This page intentionally left blank A Primer of Conservation Genetics The biological diversity of our planet is rapidly being depleted due to di- rect and indirect consequences of human activities. As the size of animal and plant populations decreases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding depres- sion an inevitable consequence for many species. This concise, entry-level text provides an introduction to the role of genetics in conservation and presents the essentials of the discipline. Topics covered include: r loss of genetic diversity in small populations r inbreeding and loss of fitness r resolution of taxonomic uncertainties r genetic management of threatened species r contributions of molecular genetics to conservation The authors assume only a basic knowledge of Mendelian genetics and simple statistics, making the book accessible to those with a limited back- ground in these areas. Connections between conservation genetics and the wider field of conservation biology are interwoven throughout the book. The text is presented in an easy-to-follow format, with main points and terms clearly highlighted. Worked examples are provided throughout to help illustrate key eq uations. A glossary and sugges tions for further reading provide additional support for the reader and many beautiful pen-and-ink portraits of endangered species help bring the material to life. Written for short, introductory-level courses in genetics, conservation genetics and conservation biology, this book will also be suitable for prac- tising conservation biologists, zoo biologists and wildlife managers need- ing a brief, accessible account of the significance of genetics to conserva- tion. dick frankham was employed in the Department of Biological Sci- ences at Macquarie University, Sydney for 31 years and was Hrdy Visiting Professor at Harvard University for spring semester 2004. He holds hon- orary professorial appointments at Macquarie University, James Cook University and the Australian Museum. jon ballou is Head of the Depar tment of Conservation Biology at the Smithsonian Institution’s National Zoological Park. david briscoe is Associate Professor at the Key Centre for Biodiversity and Bioresources, Department of Biological Sciences, Macquarie Univer- sity, Sydney. A Primer of Conservation Genetics Richard Frankham Macquarie University, Sydney Jonathan D. Ballou Smithsonian Institution, Washington, DC David A. Briscoe Macquarie University, Sydney Line drawings by Karina H. McInnes Melbourne cambridge university press Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press The Edinburgh Building, Cambridge cb2 2ru, UK First published in print format isbn-13 978-0-521-83110-9 isbn-13 978-0-521-53827-5 isbn-13 978-0-511-18661-5 © R. Frankham, Smithsonian Institution, D. Briscoe 2004 2004 Information on this title: www.cambrid g e.or g /9780521831109 This publication is in copyright. Subject to statutory exception and to the provision of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. isbn-10 0-511-18661-4 isbn-10 0-521-83110-5 isbn-10 0-521-53827-0 Cambridge University Press has no responsibility for the persistence or accuracy of urls for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. Published in the United States of America by Cambridge University Press, New York www.cambridge.org hardback p a p erback p a p erback eBook (EBL) eBook (EBL) hardback Contents Preface page ix Take-home messages xi Acknowledgments xiii Chapter 1 Introduction 1 The ‘sixth extinction’ 2 Why conserve biodiversity? 2 Endangered and extinct species 3 What is a threatened species? 4 What causes extinctions? 6 What is conservation genetics? 6 Suggested further reading 10 Chapter 2 Genetic diversity 12 Importance of genetic diversity 13 What is genetic diversity? 13 Measuring genetic diversity 13 Hardy Weinberg equilibrium 16 Extent of genetic diversity 20 Low genetic diversity in threatened species 29 What components of genetic diversity determine the ability to evolve? 30 Suggested further reading 30 Chapter 3 Evolutionary genetics of natural populations 31 Factors controlling the evolution of populations 32 Origin and regeneration of genetic diversity 33 Mutation 33 Migration and gene flow 35 Selection and adaptation 37 Genotype × environment interaction 47 Mutation selection balance 49 Suggested further reading 50 Chapter 4 Genetic consequences of small population size 52 Importance of small populations in conservation biology 53 Loss of genetic diversity 54 Chance effects and genetic drift 54 Genetic drift 55 vi CONTENTS Effects of sustained population size restrictions on genetic diversity 57 Inbreeding 58 Inbreeding in small random mating populations 63 Measuring population size 64 Population fragmentation 70 Selection in small populations 75 Suggested further reading 75 Chapter 5 Genetics and extinction 76 Genetics and the fate of endangered species 77 Inbreeding depression 77 Measuring inbreeding depression 80 Relationship between inbreeding and extinction 82 Relationship between loss of genetic diversity and extinction 86 Geneticall y viable populations 88 Population viability analysis (PVA) 93 Suggested furth er reading 99 Chapter 6 Resolving taxonomic uncertainties and defining management units 101 Importance of accurate taxonomy in conservation biology 102 What is a species? 104 Sub-species 105 How do species arise? 