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With the advent of so-called “next generation” sequencing technologies, the study of genetic variation in populations gained a new dimension, turning population genetics into population genomics. While a scaling-up in data set size accompanied this shift, population genomics is more than just “big data” population genetics: because the objects of study here are “genomes” and not only “multiple genes,” the newly emerging field of population genomics comes along with its specific biological questions and statistical models.
Developments of new statistical methods are linked to the availability of particular data sets. As the first large population genomic initiatives came from primates, the development of many new methods targeted these organisms. Following the generation of increasingly diverse data sets, it is essential to promote the application of these methods to a broader range of organisms and questions.
The goal of this volume is to present the reader with state-of-the-art inference methods in population genomics. It focuses on data analysis based on rigorous statistical techniques. Data set preparation and preprocessing are covered in other volumes such as Statistical Genomics (Mathe´ and Davis eds) and Data Production and Analysis in Population Genomics (Pompanon and Bonin eds), while Evolutionary Genomics (Anisimova Ed) provides a more general background in evolutionary genomics.
ESSENTIAL CONCEPTS
A Population Genomics Lexicon
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
4 Exploring Population Structure with Admixture Models and Principal Component Analysis
5 Detecting Positive Selection in Populations Using Genetic Data
6 polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data
7 MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent
8 Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model
9 Coalescent Simulation with msprime
10 Inference of Ancestral Recombination Graphs Using ARGweaver
ADVANCES IN POPULATION GENOMICS
11 Population Genomics of Transitions to Selfing in Brassicaceae Model Systems
12 Genomics of Long- and Short-Term Adaptation in Maize and Teosintes
13 Neurospora from Natural Populations: Population Genomics Insights into the Life History of a Model Microbial Eukaryote
14 Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments
15 Population Genomics on the Fly: Recent Advances in Drosophila
16 Genomic Access to the Diversity of Fishes
17 Avian Population Genomics Taking Off: Latest Findings and Future Prospects
18 Population Genomics of the House Mouse and the Brown Rat
19 Population Genomics in the Great Apes
Correction to: Statistical Population Genomics