DAVID J. BALDING, PhD, is Professor of Statistical Genetics at the University of Melbourne and holds an honorary appointment at University College London. IDA MOLTKE, PhD, is an Assistant Professor at the Department of Biology, University of Copenhagen. JOHN MARIONI, PhD, is a Group Leader at the European Bioinformatics Institute and the Cancer Research UK Cambridge Institute.

• Volume 1List of Contributors xxiiiEditors’ Preface to the Fourth Edition xxviiGlossary xxixAbbreviations and Acronyms xxxix1 Statistical Modeling and Inference in Genetics 1Daniel Wegmann and Christoph Leuenberger2 Linkage Disequilibrium, Recombination and Haplotype Structure 51Gil McVean and Jerome Kelleher3 Haplotype Estimation and Genotype Imputation 87Jonathan Marchini4 Mathematical Models in Population Genetics 115Nick Barton and Alison Etheridge5 Coalescent Theory 145Magnus Nordborg6 Phylogeny Estimation Using Likelihood-Based Methods 177John P. Huelsenbeck7 The Multispecies Coalescent 219Laura Kubatko8 Population Structure, Demography and Recent Admixture 247G. Hellenthal9 Statistical Methods to Detect Archaic Admixture and Identify Introgressed Sequences 275Liming Li and Joshua M. Akey10 Population Genomic Analyses of DNA from Ancient Remains 295Torsten Gunther and Mattias Jakobsson11 Sequence Covariation Analysis in Biological Polymers 325William R. Taylor, Shaun Kandathil, and David T. Jones12 Probabilistic Models for the Study of Protein Evolution 347Umberto Perron, Iain H. Moal, Jeffrey L. Thorne, and Nick Goldman13 Adaptive Molecular Evolution 369Ziheng Yang14 Detecting Natural Selection 397Aaron J. Stern and Rasmus Nielsen15 Evolutionary Quantitative Genetics 421Bruce Walsh and Michael B. Morrissey16 Conservation Genetics 457Mark Beaumont and Jinliang Wang17 Statistical Methods for Plant Breeding 501Ian Mackay, Hans-Peter Piepho, and Antonio Augusto Franco Garcia18 Forensic Genetics 531B.S.WeirVolume 219 Ethical Issues in Statistical Genetics 551Susan E. Wallace and Richard Ashcroft20 Descent-Based Gene Mapping in Pedigrees and Populations 573E.A. Thompson21 Genome-Wide Association Studies 597Andrew P. Morris and Lon R. Cardon22 Replication and Meta-analysis of Genome-Wide Association Studies 631Frank Dudbridge and Paul Newcombe23 Inferring Causal Relationships between Risk Factors and Outcomes Using Genetic Variation 651Stephen Burgess, Christopher N. Foley, and Verena Zuber24 Improving Genetic Association Analysis through Integration of Functional Annotations of the Human Genome 679Qiongshi Lu and Hongyu Zhao25 Inferring Causal Associations between Genes and Disease via the Mapping of Expression Quantitative Trait Loci 697Solveig K. Sieberts and Eric E. Schadt26 Statistical Methods for Single-Cell RNA-Sequencing 735Tallulah S. Andrews, Vladimir Yu. Kiselev, and Martin Hemberg27 Variant Interpretation and Genomic Medicine 761K. Carss, D. Goldstein, V. Aggarwal, and S. Petrovski28 Prediction of Phenotype from DNA Variants 799M.E. Goddard, T.H.E. Meuwissen, and H.D. Daetwyler29 Disease Risk Models 815Allison Meisner and Nilanjan Chatterjee30 Bayesian Methods for Gene Expression Analysis 843Alex Lewin, Leonardo Bottolo, and Sylvia Richardson31 Modelling Gene Expression Dynamics with Gaussian Process Inference 879Magnus Rattray, Jing Yang, Sumon Ahmed, and Alexis Boukouvalas32 Modelling Non-homogeneous Dynamic Bayesian Networks with Piecewise Linear Regression Models 899Marco Grzegorczyk and Dirk Husmeier33 DNA Methylation 933Kasper D. Hansen, Kimberly D. Siegmund, and Shili Lin34 Statistical Methods in Metabolomics 949Timothy M.D. Ebbels, Maria De Iorio, and David A. Stephens35 Statistical and Computational Methods in Microbiome and Metagenomics 977Hongzhe Li36 Bacterial Population Genomics 997Jukka Corander, Nicholas J. Croucher, Simon R. Harris, John A. Lees, and Gerry Tonkin-HillReference Author Index 1021Subject Index 1109