Journal of Molecular Evolution

, Volume 86, Issue 2, pp 150–165 | Cite as

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

Original Article


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).


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


Complicance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

239_2018_9833_MOESM1_ESM.pdf (422 kb)
Supplementary material 1 (PDF 422 KB)


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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Evolutionary BiologyUniversity of HaifaHaifaIsrael
  2. 2.Department of Computer ScieneceUniversity of HaifaHaifaIsrael
  3. 3.School of EngineeringKinneret CollegeTzemachIsrael

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