BT201 Handouts Complete

Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York # Oxford University Press 2006 The moral rights of the authors have been asserted Database right Oxford University Press (maker) First published 2006 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Straalen, N. M. van An introduction to ecological genomics / Nico M. van Straalen and Dick Roelofs. p. cm. ISBN-13: 978-0-19-856671-7 (alk. paper) ISBN-10: 0-19-856671-9 (alk. paper)

1. Molecular microbiology. 2. Microbiology. 3. Ecology. I. Roelofs, Dick. II. Title. QR74.S78 2006 576.508—dc22 2005029756

Cover design by Janine Marie¨n Typeset by Newgen Imaging Systems (P) Ltd., Chennai, India Printed in Great Britain on acid-free paper by Ashford Colour Press, Hampshire ISBN 0–19–856670–0 978–0–19–856670–1 ISBN 0–19–856671–9 (Pbk.) 978–0–19–856671–7 (Pbk.)

Preface

This book is an introduction to the exciting new field of ecological genomics, for use in MSc courses and by those beginning their PhD studies. When we became involved in a national research programme on ecological genomics, or ecogenomics as it became known, we realized that information on this newly emerging subject needed to be brought together. In order to start up a research programme in such a new discipline, not only the students, but also we as teachers, had to get to grips with the subject. Furthermore, although obtaining a PhD implies mastering a specialized field, the PhD student must be able to place this field in a broader context if he or she is to become a mature scientist. This approach may be called the T-model of education; the horizontal bar of the T representing a broad understanding, and the vertical bar an investigation in depth, going down to the root of the problem. Our book uses this approach. We assume a basic level of knowledge in the biological sciences to BSc level: ecology, evolutionary biology, microbiology, plant physiology, animal physiology, genetics, and molecular biology. We have tried to link up with the content of the most common textbooks in these fields, at the same time realizing that students of ecological genomics have a variety of backgrounds. However, our main targets are students with subjects closely related to ecology and evolutionary biology, which is why we place the emphasis on aspects that we judge to be particularly new to them. Evolutionary genomics and bioinformatics are companion disciplines to ecological genomics. In the last 10 years interest in both disciplines has grown enormously. Several textbooks on bioinformatics have already been published and subjects encompassed by evolutionary genomics, such as comparative genomics, phylogenetic analysis, and molecular evolution, can now be considered as fields in their own right. They are certainly too large to be covered in an introductory book on ecological genomics; indeed, evolutionary genomics deserves a textbook of its own. We have organized this book around three issues important in modern ecology, choosing questions for which the links to genomics are best developed. At the outset, we perhaps use rather ambitious phrasing to announce the genomics approach to these ecological questions. Maybe our questions cannot be answered at this stage. However, we decided not to suppress unanswered, and thus open, issues. Instead we hope to stimulate discussion as well as provide factual information. We have included an appraisal section at the end of each chapter to emphasize this questionorientated approach. Combined with information given in the introductory section, this allows the reader to grasp the main points of each chapter, even if the detailed treatment of molecular principles and case studies are left aside. Case studies are taken from literature published since the year 2000. Nevertheless, a book on genomics runs the risk of becoming outdated very quickly: the rate at which knowledge is being accrued and insight developed is unprecedented. However, we hope that our question-orientated set-up will be useful for some years to come, even when new and better case studies are available. Before this book was written, journal articles comprised the only literature on ecological genomics. These, although very inspiring, were scattered widely. Today, most textbooks on

v genetics and evolution have a chapter on genomics. Gibson and Muse published a primer on genome science in 2002, but this did not cover ecological questions. So, for us, writing this book was ploughing unknown ground. We have attempted to add structure to the field, and hopefully have put ecological genomics on the map. However, we welcome constructive criticism and suggestions from our readers. We thank the colleagues who reviewed parts of the book, suggested issues that had escaped us, or helped with correcting the English: Martin Feder, Claire Hengeveld, Jan Kammenga, Rene´ Klein Lankhorst, Bas Kooijman, Jan Kooter, Wilfred Ro¨ling, and Martijn Timmermans. We thank Desire´e Hoonhout and Karin Uyldert for checking the reference list, and Nico Schaefers, for preparation of the figures. Ian Sherman at Oxford University Press provided us with stimulating discussion. We thank members of the Animal Ecology Department at the Vrije Universiteit for your friendship and encouragement. N.M.vS. also thanks the Faculty of Earth and Life Sciences of the Vrije Universiteit for granting the sabbatical leave during which most of this book was written.

Amsterdam, July 2005 vi PREFACE