Introduction to Conservation Genetics

'This impressive author team brings the wealth of advances in conservation genetics into the new edition of this introductory text, including new chapters on Population Genomics and Genetic Issues in Introduced and Invasive Species. They continue the strong learning features for students - main points in the margin, chapter summaries, vital support with the mathematics, and further reading - and now guide the reader to software and databases. Many new references reflect the expansion of this field. With examples from mammals, birds, reptiles, fish, amphibians, plants and invertebrates, this is an ideal introduction to conservation genetics for a broad audience. The text tackles the quantitative aspects of conservation genetics, and has a host of pedagogy to support students learning the numerical side of the subject. Combined with being up-to-date, its user-friendly writing style and a first-class illustration programme, this forms a robust teaching package.'--NHBS Environment Bookstore. Introduction to Conservation Genetics, Second edition......Page 2 Title page......Page 4 Copyright page......Page 5 Contents......Page 7 Preface to the second edition......Page 17 Preface......Page 18 Copyright acknowledgments......Page 31 Chapter 1 Introduction......Page 33 Why conserve biodiversity?......Page 35 Endangered and extinct species......Page 37 What is an endangered species?......Page 41 What causes extinctions?......Page 43 Recognition of genetic factors in conservation biology......Page 45 What is conservation genetics?......Page 46 Examples of the use of genetics to aid conservation......Page 48 Genetic management of threatened species......Page 56 Methodology in conservation genetics......Page 59 Summary......Page 61 General bibliography......Page 62 Problems......Page 63 Practical exercises: categorizing endangerment of species......Page 65 Chapter 2 Genetics and extinction......Page 66 Genetics and the fate of endangered species......Page 67 Relationship between inbreeding and extinction......Page 72 Relationship between loss of genetic diversity and extinction......Page 85 Further reading......Page 94 Problems......Page 95 Practical exercises: computer projections......Page 96 Section I Evolutionary genetics of natural populations......Page 101 Chapter 3 Genetic diversity......Page 104 Importance of genetic diversity......Page 106 What is genetic diversity?......Page 108 Measuring genetic diversity......Page 114 Extent of genetic diversity......Page 130 Low genetic diversity in threatened species and bottlenecked populations......Page 141 Variation over space and time......Page 142 Genetic differences among species......Page 144 Further reading......Page 147 Practical exercise: Measuring genetic diversity using microsatellites......Page 148 Chapter 4 Characterizing genetic diversity: single loci......Page 150 Describing genetic diversity......Page 151 Frequencies of alleles and genotypes......Page 152 Hardy–Weinberg equilibrium......Page 156 Expected heterozygosity......Page 162 Deviations from Hardy–Weinberg equilibrium......Page 173 Extensions of the Hardy–Weinberg equilibrium......Page 176 More than one locus: linkage disequilibrium......Page 182 Summary......Page 188 Problems......Page 189 Chapter 5 Characterizing genetic diversity: quantitative variation......Page 192 Importance of quantitative characters......Page 193 Properties of quantitative characters......Page 196 Basis of quantitative genetic variation......Page 199 Methods for detecting quantitative genetic variation......Page 200 Partitioning genetic and environmental variation......Page 203 Partitioning of quantitative genetic variation......Page 206 Evolutionary potential, additive variation and heritability......Page 210 Dominance variance (VD)......Page 226 Correlations between molecular and quantitative genetic variation......Page 229 Genotype × environment interaction......Page 230 Further reading......Page 234 Problems......Page 235 Chapter 6 Evolutionary impacts of natural selection in large populations......Page 238 The need to evolve......Page 239 Factors controlling the evolution of populations......Page 247 Selection......Page 251 Selection on quantitative characters......Page 270 Further reading......Page 278 Problems......Page 279 Practical exercises: computer simulations......Page 280 Chapter 7 Evolutionary impacts of mutation and migration, and their interactions with selection in large populations......Page 283 Importance of mutation and migration and their interactions with selection in conservation......Page 