Data Production and Analysis in Population Genomics

Methods and Protocols

  • François Pompanon
  • Aurélie Bonin

Part of the Methods in Molecular Biology book series (MIMB, volume 888)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Sampling and Experimental Design

    1. Front Matter
      Pages 1-1
    2. Stéphanie Manel, Cécile H. Albert, Nigel G. Yoccoz
      Pages 3-12
  3. Producing Data

    1. Front Matter
      Pages 65-65
    2. Andrzej Kilian, Peter Wenzl, Eric Huttner, Jason Carling, Ling Xia, Hélène Blois et al.
      Pages 67-89
    3. Margot Paris, Claire-Lise Meyer, Christelle Blassiau, Eric Coissac, Pierre Taberlet, Laurence Després
      Pages 91-108
    4. David E. Alquezar-Planas, Sarah L. Fordyce
      Pages 109-118
    5. Zhao Lai, Yi Zou, Nolan C. Kane, Jeong-Hyeon Choi, Xinguo Wang, Loren H. Rieseberg
      Pages 119-133
  4. Analyzing Data

    1. Front Matter
      Pages 153-153
    2. Nils Arrigo, Rolf Holderegger, Nadir Alvarez
      Pages 155-175
    3. Olivier Delaneau, Jean-François Zagury
      Pages 177-196
    4. Katrina M. Dlugosch, Aurélie Bonin
      Pages 197-211
    5. Matthieu Bouaziz, Marine Jeanmougin, Mickaël Guedj
      Pages 213-233
    6. Paul A. Hohenlohe, Julian Catchen, William A. Cresko
      Pages 235-260
    7. Andrés Pérez-Figueroa, Silvia T. Rodríguez-Ramilo, Armando Caballero
      Pages 261-275

About this book

Introduction

Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough a priori data on the polymorphism, population genomics analyses will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, Data Production and Analysis in Population Genomics purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available. Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and easily accessible, Data Production and Analysis in Population Genomics serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.

Keywords

genome sequencing landscape genomics loci polymorphism population genomics

Editors and affiliations

  • François Pompanon
    • 1
  • Aurélie Bonin
    • 2
  1. 1., Laboratoire d'Ecologie AlpineUniversité Grenoble IGrenoble Cedex 09France
  2. 2.Laboratoire d'Ecologie AlpineUniversité Grenoble 1GrenobleFrance

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-61779-870-2
  • Copyright Information Springer Science+Business Media New York 2012
  • Publisher Name Humana Press, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-61779-869-6
  • Online ISBN 978-1-61779-870-2
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • About this book