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Phylogenetic Trees03:21

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A Practical Guide to Phylogenetics for Nonexperts
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Non-hereditary Maximum Parsimony trees.

Mareike Fischer1

  • 1Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr Gasse 9, 1030, Vienna, Austria. email@mareikefischer.de

Journal of Mathematical Biology
|August 16, 2011
PubMed
Summary
This summary is machine-generated.

This study investigates if Maximum Parsimony phylogenetic trees are hereditary. While confirmed for 5 taxa, counterexamples show trees are not always hereditary, impacting phylogenetic estimation.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The Maximum Parsimony (MP) method is a fundamental tool in phylogenetic estimation.
  • A 2007 conjecture by Arndt von Haeseler questioned the hereditary property of MP trees.
  • This property relates to whether subtrees of an MP tree are also most parsimonious for subalignments.

Purpose of the Study:

  • To investigate the hereditary conjecture for Maximum Parsimony trees.
  • To determine if MP trees for a given alignment contain the most parsimonious subtrees for all subalignments.
  • To explore the implications for phylogenetic inference and related methods.

Main Methods:

  • Mathematical analysis of phylogenetic tree properties.
  • Construction of counterexamples to disprove the conjecture in general cases.
  • Exploration of related concepts like subtree reduction and quartet compatibility.
  • Generalization of findings to Maximum Likelihood methods.

Main Results:

  • The conjecture is affirmed for binary alignments with 5 taxa.
  • Counterexamples demonstrate that Maximum Parsimony trees are not generally hereditary.
  • Most parsimonious trees cannot always be reduced to most parsimonious trees for fewer taxa.
  • Compatible most parsimonious quartets do not guarantee a most parsimonious supertree.

Conclusions:

  • Maximum Parsimony trees are not universally hereditary.
  • The findings necessitate caution when inferring larger phylogenetic trees from smaller subproblems.
  • Results have implications for the robustness of phylogenetic reconstruction methods.
  • The study extends to Maximum Likelihood under specific evolutionary models.