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RELAX: detecting relaxed selection in a phylogenetic framework.

Joel O Wertheim1, Ben Murrell2, Martin D Smith3

  • 1Department of Medicine, University of California, San Diego jwertheim@ucsd.edu kscheffler@ucsd.edu.

Molecular Biology and Evolution
|December 26, 2014
PubMed
Summary
This summary is machine-generated.

Relaxed selection, a reduction in natural selection

Keywords:
Daphnia pulexbornaviruscodon modelsecholocationendosymbiontsmolecular evolutionopsinphylogeneticsrelaxed selection

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Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Natural selection's intensity can decrease, leading to evolutionary changes or loss of function.
  • Existing methods struggle to detect relaxed selection accurately, potentially misinterpreting increased positive selection.
  • Understanding relaxed selection is crucial for evolutionary and functional genomics.

Purpose of the Study:

  • Introduce a novel hypothesis testing framework, RELAX, for detecting relaxed selection.
  • Differentiate between relaxed selection and intensified positive selection using molecular sequence data.
  • Apply the RELAX framework to diverse biological systems to validate its efficacy.

Main Methods:

  • Developed a codon-based phylogenetic framework for hypothesis testing.
  • Utilized simulations to establish the statistical validity and power of the RELAX test.
  • Compared selective pressures across defined phylogenetic branch subsets.

Main Results:

  • RELAX successfully distinguishes between relaxed selection and intensified positive selection.
  • Demonstrated relaxed selection in insect endosymbionts (γ-proteobacteria) compared to free-living relatives.
  • Observed relaxed selection in asexual Daphnia pulex and endogenous bornavirus-like elements.
  • Found relaxed selection on SWS1 opsin genes in bats with pseudogenization and on M/LWS1 opsin genes in all echolocating bats.

Conclusions:

  • The RELAX framework provides a robust method for detecting relaxed selection across diverse taxa.
  • Relaxed selection is a significant evolutionary force shaping genomes in various biological contexts.
  • Findings offer insights into the evolution of symbiosis, reproduction, viruses, and sensory systems.