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Molecular Ecology Molecular Ecology Joanna R. Freeland The Open University, Milton Keynes Molecular Ecology Molecular Ecology Joanna R. Freeland The Open University, Milton Keynes Copyright # 2005 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England Telephone (+44) 1243 779777 Email (for orders and customer service enquiries): [email protected] Visit our Home Page on www.wileyeurope.com or www.wiley.com 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, electronic, mechanical, photocopying, recording, scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 or under the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1T 4LP, UK, without the permission in writing of the Publisher. Requests to the Publisher should be addressed to the Permissions Department, John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England, or emailed to [email protected], or faxed to (+44) 1243 770620. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The Publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the Publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Other Wiley Editorial Offices John Wiley & Sons Inc., 111 River Street, Hoboken, NJ 07030, USA Jossey-Bass, 989 Market Street, San Francisco, CA 94103-1741, USA Wiley-VCH Verlag GmbH, Boschstr. 12, D-69469 Weinheim, Germany John Wiley & Sons Australia Ltd, 42 McDougall Street, Milton, Queensland 4064, Australia John Wiley & Sons (Asia) Pte Ltd, 2 Clementi Loop # 02-01, Jin Xing Distripark, Singapore 129809 John Wiley & Sons Canada Ltd, 22 Worcester Road, Etobicoke, Ontario, Canada M9W 1L1 Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Library of Congress Cataloging-in-Publication Data Freeland, Joanna. Molecular ecology / Joanna Freeland. p. cm. Includes bibliographical references. ISBN-13 978-0-470-09061-8 (HB) ISBN-13 978-0-470-09062-6 (PB) ISBN-10 0-470-09061-8 (HB) ISBN-10 0-470-09062-6 (PB) 1. Molecular ecology. I. Title. QH541.15.M63F74 2005 577–dc22 2005027904 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN-13 978-0-470-09061-8 (HB) ISBN-13 978-0-470-09062-6 (PB) ISBN-10 0-470-09061-8 (HB) ISBN-10 0-470-09062-6 (PB) Typeset in 10.5/13pt Minion-Regular by Thomson Press (India) Limited, New Delhi, India. Printed and bound in Great Britain by Antony Rowe Ltd, Chippenham, Wiltshire. This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production. Contents Preface ix Acknowledgements xi 1 Molecular genetics in Ecology 1 What is molecular ecology? 1 The emergence of molecular ecology 2 Protein allozymes 4 An unlimited source of data 9 Mutation and recombination 10 Polymerase chain reaction 16 Sources of DNA 20 Getting data from PCR 22 Overview 26 Chapter summary 27 Useful websites and software 28 Further reading 28 Review questions 29 2 Molecular Markers in Ecology 31 Understanding molecular markers 31 Modes of inheritance 31 Nuclear versus organelle 32 Haploid chromosomes 37 Uniparental markers: a cautionary note 41 Molecular markers 43 Co-dominant markers 44 Dominant markers 53 Overview 57 Chapter summary 57 Useful websites and software 59 Further reading 60 Review questions 60 vi CONTENTS 3 Genetic Analysis of Single Populations 63 Why study single populations? 63 What is a population? 63 Quantifying genetic diversity 67 Hardy--Weinberg equilibrium 67 Estimates of genetic diversity 72 Choice of marker 75 What influences genetic diversity? 77 Genetic drift 77 Population bottlenecks 89 Natural selection 94 Reproduction 98 Overview 103 Chapter summary 104 Useful websites and software 105 Further reading 105 Review questions 106 4 Genetic Analysis of Multiple Populations 109 Why study multiple populations? 109 Quantifying population subdivision 109 Genetic distance 110 F-Statistics 112 Quantifying gene flow 117 Direct methods 117 Indirect methods 120 Assignment tests 121 Gene flow discrepancies 123 What influences gene flow? 123 Dispersal ability 127 Barriers to dispersal 129 Reproduction 131 Fragmented habitats and metapopulations 133 Interspecific interactions 136 Population differentiation: genetic drift and natural selection 138 Gene flow and genetic drift 139 Gene flow and local adaptation 142 Overview 151 Chapter summary 151 Useful websites and software 152 Further reading 153 Review questions 153 5 Phylogeography 155 What is phylogeography? 