Hidden likelihood support in genomic data: can forty-five wrongs make a right?

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  • Author(s): Gatesy J;Gatesy J; Baker RH
  • Source:
    Systematic biology [Syst Biol] 2005 Jun; Vol. 54 (3), pp. 483-92.
  • Publication Type:
    Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 9302532 Publication Model: Print Cited Medium: Print ISSN: 1063-5157 (Print) Linking ISSN: 10635157 NLM ISO Abbreviation: Syst Biol Subsets: MEDLINE
    • Publication Information:
      Publication: 2009- : Oxford : Oxford University Press
      Original Publication: Washington, D.C., USA : Society of Systematic Biologists, [1992-
    • Subject Terms:
      Data Interpretation, Statistical* ; Genome, Fungal* ; Likelihood Functions* ; Phylogeny*; Classification/*methods ; Saccharomyces/*genetics; Computational Biology ; Models, Genetic
    • Abstract:
      Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large comparative genomic data set for yeast (genus Saccharomyces) demonstrates that hidden support can be an important factor in maximum likelihood analyses of multiple data sets as well. Emergent signal in a concatenation of 106 genes was responsible for up to 64% of the likelihood support at a particular node (the difference in log likelihood scores between optimal topologies that included and excluded a supported clade). A grouping of four yeast species (S. cerevisiae, S. paradoxus, S. mikatae, and S. kudriavzevii) was robustly supported by combined analysis of all 106 genes, but separate analyses of individual genes suggested numerous conflicts. Forty-eight genes strictly contradicted S. cerevisiae + S. paradoxus + S. mikatae + S. kudriavzevii in separate analyses, but combined likelihood analyses that included up to 45 of the "wrong" data sets supported this group. Extensive hidden support also emerged in a combined likelihood analysis of 41 genes that each recovered the exact same topology in separate analyses of the individual genes. These results show that isolated analyses of individual data sets can mask congruence and distort interpretations of clade stability, even in strictly model-based phylogenetic methods. Consensus and supertree procedures that ignore hidden phylogenetic signals are, at best, incomplete.
    • Grant Information:
      1F32GM67463-01 United States GM NIGMS NIH HHS
    • Publication Date:
      Date Created: 20050714 Date Completed: 20050818 Latest Revision: 20071114
    • Publication Date:
      20231215
    • Accession Number:
      10.1080/10635150590945368
    • Accession Number:
      16012113