Part I: Essential Concepts

1. A Population Genomics Lexicon

Gustavo Valadores Barroso, Ana Filipa Moutinho, and Julien Y Dutheil

Part II: Statistical Methods for Analyzing Genomes in Populations

2. Processing and Analyzing Multiple Genomes Alignments with MafFilter

Julien Y Dutheil

3. Data Management and Summary Statistics with PLINK

Christopher C Chang

4. Exploring Population Structure with Admixture Models and Principal Components Analysis

Chi-Chun Liu, Suyash Shringapure, Kenneth Lange, and John Novembre

5. Detecting Positive Selection in Populations using Genetic Data

Aggelos Koropoulis, Nikolaos Alachiotis, and Pavlos Pavlidis

6. polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data

Paula Tataru and Thomas Bataillon

7. MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

Stephan Schiffels and Ke Wang

8. Ancestral Population Genomics with Jocx, A Coalescent Hidden Markov Model

Jade Yu Cheng and Thomas Mailund

9. Coalescent Simulation with sprime

Jerome Kelleher and Konrad Lohse

10. Inference of Ancestral Recombination Graphs using ARGweaver

Melissa Hubisz and Adam Siepel

Part III: Advances in Population Genomics 11. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems

Tiina M. Mattila, Benjamin Laenen, and Tanja Slotte

12. Genomics of Long- and Short- Term Adaptation in Maize and Teosinte

Anne Lorant, Jeffrey Ross-Ibarra, and Maud Tenaillon

13. Neurospora from Natural Populations: Population Genomics Insights Into the Life History of a Model Microbial Eukaryote

Pierre Gladieux, Fabien De Bellis, Christopher Hann-Soden, Jesper Svedberg, Hanna Johannesson, and John W Taylor

14. Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments

Christoph J. Eschenbrenner, Alice Feurtey, and Eva H. Stukenbrock

15. Population Genomics on the Fly: Recent Advances in Drosophila

Annabelle Haudry, Stefan Laurent, and Martin Kapun

16. Genomic Access to the Diversity of Fishes

Arne W. Nolte

17. Avian Population Genomics Taking Off: Latest Findings and Future Prospects

Kira E. Delmore and Miriam Liedvogel

18. Population Genomics of the House Mouse and the Brown Rat

Kristian K Ullrich and Diethard Tautz

19. Population Genomics in the Great Apes

David Castellano and Kasper Munch