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

Sheri A. Church, Kevin Livingstone, Zhao Lai, Alexander Kozik, Steven J. Knapp, Richard W Michelmore, Loren H. Rieseberg

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Using likelihood-based variable selection models, we determined if positive selection was acting on 523 EST sequence pairs from two lineages of sunflower and lettuce. Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates. However, previous studies have shown that the likelihood ratio test (LRT) is reliable for detecting positive selection, even with low numbers of sequences. These analyses identified 56 genes that show a signature of selection, of which 75% were not identified by simpler models that average selection across codons. Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs. We discuss the validity and limitations of using variable rate models for comparisons of sequence pairs, as well as the limitations of using ESTs for identification of positively selected genes.

Original languageEnglish (US)
Pages (from-to)171-180
Number of pages10
JournalJournal of Molecular Evolution
Volume64
Issue number2
DOIs
StatePublished - Feb 2007

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Expressed Sequence Tags
Helianthus
Genes
gene
Helianthus annuus
Lettuce
genes
Codon
domestication
codons
lettuce
quantitative trait loci
Substitution reactions
substitution
rate
testing
methodology
comparison

Keywords

  • EST
  • Nonsynonymous substitutions
  • Selection
  • Synonymous substitutions

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Using variable rate models to identify genes under selection in sequence pairs : Their validity and limitations for EST sequences. / Church, Sheri A.; Livingstone, Kevin; Lai, Zhao; Kozik, Alexander; Knapp, Steven J.; Michelmore, Richard W; Rieseberg, Loren H.

In: Journal of Molecular Evolution, Vol. 64, No. 2, 02.2007, p. 171-180.

Research output: Contribution to journalArticle

Church, Sheri A. ; Livingstone, Kevin ; Lai, Zhao ; Kozik, Alexander ; Knapp, Steven J. ; Michelmore, Richard W ; Rieseberg, Loren H. / Using variable rate models to identify genes under selection in sequence pairs : Their validity and limitations for EST sequences. In: Journal of Molecular Evolution. 2007 ; Vol. 64, No. 2. pp. 171-180.
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