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Introduction to Population Genomics Methods

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2222))

Abstract

High-throughput sequencing technologies have provided an unprecedented opportunity to study the different evolutionary forces that have shaped present-day patterns of genetic diversity, with important implications for many directions in plant biology research. To manage such massive quantities of sequencing data, biologists, however, need new additional skills in informatics and statistics. In this chapter, our objective is to introduce population genomics methods to beginners following a learning-by-doing strategy in order to help the reader to analyze the sequencing data by themselves. Conducted analyses cover several main areas of evolutionary biology, such as an initial description of the evolutionary history of a given species or the identification of genes targeted by natural or artificial selection. In addition to the practical advices, we performed re-analyses of two cases studies with different kind of data: a domesticated cereal (African rice) and a non-domesticated tree species (sessile oak). All the code needed to replicate this work is publicly available on github (https://github.com/ThibaultLeroyFr/Intro2PopGenomics/).

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Acknowledgments

The analyses benefited from the Montpellier Bioinformatics Biodiversity (MBB) platform services, the genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul), the Bird Platform of the University of Nantes and Compute Canada (Graham servers). This work takes its source from a diverse range of research contributions and projects we achieved during the last 5 years. During this period, TL was supported by different postdoctoral fellowships from the French Agence Nationale de la Recherche (ANR, Genoak project, PI: Christophe Plomion, 11-BSV6-009-021 and BirdIslandGenomic, PI: Benoit Nabholz, ANR-14-CE02-0002), from the European Research Council (ERC, Treepeace, PI: Antoine Kremer, Grant Agreement no. 339728), and from the University of Vienna, Austria (PI: Christian Lexer). QR was supported by the government of Canada through Genome Canada, Genome British Columbia and Genome Quebec. QR wants to thank Louis Bernatchez for the opportunity to develop various projects during his postdoctoral research. We want to thank Jean-Marc Aury, Antoine Kremer, and Christophe Plomion for providing access to the oak sequencing data. We also thank Philippe Vigouroux and Philippe Cubry for information concerning the African rice data and Pierre-Alexandre Gagnaire and Nicolas Bierne for discussions on TreeMix. This book chapter is dedicated to Prof. Christian Lexer, who through his career greatly advanced our knowledge of population genomics and evolutionary botany.

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Authors and Affiliations

  1. Montpellier Institute of Evolutionary Sciences (ISEM), Université de Montpellier, Montpellier, France

    Thibault Leroy

  2. Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria

    Thibault Leroy

  3. Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada

    Quentin Rougemont

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  1. Thibault Leroy
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Correspondence to Thibault Leroy .

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Editors and Affiliations

  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

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Leroy, T., Rougemont, Q. (2021). Introduction to Population Genomics Methods. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_16

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