155 Molecular markers in phylogeography 155 CONTENTS vii Molecular clocks 157 Bifurcating trees 160 The coalescent 164 Applying the coalescent 166 Networks 167 Nested clade phylogeographic analysis and statistical phylogeography 170 Distribution of genetic lineages 173 Subdivided populations 173 Lineage sorting 178 Hybridization 180 Comparative phylogeography 184 Regional concordance 185 Continental concordance 188 Introduced species 193 Overview 196 Chapter summary 196 Useful websites and software 198 Further reading 198 Review questions 199 6 Molecular Approaches to Behavioural Ecology 201 Using molecules to study behaviour 201 Mating systems 202 Monogamy, polygamy and promiscuity 202 Parentage analysis 204 Mate choice 212 Social breeding 216 Manipulation of sex ratio 221 Adaptive sex ratios 222 Sex ratio conflicts 224 Sex-biased dispersal 226 Nuclear versus mitochondrial markers 227 Relatedness 228 FST Values 228 Assignment tests 228 Concordant results 230 Foraging 232 Identifying prey 233 In search of food 238 Overview 241 Chapter summary 242 Useful websites and software 243 Further reading 243 Review questions 244 viii CONTENTS 7 Conservation Genetics 247 The need for conservation 247 Taxonomy 250 Species concepts 250 Genetic barcodes 252 Subspecies 254 Conservation units 255 Population size, genetic diversity and inbreeding 257 Inbreeding depression 258 Translocations 268 Outbreeding depression 273 Captive breeding 277 Maximizing genetic diversity 278 Genetic diversity banks 280 Overview 281 Chapter summary 282 Useful websites and software 283 Further reading 283 Review questions 284 8 Molecular Ecology in a Wider Context 287 Applications of molecular ecology 287 Wildlife forensics 288 Poaching 288 Illegal trade 291 Non-human perpetrators 293 Agriculture 294 Pests and diseases 295 Law enforcement 296 Gene flow between genetically modified crops and wild relatives 297 Fishing 299 Overfishing 299 Stock enhancement 301 The future of molecular ecology 303 Chapter summary 304 Useful websites and software 305 Further reading 306 Review questions 306 Glossary 309 Answers to Review Questions 327 References 337 Index 373 Preface The theory and practice of molecular ecology draw on a number of subjects, particularly genetics, ecology and evolutionary biology. Although the foundations of molecular ecology are not particularly new, it did not emerge until the 1980s as the discipline that we now recognize. Since that time the growth of molecular ecology has been explosive, in part because molecular data are becoming increas- ingly accessible and also because it is, by its very nature, a collaborative discipline. Molecular ecology is now a broad area of research that embraces topics as varied as population genetics, conservation genetics, molecular evolution, behavioural ecology and biogeography, and has added much to our understanding of ecology. Researchers in molecular ecology now routinely publish their work in a wide range of ecological and evolutionary journals (including Molecular Ecology, first published in 1992), and also in more general publications such as Science and Nature. Although somewhat varied, the areas of research within molecular ecology are united by the fact that they all use molecular genetic data to help us understand the ecology and evolution of organisms in the wild. Although there are many excellent texts that cover general ecology and evolution, there is currently a shortage of books that provide a comprehensive overview of molecular ecology. The most important goal of this book, therefore, has been to present molecular genetics, population genetics and applied molecular ecology in a logical and uncomplicated -- but not oversimplified -- manner, using up-to-date examples from a wide range of taxa. This text is aimed at upper-level undergraduate and postgraduate students, as well as at researchers who may be relatively new to molecular ecology or are thinking about different ways to address their research questions using molecular data. Each chapter may be read in isolation, but there is a structure to the book that should be particularly useful to students who read the text in its entirety. The first two chapters provide a brief history of molecular ecology and a review of genetics, followed by an overview of molecular markers
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