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Conservation and the Genetics of Populations

663 Pages · 2007 · 7.33 MB · English

  • Conservation and the Genetics of Populations

    CATA01 28/05/2007 11:57 AM Page i


    Conservation and the Genetics of Populations CATA01 28/05/2007 11:57 AM Page ii CATA01 28/05/2007 11:57 AM Page iii


    CONSERVATION AND


    THE GENETICS OF POPULATIONS


    Fred W. Allendorf


    University of Montana


    and


    Victoria University of Wellington


    and


    Gordon Luikart


    Université Joseph Fourier, CNRS


    and


    University of Montana


    With illustrations by Agostinho Antunes CATA01 28/05/2007 11:57 AM Page iv


    © 2007 by Blackwell Publishing


    BLACKWELL PUBLISHING


    350 Main Street, Malden, MA 02148-5020, USA


    9600 Garsington Road, Oxford OX4 2DQ, UK


    550 Swanston Street, Carlton, Victoria 3053, Australia


    The right of Fred W. Allendorf and Gordon Luikart to be identified as the Authors of this Work


    has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988.


    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


    or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without


    the prior permission of the publisher.


    First published 2007 by Blackwell Publishing Ltd


    1 2007


    Library of Congress Cataloging-in-Publication Data


    Allendorf, Frederick William.


    Conservation and the genetics of populations / Fred W. Allendorf and


    Gordon Luikart.


    p. cm.


    ISBN-13: 978-1-4051-2145-3 (pbk. : alk. paper)


    ISBN-10: 1-4051-2145-9 (pbk. : alk. paper)


    1. Biological diversity conservation. 2. Population genetics. 3.


    Evolutionary genetics. I. Luikart, Gordon. II. Title.


    QH75.A42 2006



    576.58—dc22


    2006001707


    A catalogue record for this title is available from the British Library.


    Set in 10.5/12.5pt Dante


    by Graphicraft Limited, Hong Kong


    Printed and bound in UK


    by TJ International, Padstow


    The publisher’s policy is to use permanent paper from mills that operate a sustainable forestry


    policy, and which has been manufactured from pulp processed using acid-free and elementary


    chlorine-free practices. Furthermore, the publisher ensures that the text paper and cover board


    used have met acceptable environmental accreditation standards.


    For further information on


    Blackwell Publishing, visit our website:


    www.blackwellpublishing.com


    Chapter opening images remain copyright of Agostinho Antunes CATA01 28/05/2007 11:58 AM Page v


    Contents


    Authors of Guest Boxes, xi


    Preface, xiii


    List of Symbols, xvi


    PART I: INTRODUCTION


    1 Introduction, 3


    1.1 Genetics and conservation, 4


    1.2 What should we conserve?, 5


    1.3 How should we conserve biodiversity?, 10


    1.4 Applications of genetics to conservation, 11


    Guest Box 1 by L. S. Mills and M. E. Soulé: The role of genetics in conservation, 13


    2 Phenotypic Variation in Natural Populations, 15


    2.1 Color pattern, 18


    2.2 Morphology, 20


    2.3 Behavior, 23


    2.4 Differences among populations, 26


    Guest Box 2 by C. J. Foote: Looks can be deceiving: countergradient variation in


    secondary sexual color in sympatric morphs of sockeye salmon, 29


    3 Genetic Variation in Natural Populations: Chromosomes and Proteins, 33


    3.1 Chromosomes, 35


    3.2 Protein electrophoresis, 47


    3.3 Genetic variation within natural populations, 51


    3.4 Genetic divergence among populations, 52


    3.5 Strengths and limitations of protein electrophoresis, 54


    Guest Box 3 by A. Young and B. G. Murray: Management implications of polyploidy


    in a cytologically complex self-incompatible herb, 55 CATA01 28/05/2007 11:58 AM Page vi


