PRISTIONCHUS PACIFICUS – A NEMATODE MODEL FOR COMPARATIVE AND EVOLUTIONARY BIOLOGY PRISTIONCHUS PACIFICUS – A NEMATODE MODEL FOR COMPARATIVE AND EVOLUTIONARY BIOLOGY Edited by Ralf J. Sommer David J. Hunt and Roland N. Perry (Series Editors) NEMATOLOGY MONOGRAPHS AND PERSPECTIVES VOLUME 11 BRILL LEIDEN-BOSTON 2015 This book is printed on acid-free paper. Library of Congress Cataloging-in-Publication Data Pristionchus pacificus : a nematode model for comparative and evolu- tionary biology / edited by Ralf J. Sommer. pages cm. – (Nematology monographs and perspectives ; vol- ume 11) Includes bibliographical references and index. ISBN 978-90-04-26029-0 (hardback : alk. paper) – ISBN 978-90-04- 26030-6 (e-book) 1. Nematodes. 2. Evolution (Biology) I. Sommer, Ralf J., 1963- editor. QL391.N4P75 2015 592’.57–dc23 2015000351 ISBN: 978 90 04 26029 0 E-ISBN: 978 90 04 26030 6 © Copyright 2015 by Koninklijke Brill NV, Leiden, The Netherlands. Koninklijke Brill NV incorporates the imprints Brill, Brill Hes & De Graaf, Brill Nijhoff, Brill Rodopi and Hotei Publishing. All rights reserved. No part of this publication may be reproduced, translated, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without written permission of the publisher. Authorization to photocopy items for internal or personal use is granted by Brill provided that the appropriate fees are paid directly to Copyright Clearance Center, 222 Rosewood Drive, Suite 910, Danvers, MA 01923, USA. Fees are subject to change. Nematology Monographs & Perspectives, 2015, Vol. 11, v-x Contents Contributors ............................................. xi–xiv Foreword . xv–xvi Acknowledgements ....................................... xvii 1. Why Caenorhabditis elegans is great and Pristionchus pacificus might be better ........................ 1–17 Paul W. STERNBERG Introduction . ..................................... 1 Useful features of C. elegans .......................... 1 Communityresources ................................ 5 What C. elegans didforus ............................ 5 Limitations of C. elegans ............................. 7 History of Pristionchus pacificus ...................... 7 What Pristionchus didforme ......................... 8 Sciencewithothernematodes ......................... 9 Pristionchus has opened up many areas of biology . 9 Prospects............................................ 11 Acknowledgements .................................. 11 References .......................................... 12 2. Integrative evolutionary biology and mechanistic approaches in comparative biology . 19–41 Ralf J. SOMMER Thecomplexityoflife................................ 19 Thepowerofmodelsystemapproaches ................ 22 Comparative biology and a need for mechanistic approaches...................................... 26 Integrativeevolutionarybiology ....................... 29 Integrative evolutionary biology needs comparative approaches...................................... 31 Pristionchus pacificus – a nematode model to combine integrative evolutionary biology and mechanistic approachesincomparativebiology ................ 32 Conclusion.......................................... 36 © Koninklijke Brill NV, Leiden, 2015 v Contents Acknowledgements .................................. 36 References .......................................... 36 3. Diplogastrid systematics and phylogeny . 43–76 Natsumi KANZAKI and Robin M. GIBLIN-DAV I S Systematicsandphylogeny ........................... 43 Introduction . ..................................... 43 Systematics ......................................... 47 General morphology . 49 List of genera and their morphological characters . 54 Phylogeny or reconstructing evolutionary history of diplogastrids .................................... 66 Integrated systematics based on morphology and molecularphylogeny............................. 70 Acknowledgements .................................. 71 References .......................................... 71 4. Taxonomy and natural history: the genus Pristionchus . 77–120 Erik J. RAGSDALE,NatsumiKANZAKI and Matthias HERRMANN Introduction . ..................................... 77 Naturalhistory....................................... 78 Taxonomy . 90 Biogeography ....................................... 111 Acknowledgements .................................. 113 References .......................................... 113 5. The laboratory model: genetics, genetic mapping and transgenics . 121–140 Laura AURILIO and Jagan SRINIVASAN Introduction . ..................................... 121 Pristionchus pacificus: beginnings of a laboratory model system.......................................... 122 Generaldescriptionandgenetics....................... 