Molecular Ecology

by Freeland, Joanna R.; Kirk, Heather; Petersen, Stephen D.

• ISBN13: 9780470748343
• ISBN10: 0470748346
• Edition: 2nd
• Format: Hardcover
• Copyright: 2011-04-25
• Publisher: Wiley-Blackwell

Summary

This second edition provides an accessible introduction to the many diverse aspects of this subject. The book unites theory with examples from a wide range of taxa in a logical and progressive manner, and its straightforward writing style makes subjects such as population genetics and phylogenetics highly comprehensible to its readers. The first part of the book introduces the essential underpinnings of molecular ecology and opens with a review of genetics and a discussion of the molecular markers that are most frequently used in ecological research. The second half of the book then moves on to specific applications of molecular ecology, covering phylogeography, behavioural ecology and conservation genetics. The final chapter looks at molecular ecology in a wider context by using a number of case studies that are relevant to various economic and social concerns, including wildlife forensics, agriculture and overfishing.

Author Biography

Joanna R. Freeland, Associate Professor, Trent University, Canada.

Dr. Stephen D. Petersen, Visiting Fellow, Fisheries & Oceans, Canada.

Table of Contents

Preface	p. xi
Acknowledgements	p. xiii
Molecular Genetics in Ecology	p. 01
What is molecular ecology?	p. 01
The emergence of molecular ecology	p. 02
Protein allozymes	p. 04
Allozymes as generic markers	p. 06
An unlimited source of data	p. 09
Mutation and recombination	p. 10
Is genetic variation adaptive?	p. 14
Polymerase chain reaction	p. 15
Primers	p. 18
Sources of DNA	p. 20
Getting data from PCR	p. 23
DNA sequencing	p. 24
Second-generation sequencing	p. 27
Third-generation sequencing	p. 28
Quantitative PCR	p. 29
Overview	p. 31
Chapter summary	p. 31
Useful websites and software	p. 32
Further reading	p. 33
Review questions	p. 33
Molecular Markers in Ecology	p. 35
Understanding molecular markers	p. 35
Modes of inheritance	p. 35
Nuclear versus organelle	p. 36
Animal mitochondrial DNA	p. 36
Plant mitochondrial DNA	p. 39
Plastids, including chloroplast DNA	p. 41
Haploid chromosomes	p. 44
Identifying hybrids	p. 46
Uniparental markers: A cautionary note	p. 48
Molecular markers	p. 50
Co-dominant markers	p. 51
Allozymes	p. 52
RFLPs	p. 54
DNA sequences	p. 56
SNPs	p. 60
Microsatellites	p. 62
Dominant markers	p. 67
RAPDs	p. 68
AFLPs	p. 69
Overview	p. 72
Chapter summary	p. 72
Useful websites and software	p. 73
Further reading	p. 74
Online activities	p. 74
Review questions	p. 75
Genetic Analysis of Single Populations	p. 77
Why study single populations?	p. 77
What is a population?	p. 77
Quantifying genetic diversity	p. 82
Hardy-Weinberg equilibrium	p. 83
Estimates of genetic diversity	p. 87
Haploid diversity	p. 91
Choice of marker	p. 92
What influences genetic diversity?	p. 93
Genetic drift	p. 93
What is effective population size?	p. 94
Quantifying census population size	p. 95
Quantifying effective population size	p. 96
Single-Sample Estimators	p. 96
Temporal method	p. 98
Demographic influences on Ne	p. 102
Sex ratios	p. 103
Variation in reproductive success	p. 104
Fluctuating population size	p. 105
Ne, genetic drift and genetic diversity	p. 107
Population bottlenecks	p. 109
Founder effects and invasive species	p. 110
Natural selection	p. 111
The major histocompatibility complex	p. 114
Reproduction	p. 116
Inbreeding	p. 117
Polyploidy	p. 119
Overview	p. 123
Chapter summary	p. 124
Useful websites and software	p. 125
Further reading	p. 126
Online activities	p. 127
Review questions	p. 127
Genetic Analysis of Multiple Populations	p. 129
Why study multiple populations?	p. 129
Quantifying population subdivision	p. 129
Genetic distance	p. 130
F-statistics	p. 131
Interpreting FST	p. 134
Non-a priori identification of populations	p. 139
Quantifying gene flow	p. 143
Direct methods	p. 143
Indirect methods	p. 146
Assignment tests	p. 147
What influences gene flow?	p. 148
Barriers to dispersal	p. 149
