Journal of Molecular Evolution

, Volume 64, Issue 1, pp 80–89 | Cite as

Using Confidence Set Heuristics During Topology Search Improves the Robustness of Phylogenetic Inference

  • Shirley L. Pepke
  • Davin Butt
  • Isabelle Nadeau
  • Andrew J. Roger
  • Christian BlouinEmail author


We examine the impact of likelihood surface characteristics on phylogenetic inference. Amino acid data sets simulated from topologies with branch length features chosen to represent varying degrees of difficulty for likelihood maximization are analyzed. We present situations where the tree found to achieve the global maximum in likelihood is often not equal to the true tree. We use the program covSEARCH to demonstrate how the use of adaptively sized pools of candidate trees that are updated using confidence tests results in solution sets that are highly likely to contain the true tree. This approach requires more computation than traditional maximum likelihood methods, hence covSEARCH is best suited to small to medium-sized alignments or large alignments with some constrained nodes. The majority rule consensus tree computed from the confidence sets also proves to be different from the generating topology. Although low phylogenetic signal in the input alignment can result in large confidence sets of trees, some biological information can still be obtained based on nodes that exhibit high support within the confidence set. Two real data examples are analyzed: mammal mitochondrial proteins and a small tubulin alignment. We conclude that the technique of confidence set optimization can significantly improve the robustness of phylogenetic inference at a reasonable computational cost. Additionally, when either very short internal branches or very long terminal branches are present, confident resolution of specific bipartitions or subtrees, rather than whole-tree phylogenies, may be the most realistic goal for phylogenetic methods.


Phylogenetics Maximum likelihood Confidence sets Robustness Majority consensus 



The authors wish to thank Ed Susko, Associate Editor Nicholas Galtier, and the anonymous reviewers for their suggested improvements to the manuscript and, also, Matthew Spencer for helpful discussion. Thanks go to J. Leigh for providing the tree in Fig. 3a. Shirley Pepke was supported by a Genome Atlantic postdoctoral fellowship. This work was supported by NSERC discovery grant 298397-04 (CB).


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Shirley L. Pepke
    • 1
    • 2
  • Davin Butt
    • 2
  • Isabelle Nadeau
    • 1
    • 2
  • Andrew J. Roger
    • 1
  • Christian Blouin
    • 1
    • 2
    Email author
  1. 1.Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
  2. 2.Department of Computer ScienceDalhousie UniversityHalifaxCanada

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