Testing Empirical Support for Evolutionary Models that Root the Tree of Life

Derek Caetano-Anollés, Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anolles

Research output: Contribution to journalArticle

Abstract

Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Fully-reversible models use standard-ordered (additive) characters and Wagner parsimony to generate unrooted trees of proteomes that are then rooted with Weston’s generality criterion. Non-reversible models directly build rooted trees with unordered characters and asymmetric stepmatrices of transformation costs that penalize gain over loss of domains. Here, we test the empirical support for the evolutionary models with character state reconstruction methods using two published proteomic datasets. We show that the reversible models match reconstructed frequencies of character change and are faithful to the distribution of serial homologies in trees. In contrast, the non-reversible models go counter to trends in the data they must explain, attracting organisms with large proteomes to the base of the rooted trees while violating the triangle inequality of distances. This can lead to serious reconstruction inconsistencies that show model inadequacy. Our study highlights the aprioristic perils of disposing of countering evidence in natural history reconstruction.

Original languageEnglish (US)
Pages (from-to)131-142
Number of pages12
JournalJournal of Molecular Evolution
Volume87
Issue number2-3
DOIs
StatePublished - Apr 15 2019

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Proteome
proteome
testing
Censuses
Natural History
Lighting
Proteomics
proteomics
structural proteins
system optimization
Costs and Cost Analysis
homology
natural history
lighting
census
exercise
phylogenetics
protein
phylogeny
organisms

Keywords

  • Characters
  • Evolution
  • Fold superfamily
  • Phylogenetic analysis
  • Superkingdoms
  • Tree of life

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Testing Empirical Support for Evolutionary Models that Root the Tree of Life. / Caetano-Anollés, Derek; Nasir, Arshan; Kim, Kyung Mo; Caetano-Anolles, Gustavo.

In: Journal of Molecular Evolution, Vol. 87, No. 2-3, 15.04.2019, p. 131-142.

Research output: Contribution to journalArticle

Caetano-Anollés, Derek ; Nasir, Arshan ; Kim, Kyung Mo ; Caetano-Anolles, Gustavo. / Testing Empirical Support for Evolutionary Models that Root the Tree of Life. In: Journal of Molecular Evolution. 2019 ; Vol. 87, No. 2-3. pp. 131-142.
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