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Molecular Phylogenetics: Testing Evolutionary Hypotheses

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Bacteriophages

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 502))

Abstract

A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada

    David A. Walsh & Adrian K. Sharma

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  1. David A. Walsh
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  2. Adrian K. Sharma
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Editors and Affiliations

  1. University of Leicester, Leicester, UK

    Martha R.J. Clokie

  2. Public Health Agency of Canada, Guelph, Ontario, Canada

    Andrew M. Kropinski

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Walsh, D.A., Sharma, A.K. (2009). Molecular Phylogenetics: Testing Evolutionary Hypotheses. In: Clokie, M.R., Kropinski, A.M. (eds) Bacteriophages. Methods in Molecular Biology™, vol 502. Humana Press. https://doi.org/10.1007/978-1-60327-565-1_9

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  • DOI: https://doi.org/10.1007/978-1-60327-565-1_9

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