Introduction to Conservation Genetics

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