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Molecular Ecology, 3rd Edition

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Molecular Ecology, 3rd Edition

Joanna R. Freeland

ISBN: 978-1-119-42615-8 November 2019 464 Pages

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Description

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.

Glossary

Chapter 1. Molecular genetics in ecology 1

What is Molecular Ecology? 1

DNA, RNA, and protein 2

Allozymes 4

DNA: An unlimited source of data 5

Mutation and Recombination 6

Epigenetic marks 9

Genomes 10

Mitochondrial DNA (mtDNA) 11

Chloroplast DNA (cpDNA) 11

Haploid chromosomes 12

Polymerase Chain Reaction 13

Quantitative PCR 14

Sources of DNA 15

Getting data from PCR 18

Fragment sizes 18

DNA Sequencing 19

High Throughput Sequencing 20

Overview 22

Chapter summary 23

Chapter 2. Molecular markers in ecology 1

Understanding molecular markers 1

Neutral versus adaptive markers 1

Genomes 3

Animal mitochondrial DNA (mtDNA) 3

Plant mitochondrial DNA (mtDNA) 6

Chloroplast DNA (cpDNA) 7

Haploid chromosomes 9

Uniparental markers: some final considerations 10

Molecular markers 12

Early developments in molecular markers 12

Allozymes 13

PCR-RFLPs 13

Random Amplified Polymorphic DNA (RAPDs) 15

Inter Simple Sequence Repeats (ISSRs) 15

Amplified Length Fragment Polymorphisms (AFLPs) 16

Modified AFLPs: Methylation-sensitive Amplified Polymorphisms (MSAPs) 17

Microsatellites 18

DNA sequencing 23

Sequencing a single region of DNA 24

Single Nucleotide Polymorphisms (SNPs) 26

High-throughput sequencing (HTS) 29

RAD sequencing 29

Genotyping-by-Sequencing 30

Targeted sequence capture 31

Whole genome sequencing 32

Overview 33

Chapter summary 34

Chapter 3. Species 1

Species concepts 1

DNA Barcoding 3

Barcoding applications 5

Barcoding limitations 7

Metabarcoding 12

Metagenomics 13

Barcoding and metabarcoding environmental DNA (eDNA) 14

Overview 20

Chapter summary 20

Chapter 4 What is phylogeography? 1

The evolution of phylogeographic data sets 2

Molecular clocks 4

Bifurcating trees 7

The coalescent 11

Networks 12

Model-based phylogeographic inference 14

Long-term climatic fluctuations 16

Glacial-interglacial cycles 16

Marine refugia 18

Far-reaching effects of glaciation 19

Dispersal and vicariance 19

Lineage sorting 23

Hybridization 24

Applied phylogeography: Biological invasions 29

Overview 32

Chapter summary 32

Chapter 5: Genetic analysis of single populations 1

Why study single populations? 1

What is a population? 1

Quantifying genetic diversity 3

Hardy-Weinberg equilibrium 4

Estimates of genetic diversity 12

Haploid diversity 17

Choice of marker and genome 18

What influences genetic diversity? 20

Genetic drift 20

What is effective population size? 21

Census population size (Nc) 22

Effective number of breeders (Nb) 23

Estimating Ne from demographic data 24

Estimating Ne from genetic data 25

Estimating Ne: a cautionary note 30

Ne, genetic drift, and genetic diversity 33

Population bottlenecks and founder effects 35

Population size and decline 37

Natural selection 37

Reproduction 40

Inbreeding 42

Ecology and life history 46

Overview 48

Chapter summary 48

Chapter 6. Dispersal, gene flow, and landscape genetics 1

Why study multiple populations? 1

What is gene flow? 1

Why do we want to quantify gene flow? 3

Quantifying gene flow among discrete populations 4

F-statistics 5

Assignment tests 9

Relatedness and Parentage analysis 11

Non-a priori identification of populations 12

Landscape genetics and genomics 15

Data analysis in landscape genetics 16

Isolation by distance 18

Isolation by resistance 20

Genotype-environment associations 20

Contemporary versus historical influences on gene flow 24

Population differentiation: Gene flow, genetic drift and natural selection 26

Gene flow and genetic drift 26

Local adaptation and gene flow 26

Drift versus selection 29

QST and FST 29

Overview 32

Chapter summary 32

Chapter 7. Behavioural Ecology

How do genetic data help us understand behavior? 1

Mating systems 2

Monogamy 3

Polygamy 3

Parentage analysis 5

Extra-pair fertilizations 9

EPFs and male fitness 10

EPFs from the female perspective: adaptive explanations 11

EPFs from the female perspective: non-adaptive explanations 13

Social breeding 19

Cooperative breeding – indirect benefits 19

Cooperative breeding – direct benefits 23

Eusociality 24

Sex-biased dispersal 26

Sex-biased dispersal: population-level analyses 28

Male versus female genetic differentiation 28

Markers with different modes of inheritance 29

Relatedness 32

Sex-biased dispersal: individual-level analyses 33

Assignment indices 33

Spatial autocorrelation 34

Parentage analysis 35

Concordant results 36

Foraging ecology 37

Overview 40

Chapter summary 40

Chapter 8. Conservation Genetics 1

Taxonomy 3

Subspecies 4

Taxa below subspecies 7

Conservation units and adaptation 9

Genetic diversity 11

Genetic diversity and evolutionary potential 13

Transcriptomics and epigenetics 15

Genetic diversity and inbreeding 19

Inbreeding depression 22

Purging and balancing selection 25

Measuring and inferring inbreeding depression 27

Genetic differentiation and genetic rescue 31

Outbreeding depression 33

Reintroductions 34

Hybridization 36

Community genetics 39

Overview 42

Chapter summary 42

Index