122 Forward genetic screens in P. pacificus ................. 123 Positional cloning approaches and integrated maps . 126 Post-genome era P. pacificus .......................... 128 Reversegenetics ..................................... 129 Transgenicsandgenefunction......................... 130 In-situ hybridisation and immunohistochemistry . 131 vi Nematology Monographs & Perspectives Contents Whole genome sequencing and mRNA quantification using next-generation sequencing (NGS) technologies . 131 Acknowledgements .................................. 133 References .......................................... 133 Appendix ........................................... 138 Genomic resources for cloning genes of P. pacificus ..... 138 Gene nomenclature in P. pacificus ..................... 138 Genetic maintenance of P. pacificus .................... 138 Librariesforgenomiccloning ......................... 139 Sequence information of libraries and genome sequence . 139 6. Comparative and functional genomics . 141–165 Christian RÖDELSPERGER and Christoph DIETERICH Introduction . ..................................... 141 Genomesequence.................................... 143 Protein-coding genes and operons . 145 Repetitive elements and transposons . 146 Role and evolution of miRNA families . 146 Evolution of gene families . 148 Orphangenes........................................ 150 Horizontal gene transfer of cellulase genes . 152 Comparative functional genomics of the dauer stage . 156 Evolutionary comparisons at shorter time-scales . 157 Conclusions ......................................... 160 Acknowledgements .................................. 160 References .......................................... 160 7. Small-molecule signalling: encoding biological information in chemical structures . .167–196 Frank C. SCHROEDER Chemicalinformation ................................ 167 Metabolomicsformodelorganisms.................... 168 A new beginning: small-molecule signalling in C. elegans 169 The P. pacificus metabolome: adventures in structure space ........................................... 172 Specific small molecules control dauer and mouth form . 175 Modular biosynthesis is selective . 176 Natural variation of small-molecule biosynthesis and bioactivity ...................................... 178 Vol. 11, 2015 vii Contents A conserved nuclear hormone receptor downstream of ascarosides...................................... 183 Dauer towers and an extremely long-chain wax ester . 187 Conclusion.......................................... 188 Acknowledgements .................................. 190 References .......................................... 190 8. Population genetics and the La Réunion case study . 197–219 Angela MCGAUGHRAN and Katy MORGAN Introduction . ..................................... 197 Diversityanddistribution ............................. 201 Evolutionaryhistory.................................. 204 Demography ........................................ 207 Environmentalaspects................................ 210 Conclusion.......................................... 213 Futuredirections..................................... 213 References .......................................... 214 9. Evo-devo and developmental systems drift: an evolving paradigm in organ formation and tissue coordination, vulva and gonad development in Pristionchus pacificus . 221–255 David RUDEL Introduction . ..................................... 221 A comparative description of vulva development . 222 A comparative description of gonadogenesis . 233 Conclusions ......................................... 242 References .......................................... 249 10. Dauer formation and dauer-specific behaviours in Pristionchus pacificus . 257–299 Akira OGAWA and Federico BROWN Introduction . ..................................... 257 Studies on C. elegans dauerformation.................. 259 Studies on P. pacificus dauerformation................. 263 Acknowledgements .................................. 287 References .......................................... 287 11. Mouth dimorphism and the evolution of novelty and diversity . .301–329 Erik J. RAGSDALE Introduction . ..................................... 301 viii Nematology Monographs & Perspectives Contents Morphology of dimorphic mouthparts . 302 Evolutionary history of the dimorphism . 306 Ecologicalfunctionandadaptivevalue ................. 309 Environmental cues and conditional regulation . 312 Developmental regulation coupled to the dauer plasticity . 315 Regulation through a developmental switch . 316 The role of developmental plasticity in evolution . 320 Conclusions ......................................... 321 Acknowledgements .................................