    vi CONTENTS


    4 Genetic Variation in Natural Populations: DNA, 63


    4.1 Mitochondrial and chloroplast DNA, 64


    4.2 Single copy nuclear loci, 69


    4.3 Multilocus techniques, 74


    4.4 Sex-linked markers, 77


    4.5 DNA sequences, 78


    4.6 Additional techniques and the future, 78


    4.7 Genetic variation in natural populations, 81


    Guest Box 4 by N. N. FitzSimmons: Multiple markers uncover marine turtle


    behavior, 82


    PART II: MECHANISMS OF EVOLUTIONARY CHANGE


    5 Random Mating Populations: Hardy–Weinberg Principle, 93


    5.1 The Hardy–Weinberg principle, 94


    5.2 Hardy–Weinberg proportions, 97


    5.3 Testing for Hardy–Weinberg proportions, 99


    5.4 Estimation of allele frequencies, 105


    5.5 Sex-linked loci, 108


    5.6 Estimation of genetic variation, 110


    Guest Box 5 by V. Castric and L. Bernatchez: Testing alternative explanations for


    deficiencies of heterozygotes in populations of brook trout in small lakes, 112


    6 Small Populations and Genetic Drift, 117


    6.1 Genetic drift, 118


    6.2 Changes in allele frequency, 122


    6.3 Loss of genetic variation: the inbreeding effect of small populations, 123


    6.4 Loss of allelic diversity, 126


    6.5 Founder effect, 129


    6.6 Genotypic proportions in small populations, 136


    6.7 Fitness effects of genetic drift, 138


    Guest Box 6 by P. L. Leberg and D. L. Rogowski: The inbreeding effect of small


    population size reduces population growth rate in mosquitofish, 141


    7 Effective Population Size, 147


    7.1 Concept of effective population size, 148


    7.2 Unequal sex ratio, 151


    7.3 Nonrandom number of progeny, 153


    7.4 Fluctuating population size, 157


    7.5 Overlapping generations, 158


    7.6 Variance effective population size, 159


    7.7 Cytoplasmic genes, 159


    7.8 Gene genealogies and lineage sorting, 162


    7.9 Limitations of effective population size, 163


    7.10 Effective population size in natural populations, 166


    Guest Box 7 by C. R. Miller and L. P. Waits: Estimation of effective population size in


    Yellowstone grizzly bears, 167 CATA01 28/05/2007 11:58 AM Page vii


    CONTENTS vii


    8 Natural Selection, 171


    8.1 Fitness, 173


    8.2 Single locus with two alleles, 174


    8.3 Multiple alleles, 179


    8.4 Frequency-dependent selection, 184


    8.5 Natural selection in small populations, 186


    8.6 Natural selection and conservation, 188


    Guest Box 8 by C. A. Stockwell and M. L. Collyer: Rapid adaptation and


    conservation, 192


    9 Population Subdivision, 197


    9.1 F-statistics, 199


    9.2 Complete isolation, 204


    9.3 Gene flow, 205


    9.4 Gene flow and genetic drift, 206


    9.5 Cytoplasmic genes and sex-linked markers, 210


    9.6 Gene flow and natural selection, 214


    9.7 Limitations of F and other measures of subdivision, 218


    ST


    9.8 Estimation of gene flow, 220


    9.9 Population subdivision and conservation, 226


    Guest Box 9 by C. S. Baker and F. B. Pichler: Hector’s dolphin population structure


