This book provides a reference on modern statistical and data exploration methods for the population genomics. It covers a wide range of methods within the R computing environment. The readers will be assumed to have basic knowledge in population genetics, computational methods, and statistics, although some basic principles will be explained.

Emmanuel Paradis is senior researcher in the French Institute of Research for Development (IRD). His research focuses on evolutionary models and their applications. The development and publication of software associated to his research has been an important aspect of his activities for more than twenty years. He adopted R as his main software for data analysis in 2000 and has since published and maintained several packages, including ape since 2002 and pegas since 2009. He gives regular workshops and trainings in several countries.

1. Introduction. 2. Data Acquisition. 3. Genomic Data in R. 4. Data Manipulation. 5. Data Exploration and Summaries. 6. Linkage Disequilibrium and Haplotype Structure. 7. Population Genetic Structure. 8. Geographical Structure. 9. Past Demographic Events. 10. Natural Selection.