Landscape genetics	p. 150
Metapopulations	p. 154
Interspecific interactions	p. 155
Hybridization	p. 156
Population differentiation: genetic drift and natural selection	p. 159
Gene flow and genetic drift	p. 160
Gene flow and local adaptation	p. 162
Drift versus selection	p. 163
Patterns of molecular evolution	p. 165
Discordant genetic differentiation	p. 166
Clinal variations in allele frequencies: FST versus QST	p. 169
Overview	p. 173
Chapter summary	p. 173
Useful websites and software	p. 175
Further reading	p. 175
Online activities	p. 176
Review questions	p. 177
Studying Ecologically Important Traits: Ecogenomics, QTL Analysis, and Reverse Genetics	p. 179
Studying ecologically important traits	p. 179
cDNA libraries and ESTs	p. 180
Microarrays	p. 181
How do microarrays work?	p. 182
Probes	p. 188
Verifying differences in gene expression	p. 189
Microarray applications	p. 189
Variation within individuals	p. 189
Variation between species	p. 191
Sequence differences	p. 193
Differences in gene expression	p. 194
Microarrays and community ecology of microorganisms	p. 197
Microorganism functions	p. 199
Microarrays and genotyping	p. 201
Connecting genotype to phenotype	p. 203
Reverse genetics	p. 204
QTL analysis	p. 205
Linkage mapping	p. 206
QTL mapping	p. 212
QTL mapping of ecologically important traits	p. 216
Overview	p. 220
Chapter summary	p. 221
Useful websites and software	p. 222
Further reading	p. 222
Review questions	p. 223
Phylogeography	p. 225
What is phylogeography?	p. 225
Molecular markers in phylogeography	p. 225
Organelle versus nuclear markers	p. 225
Repetitive versus non-repetitive markers	p. 229
Neutral versus adaptive markers	p. 230
Molecular clocks	p. 231
Bifurcating trees	p. 235
The coalescent	p. 239
Applying the coalescent	p. 240
Networks	p. 242
Nested Clade Phylogeographic analysis and statistical phylogeography	p. 244
The distributions of genetic lineages	p. 247
Subdivided populations	p. 248
Dispersal and vicariance	p. 248
Comparative phylogeography	p. 250
Regional concordance	p. 251
Continental concordance	p. 252
European post-glacial recolonization routes	p. 253
Dispersal and invasive species	p. 255
Allele sharing between species	p. 259
Lineage sorting	p. 259
Hybrid zones	p. 261
Overview	p. 265
Chapter summary	p. 266
Useful websites and software	p. 267
Further reading	p. 268
Online activities	p. 268
Review questions	p. 269
Behavioural Ecology	p. 271
Why use molecules to study behaviour?	p. 271
Mating systems	p. 272
Parentage analysis	p. 275
Extra-pair fertilizations	p. 280
Who achieves EPFs?	p. 284
Does environment influence EPFs?	p. 285
Mate choice	p. 286
Post-copulatory mate choice	p. 288
Social breeding	p. 289
Social insects	p. 293
Manipulating sex ratios	p. 295
Sex ratio conflicts	p. 298
Sex-biased dispersal	p. 299
Nuclear and mitochondrial markers	p. 300
Relatedness	p. 302
FST values	p. 302
Assignment tests	p. 304
Spatial autocorrelation	p. 305
Concordant results	p. 307
Predators and prey	p. 309
Identifying prey	p. 309
Predation and conservation	p. 312
Overview	p. 313
Chapter summary	p. 314
Useful websites and software	p. 315
Further reading	p. 316
Online activities	p. 316
Review questions	p. 317
Conservation Genetics	p. 319
The need for conservation	p. 319
Taxonomy	p. 322
Species concepts	p. 322
DNA barcoding	p. 324
Subspecies	p. 331
Conservation units	p. 332
Hybrids	p. 333
Population size, genetic diversity and inbreeding	p. 335
Inbreeding depression	p. 337
Heterozygosity fitness correlations	p. 342
Self-fertilization	p. 344
Inbreeding avoidance	p. 345
Outbreeding depression	p. 346
Translocations	p. 348
Genetic rescue	p. 349
Source populations	p. 351
Restoration genetics	p. 354
Captive breeding	p. 356
Maximizing genetic diversity	p. 356
Captive inbreeding and outbreeding	p. 358
Genetic diversity banks	p. 359
Overview	p. 362
Chapter summary	p. 362
Useful websites and software	p. 363
Further reading	p. 364
Online activities	p. 365
Review questions	p. 365
Glossary	p. 367
Answers to Review Questions	p. 385
References	p. 395
Index	p. 433
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