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Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for

Sheri A Church1, Kevin Livingstone, Zhao Lai

  • 1Department of Biology, Indiana University, Bloomington, IN 47405, USA. schurch@gwu.edu

Journal of Molecular Evolution
|January 4, 2007
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Summary

Researchers identified 56 genes under positive selection in sunflower and lettuce using advanced models. Many of these genes, crucial for domestication traits, were missed by simpler methods, highlighting the power of variable rate models in evolutionary studies.

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Molecular Evolution

Background:

  • Detecting positive selection is key to understanding adaptation.
  • Variable rate models are challenging for sequence pair comparisons.
  • Likelihood ratio tests (LRT) are reliable for detecting positive selection, even with limited data.

Purpose of the Study:

  • To identify genes under positive selection in sunflower and lettuce lineages.
  • To compare the efficacy of variable rate models versus simpler models for detecting selection.
  • To investigate the role of selected genes in sunflower domestication.

Main Methods:

  • Analyzed 523 EST sequence pairs from sunflower and lettuce using likelihood-based variable selection models.
  • Employed the likelihood ratio test (LRT) to detect signatures of positive selection.
  • Mapped positively selected genes to quantitative trait loci (QTLs) in sunflower.

Main Results:

  • Identified 56 genes showing a signature of positive selection.
  • 75% of these selected genes were not detected by simpler, codon-averaging models.
  • Four out of five identified positively selected genes in sunflower mapped to domestication QTLs.

Conclusions:

  • Variable rate models are effective for detecting positive selection in sequence pair comparisons, despite limitations.
  • Advanced models identify genes missed by simpler methods, offering deeper evolutionary insights.
  • Positively selected genes identified are linked to important domestication traits in sunflower.