Statistical Population Genomics

ISBN-13: 9781071601983 / Angielski / Twarda / 2020 / 468 str.

Julien Dutheil

Spis treści

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

Blurb

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions.