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Evolutionary Biology from Concept to Application Pierre Pontarotti Editor Evolutionary Biology from Concept to Application 123 Editor: Dr. Pierre Pontarotti UMR 6632 Université d’Aix-Marseille/CNRS Laboratoire Evolution Biologique et Modélisation, case 19 3, Place Victor Hugo 13331 Marseille Cedex 03 France [email protected] ISBN: 978-3-540-78992-5 e-ISBN: 978-3-540-78993-2 DOI: 10.1007/978-3-540-78993-2 Library of Congress Control Number: 2008924864 c 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product liability: The publisher cannot guarantee the accuracy of any information about dosage and application contained in this book. In every individual case the user must check such information by consulting the relevant literature. Cover design: WMX Design GmbH, Heidelberg Printed on acid-free paper 987654321 springer.com Preface Every biological system is the outcome of its evolutionary history; therefore, the deciphering of the evolutionary history is of tremendous importance to understand biology. Since 1997, scientists of different disciplines who share a deep interest in evolu- tionary biology concepts and knowledge have held an “evolutionary biology meet- ing at Marseilles” in order to discuss their research, exchange ideas, and start collab- orations. Lately, scientists interested in the application of the concepts have joined the group. This book is a selection of what I think are the most representative talks of 11th meeting as they represent an up-to-date overview of concepts of evolution and how these concepts can be used to understand biology in general. The book comprises several topics that we have arranged in different subcategories: modelization of evo- lution (Yu: Chap. 1, Meade and Pagel: Chap. 2), concepts in evolutionary biology (Toll-Riera et al: Chap. 3, Erenpreisa and Cragg: Chap. 4, Mikhalevich: Chap. 5, Raineri: Chap. 6), knowledge (Shimizu: Chap. 7, Hwang et al: Chap. 8), and ap- plied evolutionary biology (Barth´el´emy et al: Chap. 9, Hilu and Barthet: Chap. 10, Kryger and Scholtz: Chap. 11, Swynghedauw: Chap. 12, Levasseur and Pontarotti: Chap. 13). I hope that this book will be useful not only to evolutionary biologists but also to biologists in general and that it will help to produce a needed epistemologi- cal shift in the different domains of biology—genomics, postgenomics, etc.—from correlative approaches to evolutionary approaches. I would like to express my sincere gratitude to the other members of the sci- entific committee—Etienne Pardoux, Philippe Monget, Bernard Swynghedauw, Etienne Danchin, Vincent Laudet, and Michel Milinkovitch, to the organiza- tional committee—Virginie Lopez-Rascol, Olivier Chabrol, and Julie Perrot, to the sponsor—Universit´e de Provence, CNRS, GDR BIM, R´egion PACA, Conseil G´en´eral 13, Marseille Provence M´etropole, and to Association pour l’Etude de l’Evolution Biologique that organizes the meetings. I also wish to thank the staff at Springer for their cooperation. v vi Preface Last but not least I thank the meeting coordinator Axelle Pontarotti for her work and also, as many participants said, for making us feel at home during the meeting. Marseilles, France Pierre Pontarotti February 2008 Contents Part I Modelization of Evolution 1 Rate of Adaptation of Large Populations ........................ 3 Feng Yu and Alison Etheridge 2 A Phylogenetic Mixture Model for Heterotachy .................. 29 Andrew Meade and Mark Pagel Part II Concepts in Evolutionary Biology 3 Accelerated Evolution of Genes of Recent Origin ................. 45 Macarena Toll-Riera, Jose Castresana, and M. Mar Alb`a 4 Life-Cycle Features of Tumour Cells ........................... 61 Jekaterina Erenpreisa and Mark S. Cragg 5 General Evolutionary Regularities of Organic and Social Life ...... 73 Valeria I. Mikhalevich 6 Old and New Concepts in EvoDevo ............................. 95 Margherita Raineri Part III Knowledge 7 Overturning the Prejudices about Hydra and Metazoan Evolution .. 117 Hiroshi Shimizu 8 The Search for the Origin of Cnidarian Nematocysts in Dinoflagellates ............................................ 135 Jung Shan Hwang, Satoshi Nagai, Shiho Hayakawa, Yasuharu Takaku, and Takashi Gojobori vii viii Contents Part IV Applied Evolutionary Biology 9 A Possible Relationship Between the Phylogenetic Branch Lengths and the Chaetognath rRNA Paralog Gene Functionalities: Ubiquitous, Tissue-Specific or Pseudogenes ...................... 155 Roxane-Marie Barth´el´emy(¬), Michel Grino, Pierre Pontarotti, Jean-Paul Casanova, and Eric Faure 10 Mode and Tempo of matK: Gene Evolution and Phylogenetic Implications ................................................ 165 Khidir W. Hilu and Michelle M. Barthet 11 Phylogeography and Conservation of the Rare South African Fruit Chafer Ichnestoma stobbiai (Coleoptera: Scarabaeidae) ........... 181 Ute Kryger and Clarke H. Scholtz 12 Nothing in Medicine Makes Sense Except in the Light of Evolution: AReview .................................................. 197 Bernard Swynghedauw 13 An Overview of Evolutionary Biology Concepts for Functional Annotation: Advances and Challenges .......................... 209 Anthony Levasseur and Pierre Pontarotti Index .............................................................217 Contributors M. Mar Alb`a Research Unit on Biomedical Informatics, Institut Municipal d’Investigaci´o M`edica, Universitat Pompeu Fabra, E-08003 Barcelona, Spain, and Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain, [email protected] Roxane-Marie Barth´el´emy Laboratoire Evolution Biologique et Mod´elisation, Case 19, UMR 6632, Universit´e d’Aix-Marseille/CNRS, 3 Place Victor Hugo, 13331 Marseille CEDEX 03, France, [email protected] Michelle M. Barthet ARC Centre of Excellence in Plant Energy Biology, School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia, [email protected] Jean-Paul Casanova Laboratoire Evolution Biologique et Mod´elisation, Case 19, UMR 6632, Universit´e d’Aix-Marseille/CNRS, 3 Place Victor Hugo, 13331 Marseille CEDEX 03, France, [email protected] Jose Castresana Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain, [email protected] Mark S. Cragg Tenovus Research Laboratory, Southampton University Hospital; Tremona Road, Southampton SO16 6YD, UK, [email protected] Jekaterina Erenpreisa Latvian Biomedicine Research and Study Centre, Ratsupites str. 1, 1067 Riga, Latvia, [email protected] ix x Contributors Alison Etheridge Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK, [email protected] Eric Faure Laboratoire Evolution Biologique et Mod´elisation, Case 19, UMR 6632, Universit´e d’Aix-Marseille/CNRS, 3 Place Victor Hugo, 13331 Marseille CEDEX 03, France, [email protected] Michel Grino Inserm UMR 626, UFR de M´edecine Secteur Timone, 27 Bd Jean Moulin, 13385 Marseille CEDEX 5, France, [email protected] Takashi Gojobori Center for Information Biology and DDBJ, National Institute of Genetics, Mishima, 411–8540 Shizuoka, Japan, [email protected] Shiho Hayakawa Center for Information Biology and DDBJ, National Institute of Genetics, Mishima, 411–8540 Shizuoka, Japan, [email protected] Khidir W. Hilu Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA, [email protected] Jung Shan Hwang Center for Information Biology and DDBJ, National Institute of Genetics, Mishima, 411–8540 Shizuoka, Japan, [email protected] Ute Kryger Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa, [email protected] Anthony S.G. Levasseur Laboratoire Evolution Biologique et Mod´elisation, Case 19, UMR 6632, Universit´e d’Aix-Marseille/CNRS, 3 Place Victor Hugo, 13331 Marseille CEDEX 03, France, [email protected] Andrew Meade School of Biological Sciences, Philip Lyle Building, The University of Reading, Reading RG6 6BX, UK, [email protected] Valeria I. Mikhalevich Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199134, Russia, [email protected] Satoshi Nagai National Research Institute of Fisheries and Environment of Inland Sea, Maruishi 2-17-5, Hatsukaichi, 739-0452 Hiroshima, Japan, [email protected] Contributors xi Mark Pagel School of Biological Sciences, Philip Lyle Building, The University of Reading, Reading RG6 6BX, UK, [email protected] Pierre Pontarotti Laboratoire Evolution Biologique et Mod´elisation, Case 19, UMR 6632, Universit´e d’Aix-Marseille/CNRS, 3 Place Victor Hugo, 13331 Marseille CEDEX 03, France, [email protected] Margherita Raineri Department
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