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  • Book
  • Open Access
  • © 2020

Statistical Population Genomics

Editors:

  1. Julien Y. Dutheil

    1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany

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  • Includes cutting-edge methods and protocols

  • Provides step-by-step detail essential for reproducible results

  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2090)

Sections

Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)
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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xii
    PDF

  2. Essential Concepts

    1. Front Matter

      Pages 1-1
      PDF

    2. A Population Genomics Lexicon

      • Gustavo V. Barroso, Ana Filipa Moutinho, Julien Y. Dutheil
      Pages 3-17Open Access

  3. Statistical Methods for Analyzing Genomes in Populations

    1. Front Matter

      Pages 19-19
      PDF

    3. Data Management and Summary Statistics with PLINK

      • Christopher C. Chang
      Pages 49-65Open Access

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

      • Chi-Chun Liu, Suyash Shringarpure, Kenneth Lange, John Novembre
      Pages 67-86Open Access

    5. Detecting Positive Selection in Populations Using Genetic Data

      • Angelos Koropoulis, Nikolaos Alachiotis, Pavlos Pavlidis
      Pages 87-123Open Access

    7. MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

      • Stephan Schiffels, Ke Wang
      Pages 147-166Open Access

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

      • Jade Yu Cheng, Thomas Mailund
      Pages 167-189Open Access

    9. Coalescent Simulation with msprime

      • Jerome Kelleher, Konrad Lohse
      Pages 191-230Open Access

    10. Inference of Ancestral Recombination Graphs Using ARGweaver

      • Melissa Hubisz, Adam Siepel
      Pages 231-266Open Access

  4. Advances in Population Genomics

    1. Front Matter

      Pages 267-267
      PDF

    2. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems

      • Tiina M. Mattila, Benjamin Laenen, Tanja Slotte
      Pages 269-287Open Access

    3. Genomics of Long- and Short-Term Adaptation in Maize and Teosintes

      • Anne Lorant, Jeffrey Ross-Ibarra, Maud Tenaillon
      Pages 289-311Open Access

    4. 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, John W. Taylor
      Pages 313-336Open Access

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

      • Christoph J. Eschenbrenner, Alice Feurtey, Eva H. Stukenbrock
      Pages 337-355Open Access

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

      • Annabelle Haudry, Stefan Laurent, Martin Kapun
      Pages 357-396Open Access

    7. Genomic Access to the Diversity of Fishes

      • Arne W. Nolte
      Pages 397-411Open Access
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About this book

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.


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Keywords

  • VCFTools
  • MafFilter
  • PLINK
  • SCRM
  • ARGweaver
  • open access
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Editors and Affiliations

  • Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany

    Julien Y. Dutheil

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Bibliographic Information

  • Book Title: Statistical Population Genomics

  • Editors: Julien Y. Dutheil

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0199-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s) 2020

  • License: CC BY

  • Hardcover ISBN: 978-1-0716-0198-3Published: 24 January 2020

  • Softcover ISBN: 978-1-0716-0201-0Published: 18 September 2020

  • eBook ISBN: 978-1-0716-0199-0Published: 23 January 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 468

  • Number of Illustrations: 105 b/w illustrations, 98 illustrations in colour

  • Topics: Bioinformatics, Genetics and Genomics

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Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)
Learn about institutional subscriptions