BookKirk E. Lohmueller, Rasmus Nielsen, editors.
Springer Nature eBook.
Summary: This textbook provides a concise introduction and useful overview of the field of human population genomics, making the highly technical and contemporary aspects more accessible to students and researchers from various fields. Over the past decade, there has been a deluge of genetic variation data from the entire genome of individuals from many populations. These data have allowed an unprecedented look at human history and how natural selection has impacted humans during this journey. Simultaneously, there have been increased efforts to determine how genetic variation affects complex traits in humans. Due to technological and methodological advances, progress has been made at determining the architecture of complex traits. Split in three parts, the book starts with the basics, followed by more advanced and current research. The first part provides an introduction to essential concepts in population genetics, which are relevant for any organism. The second part covers the genetics of complex traits in humans. The third part focuses on applying these techniques and concepts to genetic variation data to learn about demographic history and natural selection in humans. This new textbook aims to serve as a gateway to modern human population genetics research for those new to the field. It provides an indispensable resource for students, researchers and practitioners from disparate areas of expertise.
Contents:
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