期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 18, 期 12, 页码 2179-2185出版社
SOC MOLECULAR BIOLOGY EVOLUTION
DOI: 10.1093/oxfordjournals.molbev.a003764
关键词
positive selection; human leukocyte antigen; parsimony; likelihood
资金
- NIGMS NIH HHS [GM20293] Funding Source: Medline
The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different evolutionary models and generally more reliable than that by likelihood-based methods. In contrast, the results obtained by likelihood-based methods depend on the models and on the initial parameter values used. It is sometimes difficult to obtain the maximum likelihood estimates of parameters for a given model, and the results obtained may be false negatives or false positives depending on the initial parameter-values. It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths: of the phylogenetic tree are relatively small.
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