Molecular Population Genetics

PREFACE
CHAPTER 1: MODELS OF EVOLUTION
BASIC SEQUENCE TERMINOLOGY
MODELS OF EVOLUTIONARY PROCESSES
Models of populations
The effective size of a population
Models of mutation
Models of recombination
Models of natural selection
Models of migration
Models of mating
MODELS OF MOLECULAR EVOLUTION
The neutral theory of molecular evolution
Misunderstanding and misuse of the neutral theory
Alternative models of molecular evolution
CHAPTER 2: EXPERIMENTAL DESIGN
POPULATION SAMPLING
DNA SEQUENCING
Sanger sequencing
Haplotypes
Next-generation sequencing
The effect of short sequence reads
The effect of high error rates
Diverse experimental designs for next-generation genome sequencing
GENOTYPING
CHAPTER 3: DESCRIBING VARIATION
MEASURES OF SEQUENCE DIVERSITY
Common estimators of ? for SNPs under the infinite sites model
The frequency spectrum of alleles
Estimators of ? for SNPs under finite sites models and incorporating sequencing error
Interpreting measures of nucleotide variation
ADDITIONAL MEASURES OF DIVERSITY
Microsatellite variation
Haplotype variation
CHAPTER 4: RECOMBINATION
MEASURING LINKAGE DISEQUILIBRIUM
Linkage and linkage disequilibrium
Measures of pairwise linkage disequilibrium
Summarizing pairwise linkage disequilibrium
Extensions to multiple alleles, multiple loci, and genotypes
ESTIMATING RECOMBINATION
Finding the minimum number of recombination events in a sample
The population recombination parameter
Estimating the population recombination parameter
GENE CONVERSION
CHAPTER 5: POPULATION STRUCTURE
POPULATION DIFFERENTIATION
Populations, subpopulations, and demes
The Wahlund effect
MEASURING POPULATION DIFFERENTIATION
Measuring population differentiation using FST
Alternative measures of population differentiation
Is there evidence for population differentiation at a locus?
THE EFFECT OF EVOLUTIONARY PROCESSES ON DIFFERENTIATION
The effects of natural selection on population differentiation
The effects of migration and drift on population differentiation
Distinguishing between migration and drift: The isolation-with-migration model
Additional methods for detecting migration between pairs of populations
DEFINING POPULATIONS
Identifying populations and the individuals within them
Using the Wahlund effect to identify population structure
Evolutionary inference from the determination of population structure
CHAPTER 6: THE COALESCENT
SIMULATING SAMPLES OF DNA SEQUENCES
SIMULATING THE COALESCENT
Coalescent genealogies
Genealogies and phylogenies
UNDERSTANDING THE COALESCENT
Important genealogical quantities
The coalescent and measures of polymorphism
The effects of ascertainment bias on the allele frequency spectrum
EXTENDING THE COALESCENT
The coalescent with recombination
The coalescent and reference genomes
CHAPTER 7: DIRECT SELECTION
THE ACCUMULATION OF SEQUENCE DIVERGENCE
The rate of nucleotide substitution
Estimating sequence divergence
DETECTING SELECTION USING DIVERGENCE
dN, dS, and dN/dS
Interpreting dN/dS
DETECTING SELECTION USING POLYMORPHISM
The effect of selection on the frequency of polymorphism
pN/pS
DETECTING SELECTION USING POLYMORPHISM AND DIVERGENCE
The McDonald-Kreitman test
Experimental design for the McDonald-Kreitman test
Expectations for levels of polymorphism and divergence
Interpreting the McDonald-Kreitman test
Methodological extensions of the MK test
Assumptions of the MK test
Biological extensions of the MK test
Summarizing selection across the genome
CHAPTER 8: LINKED SELECTION
DETECTING SELECTION USING THE AMOUNT OF POLYMORPHISM
The effects of positive selection on levels of linked neutral variation
The effects of balancing selection and strongly deleterious alleles on levels of linked neutral vari
The most underappreciated result in molecular population genetics
Detecting selection via levels of polymorphism: The HKA test
Experimental design for the HKA test
Interpreting the HKA test
DETECTING SELECTION USING THE ALLELE FREQUENCY SPECTRUM
The effects of positive selection on the allele frequency spectrum
The effects of balancing selection on the allele frequency spectrum
Detecting selection using the allele frequency spectrum: Tajima’s D and related tests
Interpreting Tajima’s D and related tests of the frequency spectrum
Detecting selection using the allele frequency spectrum: Fay and Wu’s H
The power to detect natural selection using tests of the frequency spectrum
DETECTING SELECTION USING PATTERNS OF LINKAGE DISEQUILIBRIUM
The effects of balancing selection on linkage disequilibrium
The effects of completed sweeps on linkage disequilibrium
The effects of partial sweeps on linkage disequilibrium
Detecting selection using linkage disequilibrium: Haplotype summary statistics
Detecting selection using linkage disequilibrium: Measures of pairwise LD
Detecting selection using linkage disequilibrium: Haplotype homozygosity
Interpreting tests based on haplotype structure and linkage disequilibrium
CAVEATS TO TESTS OF LINKED SELECTION
CHAPTER 9: DEMOGRAPHIC HISTORY
THE DEMOGRAPHIC HISTORY OF SINGLE POPULATIONS
Nonequilibrium demographic histories
The effect of changing population size on gene genealogies
The effect of changing population size on the allele frequency spectrum
The effect of changing population size on other measures of variation
Types of data and computational methods used in demographic inference
Inferring nonequilibrium population histories
THE DEMOGRAPHIC HISTORY OF MULTIPLE POPULATIONS
The effect of population structure on gene genealogies
The effect of population structure on the allele frequency spectrum
Inferring demographic histories for multiple populations
Multi-population histories as networks
The analysis of multiple populations in space
POPULATION GENETICS WITHOUT POLYMORPHISM
Ancestral parameters inferred from two species
Ancestral parameters inferred from gene tree discordance
Introgression inferred from gene tree discordance
CAVEATS TO INFERENCES OF DEMOGRAPHIC HISTORY
CHAPTER 10: POPULATION GENOMICS
GENOME-WIDE SCANS FOR SELECTION
Motivating questions
Selection versus demography
General approaches for identifying targets of selection
METHODS FOR CARRYING OUT GENOME-WIDE SCANS FOR SELECTION
Detecting selection using a sample from a single population
Detecting selection using samples from multiple populations
CAVEATS ABOUT NON-INDEPENDENCE IN POPULATION GENOMICS
FUTURE APPROACHES
The application of machine learning to population genetics
Ancient DNA and genetic variation through time
Populations of whole assembled genomes
Deep population sequencing
REFERENCES
INDEX

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