285 Mutation......Page 286 Mutation–selection balance and the mutation load......Page 294 Migration......Page 306 Migration–selection equilibria and clines......Page 310 Software......Page 316 Problems......Page 317 Chapter 8 Genetic consequences of small population sizes......Page 319 Importance of small populations in conservation biology......Page 320 Chance effects......Page 323 Fixation......Page 331 Effects of population bottlenecks......Page 332 Inbreeding......Page 341 Measuring population size......Page 343 Selection in small populations......Page 346 Mutation–selection equilibrium in small populations......Page 348 Computer simulation......Page 350 Summary......Page 352 Software......Page 353 Problems......Page 354 Practical exercises: computer simulations......Page 355 Chapter 9 Maintenance of genetic diversity......Page 357 Conservation of genetic diversity......Page 358 Fate of different classes of mutations......Page 360 Neutral mutations under random genetic drift......Page 363 Selection intensities vary among characters......Page 370 Balancing selection......Page 372 Reproductive fitness......Page 387 Maintenance of genetic diversity in small populations......Page 388 Summary......Page 397 Software......Page 398 Problems......Page 399 Practical exercises: Computer simulations......Page 400 Chapter 10 Population genomics......Page 403 Genome sequencing and population genomics......Page 404 cDNA expression microarrays......Page 409 What conservation benefits might be gained from genomics?......Page 411 Genome organization......Page 413 Insights into evolution from genomics......Page 420 Insights from gene expression studies......Page 430 Prospects for individual-locus genetic management......Page 433 Summary......Page 439 Software......Page 440 Problems......Page 441 Section II Effects of population size reduction......Page 442 Chapter 11 Loss of genetic diversity in small populations......Page 445 Changes in genetic diversity over time......Page 446 Relationship between loss of genetic diversity and reduced fitness......Page 448 Effects of sustained population size restrictions on genetic diversity......Page 452 Relationship between population size and genetic diversity in wild populations......Page 461 Effective population size......Page 466 Measuring effective population size......Page 469 Gene trees and coalescence......Page 489 Summary......Page 493 Software......Page 494 Problems......Page 495 Practical exercises: computer simulations......Page 496 Chapter 12 Inbreeding......Page 497 What is inbreeding?......Page 498 Conservation concerns with inbreeding......Page 501 Measuring inbreeding: inbreeding coefficient (F)......Page 502 Genetic consequences of inbreeding......Page 506 Inbreeding in small random mating populations......Page 513 Pedigrees......Page 523 Regular systems of inbreeding......Page 528 Mutation–selection balance with inbreeding......Page 534 Inbreeding in polyploids......Page 536 Relationships between inbreeding, heterozygosity, genetic diversity and population size......Page 538 Summary......Page 539 Software......Page 540 Problems......Page 541 Chapter 13 Inbreeding depression......Page 544 Inbreeding depression in naturally outbreeding species......Page 545 Inbreeding depression in the wild......Page 548 Inbreeding depression due to small population size......Page 552 Inbreeding, population viability and extinction......Page 553 Characteristics of inbreeding depression......Page 558 Genetic basis of inbreeding depression......Page 565 Purging......Page 571 Detecting and measuring inbreeding depression......Page 578 Genetic rescue......Page 584 Summary......Page 585 Further reading......Page 586 Problems......Page 587 Chapter 14 Population fragmentation......Page 589 Population fragmentation......Page 591 Population structure......Page 596 Completely isolated population fragments......Page 599 Measuring population fragmentation: F statistics......Page 615 Gene flow among population fragments......Page 621 Measuring gene flow......Page 627 Landscape genetics......Page 635 Impacts of different population structures on reproductive fitness......Page 637 Further reading......Page 640 Software......Page 641 Problems......Page 642 Chapter 15 Genetically viable populations......Page 644 Shortage of space for threatened species......Page 645 How large?......Page 649 Retaining reproductive fitness......Page 650 Retaining evolutionary potential......Page 652 How large are threatened populations?......Page 655 Time to regenerate genetic diversity......Page 664 Avoiding accumulation of new deleterious