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A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution.

Keren Halabi1, Eli Levy Karin2, Laurent Guéguen3,4

  • 1School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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|November 30, 2020
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Summary
This summary is machine-generated.

TraitRELAX, a new phylogenetic model, detects evolutionary selection changes linked to trait shifts. It identified intensified selection in primate SEMG2 genes and altered selection in bacterial genes during lifestyle transitions.

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Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Detecting selection signatures in coding sequences helps identify genes for complex traits.
  • Phylogenetic branch-site codon models are used to find selection changes but assume resolved trait evolution.
  • Existing methods often overlook uncertainty in trait and sequence evolution, limiting the detection of repeated trait transitions.

Purpose of the Study:

  • To introduce TraitRELAX, a novel phylogenetic model addressing limitations of current methods.
  • To enable detection of selection intensity changes associated with repeated trait transitions.
  • To account for uncertainty in both trait and coding sequence evolution.

Main Methods:

  • Developed TraitRELAX, a joint statistical framework for phylogenetic analysis.
  • The model explicitly handles uncertainty in trait and coding sequence evolution.
  • Evaluated TraitRELAX performance through simulations and applied it to empirical data.

Main Results:

  • TraitRELAX identified intensified selection in the primate SEMG2 gene in polygynandrous species.
  • Detected changes in purifying selection intensity for sixteen bacterial genes during the free-living to endosymbiotic transition.
  • Demonstrated the model's ability to detect selection changes upon repeated trait transitions.

Conclusions:

  • TraitRELAX offers a more robust approach to studying evolutionary selection by accounting for evolutionary uncertainty.
  • The model successfully revealed adaptive evolutionary changes linked to specific phenotypic shifts in primates and bacteria.
  • This framework advances our understanding of genotype-phenotype evolution and the genetic basis of complex traits.