106 Use of genetic analyses in delineating species 108 Genetic distance 112 Constructing phylogenetic trees 114 Outbreeding depression 116 Defining management units within species 118 Suggested further reading 121 Chapter 7 Genetic management of endangered species in the wild 123 Genetic issues in endangered populations 124 Increasing population size 126 Diagnosing genetic problems 128 Recovering small inbred populations with low genetic diversity 129 Genetic management of fragmented populations 131 Genetic issues in reserve design 136 Introgression and hybridization 137 Impacts of harvesting 138 Genetic management of species that are not outbreeding diploids 139 CONTENTS vii Evaluating recovery strategies 140 Supplemental breeding and assisted reproductive technologies 142 Suggested further reading 144 Chapter 8 Captive breeding and reintroduction 145 Why captive breed? 146 Stages in captive breeding and reintroduction 147 Founding captive populations 148 Growth of captive populations 149 Genetic management during the maintenance phase 149 Ex situ conservation of plants 155 Management of inherited diseases 155 Reintroductions 157 Case studies in captive breeding and reintroduction 165 Suggested further reading 167 Chapter 9 Molecular genetics in forensics and understanding species biology 168 Forensics: detecting illegal hunting and collecting 169 Understan d ing species’ b iology is critical to its conservation 171 Gene trees and coalescence 172 Population size and demographic history 177 Gene flow and population structure 180 Reintroduction and translocation 184 Breeding systems, parentage, founder relationships and sexing 185 Disease 191 Diet 192 Suggested further reading 192 Final messages 193 Glossary 194 Sources and copyright acknowledgments 206 Index 212 [...]... relative frequency of a particular allele in a population (often referred to as gene frequency) For example, if a population of a diploid species has 8 A1 A1 individuals and 2 A1 A2 individuals, then there are 18 copies of the A1 allele and 2 of the A2 allele Thus, the A1 allele has a frequency of 0.9 and the A2 allele a frequency of 0.1 Polymorphic The presence in a species of two or more alleles at... populations are considered to be a valuable genetic resource for re-establishing mainland populations, particularly in Australia and New Zealand However, molecular genetic analyses revealed that the black-footed rock wallaby population on Barrow Island, Australia (a potential source of individuals for reintroductions onto the mainland) has extremely low genetic variation and reduced reproductive rate... breeds All derive from the gray wolf Genetic diversity can be measured at a number of different levels This includes diversity in measurable characters (quantitative variation), the visible direct effects of deleterious alleles, variation in proteins, and direct measurement of variation in DNA sequences Quantitative variation The characters of most importance in conservation are quantitative characters... years When extinctions are balanced by the origin of new species (speciation), biodiversity is maintained Mass extinctions, such as the cosmic cataclysm that eliminated much of the flora and fauna at the end of the Cretaceous, 65 million years ago, are different It took many millions of years for proliferation of mammals and angiosperm plants to replace the pre-existing dinosaurs and gymnosperm plants... , A1 A2 or A2 A2 Genotypes are heterozygous (A1 A2 ) or homozygous (A1 A1 or A2 A2 ) Genome The complete genetic material of a species, or individual; the entire DNA nucleotide sequence, including all of the loci and all of the chromosomes Homozygote An individual with two copies of the same allele at a locus, e.g A1 A1 Heterozygote An individual with two different alleles at a locus, e.g A1 A2 Allele... stochasticity, inbreeding, inbreeding depression, purging, speciation, stochastic, threatened, vulnerable Selection of threatened species: Clockwise: panda (China), an Australian orchid, palm cockatoo (Australia), tuatara (New Zealand), poison arrow frog (South America), lungfish (Australia), Wollemi pine (Australia) and Corsican swallow-tail butterfly 2 INTRODUCTION The ‘sixth extinction’ The biological... inbreeding) Some numerically smaller and more endangered mainland populations are genetically healthier and are therefore a more suitable source of animals for reintroductions to other mainland localities Alternatively, the pooling of several different Black-footed rock wallaby 9 10 INTRODUCTION island populations of this wallaby could provide a genetically healthy population suitable for reintroduction... and a substantial proportion of currently threatened species, are on islands (Table 1.1) For example, 81% of all extinct birds lived on islands, four-fold greater than the proportion of bird species that have lived on islands Extent of endangerment 18% of vertebrate animal species, 29% of invertebrates and 49% of plant species are classified as threatened IUCN, the World Conservation Union, defines as... reintroduction Molecular analyses may provide additional information on the historical distribution of species, expanding possibilities for conservation action For ecological reasons, reintroductions should preferably occur within a species’ historical range The northern hairy-nosed wombat exists in a single population of approximately 100 animals at Clermont in Queensland, Australia DNA samples obtained from... population genetics (allele frequencies and Hardy Weinberg equilibrium) Conservation professionals with little genetics background wishing for a brief authoritative introduction to conservation genetics should find it understandable These include wildlife biologists and ecologists, zoo staff undertaking captive breeding programs, planners and managers of national parks, water catchments and local government areas, . species Selection of threatened species: Clockwise: panda (China), an Australian orchid, palm cockatoo (Australia), tuatara (New Zealand), poison arrow frog (South America),. species that are incapable of surviving in their natural habitats. Captive popula- tions of threatened species are typically managed to retain 90% of their