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Phylogenetic Methods for Genome-Wide Association Studies in Bacteria

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2242))

Abstract

Genome-wide association studies in bacteria have great potential to deliver a better understanding of the genetic basis of many biologically important phenotypes, including antibiotic resistance, pathogenicity, and host adaptation. Such studies need however to account for the specificities of bacterial genomics, especially in terms of population structure, homologous recombination, and genomic plasticity. A powerful way to tackle this challenge is to use a phylogenetic approach, which is based on long-standing methodology for the evolutionary analysis of bacterial genomic data. Here we present both the theoretical and practical aspects involved in the use of phylogenetic methods for bacterial genome-wide association studies.

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Author information

Authors and Affiliations

  1. School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK

    Xavier Didelot

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  1. Xavier Didelot
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Correspondence to Xavier Didelot .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Alessio Mengoni

  2. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Giovanni Bacci

  3. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Marco Fondi

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Didelot, X. (2021). Phylogenetic Methods for Genome-Wide Association Studies in Bacteria. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_13

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1098-5

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