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Cases in which ancestral maximum likelihood will be confusingly misleading.

Tomer Handelman1, Benny Chor1

  • 1School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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Summary
This summary is machine-generated.

Ancestral maximum likelihood (AML) is statistically inconsistent and misleading. This study demonstrates AML can favor incorrect phylogenetic trees, unlike maximum parsimony

Keywords:
Ancestral maximum likelihoodMaximum parsimonyPhylogenetic reconstructionStatistical consistency

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Maximum likelihood (ML) is statistically consistent for phylogenetic tree reconstruction.
  • Maximum parsimony (MP) is known to be statistically inconsistent and misleading.
  • The statistical consistency of Ancestral Maximum Likelihood (AML) has remained an open question.

Purpose of the Study:

  • To investigate the statistical consistency of Ancestral Maximum Likelihood (AML).
  • To determine if AML is misleading in phylogenetic tree reconstruction.

Main Methods:

  • Analysis of AML criteria on simplified four-taxa phylogenetic trees.
  • Mathematical evaluation of tree topology optimization under AML.

Main Results:

  • AML can be statistically inconsistent, favoring incorrect tree topologies.
  • AML can be misleading, optimizing on incorrect resolved and star trees.
  • Unlike MP's "long edge attraction," AML exhibits "long edge repulsion."

Conclusions:

  • Ancestral Maximum Likelihood (AML) is statistically inconsistent and misleading.
  • AML's inconsistencies differ mechanistically from Maximum Parsimony.
  • This research clarifies the statistical properties of AML in phylogenetics.