A fully updated guide to the increasingly prevalent use of molecular data in ecological studies
Molecular ecology is concerned with how molecular biology and population genetics may help us to better understand aspects of ecology and evolution including local adaptation, dispersal across landscapes, phylogeography, behavioral ecology, and conservation biology. As the technology driving genetic science has advanced, so too has this fast-moving and innovative discipline, providing important insights into virtually all taxonomic groups. This third edition of Molecular Ecology takes account of the breakthroughs achieved in recent years to give readers a thorough and up-to-date account of the field as it is today.
New topics covered in this book include next-generation sequencing, metabarcoding, environmental DNA (eDNA) assays, and epigenetics. As one of molecular ecology's leading figures, author Joanna Freeland also provides those new to the area with a full grounding in its fundamental concepts and principles. This important text:
Is presented in an accessible, user-friendly manner
Offers a comprehensive introduction to molecular ecology
Has been revised to reflect the field's most recent studies and research developments
Includes new chapters covering topics such as landscape genetics, metabarcoding, and community genetics
Rich in insights that will benefit anyone interested in the ecology and evolution of natural populations, Molecular Ecology is an ideal guide for all students and professionals who wish to learn more about this exciting field.
About the Companion Website Page xiii
1 Molecular Genetics in Ecology 1
What is Molecular Ecology? 1
DNA, RNA, and Protein 2
Allozymes 5
DNA: An Unlimited Source of Data 7
Mutation and Recombination 8
Epigenetic Marks 10
Genomes 12
Mitochondrial DNA (mtDNA) 13
Chloroplast DNA (cpDNA) 13
Haploid Chromosomes 16
Polymerase Chain Reaction 16
Quantitative PCR 19
Sources of DNA 21
Getting Data from PCR 22
Fragment Sizes 22
DNA Sequencing 25
High Throughput Sequencing 26
Overview 28
Chapter Summary 29
References 29
2 Molecular Markers in Ecology 35
Understanding Molecular Markers 35
Neutral Versus Adaptive Markers 35
Genomes 36
Animal Mitochondrial DNA (mtDNA) 36
Plant Mitochondrial DNA (mtDNA) 39
Chloroplast DNA (cpDNA) 39
Haploid Chromosomes 42
Uniparental Markers: Some Final Considerations 43
Molecular Markers 44
Early Developments in Molecular Markers 45
Allozymes 46
PCR-RFLPs 46
Random Amplified Polymorphic DNA (RAPDs) 47
Inter Simple Sequence Repeats (ISSRs) 48
Amplified Length Fragment Polymorphisms (AFLPs) 49
Modified AFLPs: Methylation-Sensitive Amplified Polymorphisms (MSAPs) 50
Microsatellites 51
DNA Sequencing 56
Sequencing a Single Region of DNA 56
Single Nucleotide Polymorphisms (SNPs) 59
High Throughput Sequencing (HTS) 61
RAD Sequencing 62
Genotyping-by-Sequencing (GBS) 63
Targeted Sequence Capture 63
Whole-Genome Sequencing 64
Overview 65
Chapter Summary 65
References 66
3 Species 71
Species Concepts 71
DNA Barcoding 73
Barcoding Applications 76
Barcoding Limitations 79
Metabarcoding 81
Metagenomics 84
Barcoding and Metabarcoding Environmental DNA (eDNA) 87
Overview 91
Chapter Summary 91
References 92
4 Phylogeography 101
What is Phylogeography? 101
The Evolution of Phylogeographic Data Sets 102
Molecular Clocks 104
Bifurcating Trees 109
The Coalescent 115
Networks 117
Model-Based Phylogeographic Inference 120
Long-Term Climatic Fluctuations 121
Glacial-Interglacial Cycles 121
Marine Refugia 123
Far-Reaching Effects of Glaciation 125
Dispersal and Vicariance 125
Lineage Sorting 127
Hybridization 130
Applied Phylogeography: Biological Invasions 133
Overview 136
Chapter Summary 136
References 137
5 Genetic Analysis of Single Populations 149
Why Study Single Populations? 149
What is a Population? 149
Quantifying Genetic Diversity 151
Hardy-Weinberg Equilibrium 152
Estimates of Genetic Diversity 157
Haploid Diversity 160
Choice of Marker and Genome 162
What Influences Genetic Diversity? 163
Genetic Drift 163
What is Effective Population Size? 164
Census Population Size (Nc) 165
Effective Number of Breeders (Nb) 165
Estimating Ne from Demographic Data 165
Estimating Ne from Genetic Data 166
Estimating Ne: A Cautionary Note 170
Ne, Genetic Drift, and Genetic Diversity 173
Population Bottlenecks and Founder Effects 174
Population Size and Decline 176
Natural Selection 178
Reproduction 180
Inbreeding 182
Ecology and Life History 186
Overview 188
Chapter Summary 188
References 189
6 Dispersal, Gene Flow, and Landscape Genetics 197
Why Study Multiple Populations? 197
What is Gene Flow? 197
Why Do We Want to Quantify Gene Flow? 199
Quantifying Gene Flow Among Discrete Populations 200
F-Statistics 201
Assignment Tests 204
Relatedness and Parentage Analysis 206
Non-a Priori Identification of Populations 207
Landscape Genetics and Genomics 209
Data Analysis in Landscape Genetics 214
Isolation by Distance 216
Isolation by Resistance 217
Genotype-Environment Associations 218
Contemporary Versus Historical Influences on Gene Flow 221
Population Differentiation: Gene Flow, Genetic Drift, and Natural Selection 223
Gene Flow and Genetic Drift 223
Local Adaptation and Gene Flow 223
Drift Versus Selection 225
QST and FST 226
Overview 228
Chapter Summary 228
References 229
7 Behavioral Ecology 237
How Do Genetic Data Help Us Understand Behavior? 237
Mating Systems 238
Monogamy 239
Polygamy 239
Parentage Analysis 241
Extra-Pair Fertilizations 244
EPFs and Male Fitness 244
EPFs from the Female Perspective: Adaptive Explanations 245
EPFs from the Female Perspective: Non-adaptive Explanations 247
Social Breeding 252
Cooperative Breeding - Indirect Benefits 253
Cooperative Breeding - Direct Benefits 257
Eusociality 257
Sex-Biased Dispersal 260
Sex-Biased Dispersal: Population-Level Analyses 262
Male Versus Female Genetic Differentiation 262
Markers with Different Modes of Inheritance 263
Relatedness 264
Sex-Biased Dispersal: Individual-Level Analyses 266
Assignment Indices 266
Spatial Autocorrelation 268
Parentage Analysis 268
Concordant Results 270
Foraging Ecology 271
Overview 276
Chapter Summary 276
References 277
8 Conservation Genetics 289
Taxonomy 292
Subspecies 294
Taxa Below Subspecies 297
Conservation Units and Adaptation 299
Genetic Diversity 300
Genetic Diversity and Evolutionary Potential 301
Transcriptomics and Epigenetics 303
Genetic Diversity and Inbreeding 307
Inbreeding Depression 310
Purging and Balancing Selection 312
Measuring and Inferring Inbreeding Depression 315
Genetic Differentiation and Genetic Rescue 317
Outbreeding Depression 320
Reintroductions 321
Hybridization 324
Community Genetics 326
Overview 330
Chapter Summary 330
References 331
Glossary 343
Index 359
