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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Published on: August 14, 2018

On phylogenetic tests of irreversible evolution.

Emma E Goldberg1, Boris Igić

  • 1Department of Biology, Biology/Psychology Bldg. #144, University of Maryland, College Park, Maryland 20742, USA. eeg@umd.edu

Evolution; International Journal of Organic Evolution
|September 4, 2008
PubMed
Summary

Dollo's law, concerning trait evolution, is often incorrectly rejected in phylogenetic studies. This research reveals flaws in common statistical methods, highlighting the need for improved approaches to evolutionary analysis.

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Computational Biology

Background:

  • Dollo's law posits that complex traits, once lost, do not reevolve identically.
  • Recent phylogenetic methods have challenged the validity of Dollo's law.
  • Statistical phylogenetic analyses are increasingly used to test evolutionary hypotheses.

Purpose of the Study:

  • To evaluate the accuracy of statistical phylogenetic methods used to test Dollo's law.
  • To identify sources of error in phylogenetic reconstructions of trait evolution.
  • To propose improvements for testing evolutionary irreversibility.

Main Methods:

  • Simulation studies using an irreversible binary character.
  • Likelihood-ratio tests of transition rate constraints.
  • Reconstruction of ancestral states.
  • Analysis of root state frequencies and character-dependent speciation/extinction rates.

Main Results:

  • Rejections of Dollo's law based on current phylogenetic methods are frequently incorrect.
  • Key errors stem from incorrect root state frequency assignment and neglecting character state effects on diversification rates.
  • False rejections of Dollo's law can be reduced using appropriate models and model selection.

Conclusions:

  • Significant methodological flaws exist in phylogenetic studies challenging Dollo's law.
  • Existing models and proper model selection can improve the reliability of tests for evolutionary irreversibility.
  • More robust tests require data beyond phylogenies and extant taxa character states.