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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
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