PMID- 15014169
OWN - NLM
STAT- MEDLINE
DCOM- 20041210
LR  - 20240109
IS  - 0737-4038 (Print)
IS  - 0737-4038 (Linking)
VI  - 21
IP  - 5
DP  - 2004 May
TI  - False-positive selection identified by ML-based methods: examples from the Sig1 
      gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell 
      lymphotropic virus.
PG  - 914-21
AB  - Sexually induced gene 1 (Sig1) in the centric diatom Thalassiosira weissflogii is 
      considered to encode a gamete recognition protein. Sorhannus (2003) analyzed 
      nucleotide sequences of Sig1 using parsimony analysis and the maximum-likelihood 
      (ML)-based Bayesian method for inferring positive selection at single amino acid 
      sites and reported that positively selected sites were detected by the latter 
      method but not by the former. He then concluded that for this type of study, the 
      ML-based method is more reliable than parsimony analysis. Here we show that his 
      results apparently represent false-positive cases of the ML-based method and that 
      there is no solid evidence that this gene contains positively selected sites. We 
      further demonstrate that in the tax gene of human T-cell lymphotropic virus type 
      I (HTLV-I), all codon sites, including invariable sites, can be inferred as 
      positively selected sites by the ML-based method. These observations indicate 
      that the ML-based method may produce many false-positive sites. One of the main 
      reasons for the occurrence of false positives is that in the ML-based method, 
      codon sites are grouped into several categories, with different 
      nonsynonymous/synonymous rate ratios (omegas), on a purely statistical basis, and 
      positive selection is inferred indirectly by examining whether the average omega 
      for each category is greater than 1. In parsimony analysis, however, the 
      evolutionary change of nucleotides at each codon site is examined. For this 
      reason, parsimony-based methods rarely produce false positives and are safer than 
      ML-based methods for detecting positive selection at individual codon sites, 
      although a large number of sequences are necessary.
FAU - Suzuki, Yoshiyuki
AU  - Suzuki Y
AD  - Center for Information Biology and DNA Data Bank of Japan, National Institute of 
      Genetics, Japan. yossuzuki@lab.nig.ac.jp
FAU - Nei, Masatoshi
AU  - Nei M
LA  - eng
GR  - GM 29332/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, U.S. Gov't, P.H.S.
DEP - 20040310
PL  - United States
TA  - Mol Biol Evol
JT  - Molecular biology and evolution
JID - 8501455
RN  - 0 (Codon)
RN  - 0 (Proteins)
RN  - 0 (Protozoan Proteins)
RN  - 0 (Sexually induced protein 1, Thalassiosira weissflogii)
SB  - IM
MH  - Bayes Theorem
MH  - Binding Sites
MH  - Codon
MH  - Databases as Topic
MH  - Diatoms/*genetics
MH  - *Evolution, Molecular
MH  - False Positive Reactions
MH  - Genes, pX/*genetics
MH  - Genetic Techniques
MH  - *Likelihood Functions
MH  - Models, Genetic
MH  - Phylogeny
MH  - Proteins/*genetics
MH  - Protozoan Proteins
MH  - Sequence Analysis, DNA
EDAT- 2004/03/12 05:00
MHDA- 2004/12/16 09:00
CRDT- 2004/03/12 05:00
PHST- 2004/03/12 05:00 [pubmed]
PHST- 2004/12/16 09:00 [medline]
PHST- 2004/03/12 05:00 [entrez]
AID - msh098 [pii]
AID - 10.1093/molbev/msh098 [doi]
PST - ppublish
SO  - Mol Biol Evol. 2004 May;21(5):914-21. doi: 10.1093/molbev/msh098. Epub 2004 Mar 
      10.