Table of Contents

A Population Genomics Lexicon.- Processing and Analyzing Multiple Genomes Alignments with MafFilter.- Data Management and Summary Statistics with PLINK.- Exploring Population Structure with Admixture Models and Principal Components Analysis.- Detecting Positive Selection in Populations using Genetic Data.- polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations  from Polymorphism Data.- MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent.-Ancestral Population Genomics with Jocx, A Coalescent Hidden Markov Model.- Coalescent Simulation with sprime.- Inference of Ancestral Recombination Graphs using ARGweaver.- Population Genomics of Transitions to Selfing in Brassicaceae Model Systems.- Genomics of Long- and Short- Term Adaptation in Maize and Teosinte.- Neurospora from Natural Populations: Population Genomics Insights Into the Life History of a Model Microbial Eukaryote.- Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments.- Population Genomics on the Fly: Recent Advances in Drosophila.- Genomic Access to the Diversity of Fishes.- Avian Population Genomics Taking Off: Latest Findings and Future Prospects.- Population Genomics of the House Mouse and the Brown Rat.- Population Genomics in the Great Apes.