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

Eliran Avni, Zahi Yona, Reuven Cohen, Sagi Snir

Research output: Contribution to journalArticlepeer-review


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).

Original languageEnglish
Pages (from-to)150-165
Number of pages16
JournalJournal of Molecular Evolution
Issue number2
StatePublished - 1 Feb 2018

Bibliographical note

Publisher Copyright:
© 2018, Springer Science+Business Media, LLC, part of Springer Nature.


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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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