    and conservation, 227


    10 Multiple Loci, 233


    10.1 Gametic disequilibrium, 234


    10.2 Small population size, 239


    10.3 Natural selection, 240


    10.4 Population subdivision, 245


    10.5 Hybridization, 246


    10.6 Estimation of gametic disequilibrium, 250


    Guest Box 10 by S. H. Forbes: Dating hybrid populations using gametic


    disequilibrium, 252


    11 Quantitative Genetics, 257


    11.1 Heritability, 258


    11.2 Selection on quantitative traits, 264


    11.3 Quantitative trait loci (QTLs) , 269


    11.4 Genetic drift and bottlenecks, 274


    11.5 Divergence among populations (Q ), 276


    ST


    11.6 Quantitative genetics and conservation, 278


    Guest Box 11 by D. W. Coltman: Response to trophy hunting in bighorn sheep, 282


    12 Mutation, 285


    12.1 Process of mutation, 286


    12.2 Selectively neutral mutations, 291


    12.3 Harmful mutations, 296


    12.4 Advantageous mutations, 297 CATA01 28/05/2007 11:58 AM Page viii


    viii CONTENTS


    12.5 Recovery from a bottleneck, 297


    Guest Box 12 by M. W. Nachman: Color evolution via different mutations in


    pocket mice, 299


    PART III: GENETICS AND CONSERVATION


    13 Inbreeding Depression, 305


    13.1 Pedigree analysis, 307


    13.2 Gene drop analysis, 310


    13.3 Estimation of Fand relatedness with molecular markers, 313


    13.4 Causes of inbreeding depression, 315


    13.5 Measurement of inbreeding depression, 317


    13.6 Genetic load and purging, 323


    Guest Box 13 by R. C. Lacy: Understanding inbreeding depression: 20 years of


    experiments with Peromyscusmice, 327


    14 Demography and Extinction, 334


    14.1 Estimation of population size, 336


    14.2 Inbreeding depression and extinction, 338


    14.3 Population viability analysis, 342


    14.4 Loss of phenotypic variation, 350


    14.5 Loss of evolutionary potential, 355


    14.6 Mitochondrial DNA, 355


    14.7 Mutational meltdown, 357


    14.8 Long-term persistence, 357


    14.9 The 50/500 rule, 359


    Guest Box 14 by A. C. Taylor: Noninvasive population size estimation in wombats, 360


    15 Metapopulations and Fragmentation, 363


    15.1 The metapopulation concept, 364


    15.2 Genetic variation in metapopulations, 365


    15.3 Effective population size, 369


    15.4 Population divergence and fragmentation, 371


    15.5 Genetic rescue, 372


    15.6 Long-term population viability, 374


    Guest Box 15 by R. C. Vrijenhoek: Fitness loss and genetic rescue in


    stream-dwelling topminnows, 377


    16 Units of Conservation, 380


    16.1 What should we try to protect?, 382


    16.2 Systematics and taxonomy, 385


    16.3 Phylogeny reconstruction, 387


    16.4 Description of genetic relationships within species, 392


    16.5 Units of conservation, 404


    16.6 Integrating genetic, phenotypic, and environmental information, 415


    Guest Box 16 by R. S. Waples: Identifying conservation units in Pacific salmon, 417 CATA01 28/05/2007 11:58 AM Page ix


    CONTENTS ix


    17 Hybridization, 421


    17.1 Natural hybridization, 423


    17.2 Anthropogenic hybridization, 428


    17.3 Fitness consequences of hybridization, 429


    17.4 Detecting and describing hybridization, 434


    17.5 Hybridization and conservation, 443


    Guest Box 17 by L. H. Rieseberg: Hybridization and the conservation of plants, 446


    18 Conservation Breeding and Restoration, 449


    18.1 The role of conservation breeding, 452


    18.2 Reproductive technologies and genome banking, 457


    18.3 Founding populations for conservation breeding programs, 459


    18.4 Genetic drift in captive populations, 461


    18.5 Natural selection and adaptation to captivity, 464


    18.6 Genetic management of conservation breeding programs, 466


    18.7 Supportive breeding, 470


    18.8 Reintroductions and translocations, 472


    Guest Box 18 by J. V. Briskie: Effects of population bottlenecks on introduced species


    of birds, 479


    19 Invasive Species, 482


    19.1 Why are invasive species so successful?, 484


    19.2 Genetic analysis of introduced species, 487


    19.3 Establishment and spread of invasive species, 491


    19.4 Hybridization as a stimulus for invasiveness, 492


    19.5 Eradication, management, and control, 494


    Guest Box 19 by J. L. Maron: Rapid adaptation of invasive populations of


    St John’s Wort, 499


    20 Forensic and Management Applications of Genetic Identification, 502


    20.1 Species identification, 504


    20.2 Individual identification and probability of identity, 509


    20.3 Parentage testing, 513


    20.4 Sex identification, 515


    20.5 Population assignment, 515


    20.6 Population composition analysis, 518


    Guest Box 20 by L. P. Waits: Microsatellite DNA genotyping identifies problem bear


    and cubs, 521


    Glossary, 526


    Appendix: Probability and Statistics, 543


    A1 Probability, 546


    A2 Statistical measures and distributions, 548


    A3 Frequentist hypothesis testing, statistical errors, and power, 557


    A4 Maximum likelihood, 561


    A5 Bayesian approaches and MCMC (Markov chain Monte Carlo), 562


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