Molecular Ecology

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.

Auteur

JOANNA R. FREELAND is a Professor in the Department of Biology at Trent University, Peterborough, ON, Canada. She has been a researcher in the field of molecular ecology for more than 20 years, with particular interests in invasive species and conservation genetics.

Contenu
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

PCRRFLPs 46

Random Amplified Polymorphic DNA (RAPDs) 47

Inter Simple Sequence Repeats (ISSRs) 48

Amplified Length Fragment Polymorphisms (AFLPs) 49

Modified AFLPs: MethylationSensitive 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

GenotypingbySequencing (GBS) 63

Targeted Sequence Capture 63

WholeGenome 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

ModelBased Phylogeographic Inference 120

LongTerm Climatic Fluctuations 121

GlacialInterglacial Cycles 121

Marine Refugia 123

FarReaching 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

HardyWeinberg 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</p&g...