Molecular Ecology

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 (N_c) 165

Effective Number of Breeders (N_b) 165

Estimating N_e from Demographic Data 165

Estimating N_e from Genetic Data 166

Estimating N_e: A Cautionary Note 170

N_e, 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

Q_ST and F_ST 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