Conservation and the Genetics of Populations

Conservation and the Genetics of Populations

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


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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