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The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input

Journal of Molecular Evolution volume 86, pages 150–165 (2018)Cite this article

Abstract

Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. The availability of enormous quantities of molecular data has made large-scale phylogenetic reconstruction involving thousands of species, a more viable goal. For this goal, separate trees over different, overlapping subsets of species, representing histories of various markers of these species, are collected. These trees, typically with conflicting signals, are subsequently combined into a single tree over the full set, an operation denoted as supertree construction. The amalgamation of such trees into a single tree lies at the heart of many tasks in phylogenetics, yet remains a daunting endeavor, especially in light of conflicting signals. In this work, we study the performance of matrix representation with parsimony (MRP), the most widely used supertree method to date, when confronted with quartet trees. Quartet trees are the most basic informational unit when amalgamation of unrooted trees is attempted, and they remain relevant in more general settings even though standard supertree methods are not necessarily confined to quartets. This study involves both real and simulated data, and the effects of several parameters on the results are evaluated, revealing a number of anomalies associated with MRP. We show that these anomalies are surmountable when using a recently introduced supertree method, weighted quartet MaxCut (wQMC).

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Author notes

  1. Eliran Avni and Zahi Yona are equal contribution.

Affiliations

  1. Department of Evolutionary Biology, University of Haifa, 31905, Haifa, Israel

    Eliran Avni & Sagi Snir

  2. Department of Computer Scienece, University of Haifa, 31905, Haifa, Israel

    Zahi Yona

  3. School of Engineering, Kinneret College, 15132, Tzemach, Israel

    Reuven Cohen

Authors
  1. Eliran Avni
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  2. Zahi Yona
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  3. Reuven Cohen
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  4. Sagi Snir
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Correspondence to Sagi Snir.

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Avni, E., Yona, Z., Cohen, R. et al. The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input. J Mol Evol 86, 150–165 (2018). https://doi.org/10.1007/s00239-018-9833-0

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  • DOI: https://doi.org/10.1007/s00239-018-9833-0

Keywords

  • Phylogenetic reconstruction
  • Matrix representation with parsimony (MRP)
  • Weighted quartet MaxCut (wQMC)
  • Supertree reconstruction
  • Weighted tree similarity.