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Derek Caetano-Anollés1, Arshan Nasir2, Kyung Mo Kim3

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Fully-reversible models accurately reconstruct evolutionary relationships using protein domain data. Non-reversible models lead to inconsistencies, highlighting the importance of empirical evidence in phylogenetic tree construction.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Constructing rooted Trees of Life (ToLs) requires direct methods optimizing character state information.
  • Protein structural domains in proteomes are used to build ToLs with different evolutionary models.

Purpose of the Study:

  • To empirically test the support for reversible and non-reversible evolutionary models in phylogenetic reconstruction.
  • To evaluate model adequacy using character state reconstruction methods and proteomic datasets.

Main Methods:

  • Utilized character state reconstruction methods on two published proteomic datasets.
  • Compared fully-reversible models (additive characters, Wagner parsimony) with non-reversible models (unordered characters, asymmetric stepmatrices).
  • Rooted unrooted trees using Weston's generality criterion for reversible models.

Main Results:

  • Reversible models align with reconstructed character change frequencies and the distribution of serial homologies.
  • Non-reversible models produce inconsistencies, placing organisms with large proteomes at the tree base and violating distance inequalities.
  • Demonstrated model inadequacy of non-reversible approaches.

Conclusions:

  • Fully-reversible models provide a more faithful representation of evolutionary history based on proteomic data.
  • Non-reversible models exhibit significant limitations and can lead to erroneous phylogenetic reconstructions.
  • Emphasizes the critical need to incorporate empirical evidence and avoid aprioristic assumptions in natural history reconstruction.