TY - JOUR
T1 - Using variable rate models to identify genes under selection in sequence pairs
T2 - Their validity and limitations for EST sequences
AU - Church, Sheri A.
AU - Livingstone, Kevin
AU - Lai, Zhao
AU - Kozik, Alexander
AU - Knapp, Steven J.
AU - Michelmore, Richard W.
AU - Rieseberg, Loren H.
PY - 2007/2
Y1 - 2007/2
N2 - 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.
AB - 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.
KW - EST
KW - Nonsynonymous substitutions
KW - Selection
KW - Synonymous substitutions
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U2 - 10.1007/s00239-005-0299-5
DO - 10.1007/s00239-005-0299-5
M3 - Article
C2 - 17200807
AN - SCOPUS:33846438205
SN - 0022-2844
VL - 64
SP - 171
EP - 180
JO - Journal of Molecular Evolution
JF - Journal of Molecular Evolution
IS - 2
ER -