, UK. 8 4 CIBIO/InBIO (Centro de Investigacao em Biodiversidade e Recursos Genticos), Universide do Porto , 9 Vairao 4485-661, Portugal. 10 *[email protected] 11 ABSTRACT 12 Recent reviews on sexual dichromatism in frogs included Mannophryne trinitatis as the only example 13 they could find of dynamic dichromatism (males turn black when calling) within the family 14 Aromobatidae and found no example of ontogenetic dichromatism in this group. We demonstrate 15 ontogenetic dichromatism in M. trinitatis by rearing post-metamorphic froglets to near maturity: the 16 throats of all individuals started as grey coloured; at around seven weeks, the throat became pale 17 yellow in some, and more strongly yellow as development proceeded; the throats of adults are grey 18 in males and variably bright yellow in females, backed by a dark collar.
    [Show full text]
  • Breakdown of Phylogenetic Signal: a Survey of Microsatellite
    Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species Emese Meglécz, Gabriel Nève, Ed Biffin, Michael Gardner To cite this version: Emese Meglécz, Gabriel Nève, Ed Biffin, Michael Gardner. Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species. PLoS ONE, Public Library of Science, 2012, 7 (7), 10.1371/journal.pone.0040861. hal-01794109 HAL Id: hal-01794109 https://hal-amu.archives-ouvertes.fr/hal-01794109 Submitted on 17 May 2018 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. Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species Emese Megle´ cz1,2*, Gabriel Ne`ve1,2, Ed Biffin3, Michael G. Gardner2,3,4 1 IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France, 2 School of Biological Sciences, Flinders University, Adelaide, Australia, 3 Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, Australia, 4 Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia Abstract Microsatellites are ubiquitous in Eukaryotic genomes.
    [Show full text]
  • A Review of Chemical Defense in Poison Frogs (Dendrobatidae): Ecology, Pharmacokinetics, and Autoresistance
    Chapter 21 A Review of Chemical Defense in Poison Frogs (Dendrobatidae): Ecology, Pharmacokinetics, and Autoresistance Juan C. Santos , Rebecca D. Tarvin , and Lauren A. O’Connell 21.1 Introduction Chemical defense has evolved multiple times in nearly every major group of life, from snakes and insects to bacteria and plants (Mebs 2002 ). However, among land vertebrates, chemical defenses are restricted to a few monophyletic groups (i.e., clades). Most of these are amphibians and snakes, but a few rare origins (e.g., Pitohui birds) have stimulated research on acquired chemical defenses (Dumbacher et al. 1992 ). Selective pressures that lead to defense are usually associated with an organ- ism’s limited ability to escape predation or conspicuous behaviors and phenotypes that increase detectability by predators (e.g., diurnality or mating calls) (Speed and Ruxton 2005 ). Defended organisms frequently evolve warning signals to advertise their defense, a phenomenon known as aposematism (Mappes et al. 2005 ). Warning signals such as conspicuous coloration unambiguously inform predators that there will be a substantial cost if they proceed with attack or consumption of the defended prey (Mappes et al. 2005 ). However, aposematism is likely more complex than the simple pairing of signal and defense, encompassing a series of traits (i.e., the apose- matic syndrome) that alter morphology, physiology, and behavior (Mappes and J. C. Santos (*) Department of Zoology, Biodiversity Research Centre , University of British Columbia , #4200-6270 University Blvd , Vancouver , BC , Canada , V6T 1Z4 e-mail: [email protected] R. D. Tarvin University of Texas at Austin , 2415 Speedway Stop C0990 , Austin , TX 78712 , USA e-mail: [email protected] L.
    [Show full text]
  • Amphibian Ark Number 43 Keeping Threatened Amphibian Species Afloat June 2018
    AArk Newsletter NewsletterNumber 43, June 2018 amphibian ark Number 43 Keeping threatened amphibian species afloat June 2018 In this issue... Reintroduction of the Northern Pool Frog to the UK - Progress Report, April 2018 ............... 2 ® Establishment of a captive breeding program for the Kroombit Tinkerfrog .............................. 4 In situ conservation of the Lemur Leaf Frog through habitat improvement and forest management practices in the Guayacán Rainforest Reserve in Costa Rica .................... 6 Neotropical amphibian biology, management and conservation course .................................. 8 Donation provides for equipment upgrades within the Biogeos Foundation facilities, at the Rescue of Endangered Venezuelan Amphibians program in Venezuela ................... 9 New AArk Conservation Grants program, and call for applications .................................. 10 Amphibian Advocates - José Alfredo Hernández Díaz, Africam Safari, Mexico ........ 11 Amphibian Advocates - Dr. Phil Bishop, Co-Chair IUCN SSC ASG............................... 12 AArk Newsletter - Instructions for authors ...... 13 A private donation helps the Valcheta Frog program in Argentina ...................................... 14 A rich food formula to raise tadpoles in captivity........................................................... 16 Vibicaria Conservation Program: creation of an ex situ model for a rediscovered species in Costa Rica ...................................................... 18 Reproduction of Dendropsophus padreluna at
    [Show full text]