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Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

Z Yang1

  • 1Department of Biology, University College, London, United Kingdom. z.yang@ucl.ac.uk

Molecular Biology and Evolution
|May 15, 1998
PubMed
Summary
This summary is machine-generated.

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Positive selection drives evolution, indicated by an excess of nonsynonymous over synonymous substitutions. Analysis of primate lysozyme genes reveals episodic evolution, particularly in the hominoid lineage, suggesting Darwinian selection.

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Positive selection at the molecular level is indicated by an excess of nonsynonymous over synonymous substitutions.
  • The nonsynonymous/synonymous rate ratio (dN/dS) can reveal lineages undergoing Darwinian selection.

Purpose of the Study:

  • Develop and apply codon-based likelihood models to detect variable dN/dS ratios among evolutionary lineages.
  • Test for episodic evolution and positive selection in primate lysozyme genes.

Main Methods:

  • Developed codon-based likelihood models for analyzing dN/dS ratios.
  • Constructed likelihood ratio tests to assess lineage-specific dN/dS variation.
  • Applied tests to lysozyme genes from 24 primate species.

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Main Results:

  • Primate lysozyme gene evolution shows significant variation in dN/dS ratios among lineages, indicating episodic evolution.
  • The hominoid lineage exhibits a dN/dS ratio significantly greater than one, with 9 nonsynonymous and 0 synonymous substitutions.
  • The ancestral colobine monkey lineage shows a higher dN/dS ratio than the background, but not significantly greater than one.

Conclusions:

  • Primate lysozyme evolution is episodic and not explained by neutral theory.
  • Evidence supports positive selection in the hominoid lineage.
  • Likelihood analysis largely confirms previous findings but highlights nuances in evolutionary rates.