mutations......Page 665 Genetic goals in the management of wild populations......Page 668 Genetic goals in management of captive populations: a compromise......Page 671 The fallacy of small surviving populations......Page 678 Summary......Page 679 Further reading......Page 680 Problems......Page 681 Section III From theory to practice......Page 683 Chapter 16 Resolving taxonomic uncertainties and defining management units......Page 686 Importance of accurate taxonomy in conservation biology......Page 687 What is a species?......Page 695 Sub-species......Page 701 How do species arise?......Page 702 Delineating sympatric species......Page 708 Delineating allopatric species......Page 710 Genetic distance......Page 712 Constructing phylogenetic trees......Page 716 Outbreeding depression......Page 720 Defining management units within species......Page 727 Summary......Page 732 Further reading......Page 733 Software......Page 734 Problems......Page 735 Practical exercise: building a phylogenetic tree......Page 736 Chapter 17 Genetic management of wild populations......Page 738 Genetic issues in wild populations......Page 740 Increasing population size......Page 745 Diagnosing genetic problems......Page 748 Genetic rescue of small inbred populations by outcrossing......Page 750 Genetic management of fragmented populations......Page 754 Genetic issues in reserve design......Page 764 Impacts of harvesting......Page 766 Genetic management of species that are not outbreeding diploids......Page 769 Summary......Page 779 Further reading......Page 780 Problems......Page 781 Chapter 18 Genetic issues in introduced and invasive species......Page 783 Impact of invasive species on biodiversity......Page 784 Phases in establishment of invasive species......Page 786 Genetic issues in invasion biology......Page 789 Evolution of native species in response to introduced species......Page 793 Control of invasive species......Page 796 Introgression and hybridization......Page 805 Summary......Page 809 Software......Page 810 Problems......Page 811 Chapter 19 Genetic management of captive populations......Page 812 Why captive breed?......Page 814 Stages in captive breeding and reintroduction......Page 819 Founding captive populations......Page 821 Growth of captive populations......Page 826 Genetic management during the maintenance phase......Page 828 Captive management of groups......Page 840 Ex situ conservation of plants......Page 844 Reproductive technology and genome resource banks......Page 845 Managing inherited diseases in endangered species......Page 850 Further reading......Page 853 Software......Page 854 Problems......Page 855 Chapter 20 Genetic management for reintroduction......Page 857 Reintroductions......Page 859 Genetic changes in captivity that affect reintroduction success......Page 863 Genetic adaptation to captivity......Page 866 Genetic management of reintroductions......Page 873 How successful are reintroductions?......Page 880 Supportive breeding......Page 882 Case studies in captive breeding and reintroduction......Page 883 Summary......Page 891 Software......Page 892 Problems......Page 893 Chapter 21 Use of molecular genetics in forensics and to understand species biology......Page 894 Forensics: detecting illegal hunting and collecting......Page 895 Understanding a species’ biology is critical to its conservation......Page 898 Population size and demographic history......Page 904 Gene flow and population structure......Page 911 Reintroduction and translocation......Page 919 Breeding systems, parentage, founder relationships and sexing......Page 920 Disease......Page 931 Diet......Page 932 Dating using molecular clocks......Page 933 Summary......Page 935 Software......Page 936 Problems......Page 937 Chapter 22 The broader context: population viability analysis (PVA)......Page 939 What causes endangerment and extinction?......Page 941 Predicting extinction probabilities: population viability analysis (PVA)......Page 946 Genetics and PVA......Page 955 Insights into the causes of extinction from PVA......Page 958 Recovering threatened populations......Page 965 Using PVA to evaluate management options: case studies......Page 966 How useful are the predictions of PVA?......Page 973 Lessons learned......Page 977 Minimum viable population sizes (MVP)......Page 979 Summary......Page 982 Software......Page 983 Problems......Page 984 Practical exercises: population viability analyses......Page 985 Take home messages from this book......Page 986 Revision problems......Page 989 Glossary......Page 992 References......Page 1020 Index......Page 1123