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The likelihood node density effect and consequences for evolutionary studies of molecular rates.

Andrew F Hugall1, Michael S Y Lee

  • 1CEBB, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia. andrew.hugall@adelaide.edu.au

Evolution; International Journal of Organic Evolution
|August 23, 2007
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The node density effect (NDE) is an artifact in phylogenetic tree reconstruction, causing longer root-to-tip lengths in species-rich groups. This artifact, present in maximum likelihood and Bayesian methods, can skew molecular evolutionary rate studies.

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Area of Science:

  • Molecular evolution
  • Phylogenetics
  • Computational biology

Background:

  • Species-rich clades often exhibit longer root-to-tip path lengths in molecular phylogenies.
  • This pattern has been interpreted as evidence for accelerated molecular evolution linked to cladogenesis.
  • An alternative explanation is the node density effect (NDE), a reconstruction artifact.

Purpose of the Study:

  • To investigate whether maximum likelihood and Bayesian phylogenetic reconstruction methods are susceptible to the node density effect (NDE).
  • To quantify the impact of model disparity and taxon sampling on NDE.
  • To assess the implications of NDE for studies of molecular evolutionary rates.

Main Methods:

  • Simulations using mismatched simulation and reconstruction models to assess NDE.
  • Taxon sampling manipulation on empirical datasets to evaluate NDE under optimized models.
  • Comparison of NDE prevalence and strength across different phylogenetic methods (parsimony, maximum likelihood, Bayesian).

Main Results:

  • Both maximum likelihood and Bayesian methods demonstrate the node density effect (NDE).
  • Greater model disparity between simulation and reconstruction significantly increases NDE.
  • NDE is prevalent in empirical data, even with optimized models, affecting a majority of sister path comparisons.
  • A 10% underestimation of tree length can lead to NDE in over 80% of simulated phylogenies.
  • Bayesian methods exhibit a slightly stronger NDE than maximum likelihood.

Conclusions:

  • The node density effect (NDE) is a pervasive artifact in phylogenetic tree reconstruction, affecting common methods beyond parsimony.
  • NDE can lead to an overestimation of molecular evolutionary rate heterogeneity.
  • Findings challenge the interpretation of longer root-to-tip lengths in species-rich groups as solely indicative of accelerated evolution.
  • Methodological improvements are needed to mitigate NDE and ensure accurate inferences of molecular evolutionary processes.