Molecular population genetics

Cover......Page 1
MOLECULAR POPULATION GENETICS......Page 2
DEDICATION......Page 6
CONTENTS......Page 8
PREFACE......Page 16
CHAPTER 1: MODELS OF EVOLUTION......Page 20
 BASIC SEQUENCE TERMINOLOGY......Page 21
  Models of populations......Page 22
  The effective size of a population......Page 25
  Models of mutation......Page 26
  Models of recombination......Page 30
  Models of natural selection......Page 31
  Models of migration......Page 33
  Models of mating......Page 36
  The neutral theory of molecular evolution......Page 37
  Misunderstanding and misuse of the neutral theory......Page 40
  Alternative models of molecular evolution......Page 42
 POPULATION SAMPLING......Page 44
 DNA SEQUENCING......Page 45
  Sanger sequencing......Page 46
  Haplotypes......Page 49
  Next-generation sequencing......Page 50
  The effect of short sequence reads......Page 52
  The effect of high error rates......Page 54
  Diverse experimental designs for next-generation genome sequencing......Page 55
 GENOTYPING......Page 59
CHAPTER 3: DESCRIBING VARIATION......Page 62
  Common estimators of θ for SNPs under the infinite sites model......Page 63
  The frequency spectrum of alleles......Page 66
  Estimators of θ for SNPs under finite sites models and incorporating sequencing error......Page 69
  Interpreting measures of nucleotide variation......Page 72
  Microsatellite variation......Page 74
  Haplotype variation......Page 76
  Linkage and linkage disequilibrium......Page 78
  Measures of pairwise linkage disequilibrium......Page 80
  Summarizing pairwise linkage disequilibrium......Page 82
  Extensions to multiple alleles, multiple loci, and genotypes......Page 85
  Finding the minimum number of recombination events in a sample......Page 87
  The population recombination parameter......Page 89
  Estimating the population recombination parameter......Page 90
 GENE CONVERSION......Page 96
  Populations, subpopulations, and demes......Page 98
  The Wahlund effect......Page 99
  Measuring population differentiation using FST......Page 100
  Alternative measures of population differentiation......Page 105
  Is there evidence for population differentiation at a locus?......Page 108
  The effects of natural selection on population differentiation......Page 110
  The effects of migration and drift on population differentiation......Page 112
  Distinguishing between migration and drift: The isolation-with-migration model......Page 116
  Additional methods for detecting migration between pairs of populations......Page 119
  Identifying populations and the individuals within them......Page 123
  Using the Wahlund effect to identify population structure......Page 124
  Evolutionary inference from the determination of population structure......Page 126
 SIMULATING SAMPLES OF DNA SEQUENCES......Page 130
  Coalescent genealogies......Page 133
  Important genealogical quantities......Page 137
  The coalescent and measures of polymorphism......Page 139
  The effects of ascertainment bias on the allele frequency spectrum......Page 141
  The coalescent with recombination......Page 143
  The coalescent and reference genomes......Page 147
  The rate of nucleotide substitution......Page 150
  Estimating sequence divergence......Page 153
  dN, dS, and dN/dS......Page 156
  Interpreting dN/dS......Page 160
  The effect of selection on the frequency of polymorphism......Page 164
  pN/pS......Page 167
  Experimental design for the McDonald-Kreitman test......Page 168
  Expectations for levels of polymorphism and divergence......Page 170
  Interpreting the McDonald-Kreitman test......Page 171
  Methodological extensions of the MK test......Page 173
  Assumptions of the MK test......Page 175
  Biological extensions of the MK test......Page 178
  Summarizing selection across the genome......Page 179
  The effects of positive selection on levels of linked neutral variation......Page 184
  The effects of balancing selection and strongly deleterious alleles on levels of linked neutral variation......Page 187
  The most underappreciated result in molecular population genetics......Page 189
  Detecting selection via levels of polymorphism: The HKA test......Page 190
  Experimental design for the HKA test......Page 191
  Interpreting the HKA test......Page 192
 DETECTING SELECTION USING THE ALLELE FREQUENCY SPECTRUM......Page 194
  The effects of positive selection on the allele frequency spectrum......Page 195
  The effects of balancing selection on the allele frequency spectrum......Page 196
  Detecting selection using the allele frequency spectrum: Tajima’s D and related tests......Page 198
  Interpreting Tajima’s D and related tests of the frequency spectrum......Page 200
  Detecting selection using the allele frequency spectrum: Fay and Wu’s H......Page 204
  The power to detect natural selection using tests of the frequency spectrum......Page 205
  The effects of balancing selection on linkage disequilibrium......Page 208
  The effects of completed sweeps on linkage disequilibrium......Page 209
  The effects of partial sweeps on linkage disequilibrium......Page 210
  Detecting selection using linkage disequilibrium: Haplotype summary statistics......Page 213
  Detecting selection using linkage disequilibrium: Measures of pairwise LD......Page 214
  Detecting selection using linkage disequilibrium: Haplotype homozygosity......Page 215
  Interpreting tests based on haplotype structure and linkage disequilibrium......Page 219
 CAVEATS TO TESTS OF LINKED SELECTION......Page 220
CHAPTER 9: DEMOGRAPHIC HISTORY......Page 222
  Nonequilibrium demographic histories......Page 223
  The effect of changing population size on gene genealogies......Page 225
  The effect of changing population size on the allele frequency spectrum......Page 227
  The effect of changing population size on other measures of variation......Page 229
  Types of data and computational methods used in demographic inference......Page 233
  Inferring nonequilibrium population histories......Page 236
 THE DEMOGRAPHIC HISTORY OF MULTIPLE POPULATIONS......Page 241
  The effect of population structure on gene genealogies......Page 242
  The effect of population structure on the allele frequency spectrum......Page 244
  Inferring demographic histories for multiple populations......Page 247
  Multi-population histories as networks......Page 249
  The analysis of multiple populations in space......Page 253
  Ancestral parameters inferred from two species......Page 258
  Ancestral parameters inferred from gene tree discordance......Page 259
  Introgression inferred from gene tree discordance......Page 263
 CAVEATS TO INFERENCES OF DEMOGRAPHIC HISTORY......Page 266
CHAPTER 10: POPULATION GENOMICS......Page 268
  Motivating questions......Page 269
  Selection versus demography......Page 270
  General approaches for identifying targets of selection......Page 273
  Detecting selection using a sample from a single population......Page 277
  Detecting selection using samples from multiple populations......Page 281
 CAVEATS ABOUT NON-INDEPENDENCE IN POPULATION GENOMICS......Page 285
  The application of machine learning to population genetics......Page 287
  Ancient DNA and genetic variation through time......Page 289
  Populations of whole assembled genomes......Page 290
  Deep population sequencing......Page 292
REFERENCES......Page 294
INDEX......Page 334