Intro
Preface
Contents
Part I Population Genetic Theory
1 Coalescent Models
1.1 Aims and Clarifications
1.2 Introduction: Gene Genealogies Within a Population or Species
1.2.1 Organismal Pedigrees and Gene Genealogies
1.3 The Standard Neutral Model: The Kingman Coalescent
1.3.1 The Sampling Structure of Coalescent Gene Genealogies
1.3.2 Including Mutations in the Coalescent
1.4 Fundamental Predictions for Single Loci in Well-Mixed Populations
1.4.1 The Size and Shape of a Gene Genealogy
1.4.2 Levels and Patterns of Genetic Variation

1.4.3 Tests of the Standard Neutral Coalescent Based on Site Frequencies
1.5 Extensions of the Standard Model
1.5.1 Fluctuations in Population Size over Time
1.5.2 Population Subdivision and Migration
1.6 Conclusion: Current Challenges of Big Data
References
2 Linkage Disequilibrium
2.1 Introduction
2.2 Tests of whether D == 0
2.3 More than Two Alleles per Locus
2.4 More than Two Loci: Haplotype Blocks and the HapMap Project
2.5 Dynamics of D
2.6 Genetic Drift and LD
2.7 Genealogical Interpretation of LD
2.8 Natural Selection and LD

2.9 Genetic Hitchhiking
2.10 Population Subdivision
2.11 Conclusion
References
3 Analysis of Population Structure
3.1 What Is Population Structure?
3.2 Individual-Based and Unsupervised Methods for Inferring Population Structure
3.2.1 Tree Construction Methods at the Individual Level
3.2.2 Principal Component Analysis and Related Approaches
3.2.3 Ancestry Component Estimation with Few Model Assumptions
3.3 Population-Based and Supervised Methods
3.3.1 Genetic Differentiation at the Population Level
3.3.1.1 FST
3.3.1.2 Other Measures of Genetic Distance

3.3.2 Formal Tests for Admixture Under a Population Tree-Model
3.3.3 More Advanced Modeling
3.3.3.1 Population Graph Fitting
3.3.3.2 Isolation-Migration Models
3.3.3.3 Approximate Bayesian Computation
3.4 Summary and Guidelines
References
4 Types of Natural Selection and Tests of Selection
4.1 Types of Selection and Their Effect on Linked Neutral Sites
4.1.1 Types of Selection
4.1.2 The Effect of Selection on Linked Neutral Sites
4.2 Tests of Selection
4.2.1 Tests of Selection Based on the Site Frequency Spectrum
4.2.1.1 Tajima's D
4.2.1.2 Fay and Wu's H

4.2.1.3 Likelihood Ratio Tests
4.2.2 Tests of Selection Based on Haplotypes
4.2.2.1 Extended Haplotype Homozygosity (EHH)
4.2.2.2 Integrated Haplotype Score (iHS)
4.2.2.3 Cross-Population EHH (XP-EHH)
4.2.3 Tests Based on both Diversity and Divergence:The McDonald-Kreitman Test
4.3 How to Choose a Specific Test of Selection?
References
Part II Association Studies and Medical Genetics
5 Methods for Association Studies
5.1 Introduction
5.2 Types of Association Studies
5.2.1 Candidate Gene Studies
5.2.2 Genome-Wide Association Studies
5.2.2.1 Background