Horizontal Gene Transfer pp 241-256

Part of the Methods in Molecular Biology book series (MIMB, volume 532)

| Cite as

Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction

  • Robert G. Beiko
  • Mark A. Ragan

Abstract

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building ‘all the trees of all the genes’ can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.

Keywords

Phylogenetics phylogenomics horizontal gene transfer subtree prune-and-regraft bipartitions model violation 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Robert G. Beiko
    • 1
  • Mark A. Ragan
    • 2
  1. 1.Department of Computer ScienceDalhousie UniversityHalifaxCanada
  2. 2.Institute for Molecular Bioscience and Australian Research Council Centre of Excellence in BioinformaticsSt. LuciaAustralia

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