The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites
Abstract
The parsimony method of Suzuki and Gojobori (1999) and the maximum likelihood method developed from the work of Nielsen and Yang (1998) are two widely used methods for detecting positive selection in homologous protein coding sequences. Both methods consider an excess of nonsynonymous (replacement) substitutions as evidence for positive selection. Previously published simulation studies comparing the performance of the two methods show contradictory results. Here we conduct a more thorough simulation study to cover and extend the parameter space used in previous studies. We also reanalyzed an HLA data set that was previously proposed to cause problems when analyzed using the maximum likelihood method. Our new simulations and a reanalysis of the HLA data demonstrate that the maximum likelihood method has good power and accuracy in detecting positive selection over a wide range of parameter values. Previous studies reporting poor performance of the method appear to be due to numerical problems in the optimization algorithms and did not reflect the true performance of the method. The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites.
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Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
An improved Bonferroni procedure for multiple tests of significance
SIMES, R. J. (1986) · Biometrika · doi:10.1093/biomet/73.3.751 · Cited by 2,396
Bjorkman, P. J., Saper, M. A., Samraoui, B., Bennett, W. S., Strominger, J. L., & Wiley, D. C. (1987) · Nature · doi:10.1038/329512a0 · Cited by 2,377
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
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A random effects branch-site model for detecting episodic diversifying selection
Kosakovsky Pond, S. L., Murrell, B., Fourment, M., Frost, S. D. W., Delport, W., & Scheffler, K. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr125 · Cited by 400
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Self-citationHundreds of genes experienced convergent shifts in selective pressure in marine mammals
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Lou, D. I., McBee, R. M., Le, U. Q., Stone, A. C., Wilkerson, G. K., Demogines, A. M., & Sawyer, S. L. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-155 · Cited by 74
Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
Sghaier, H., Ghedira, K., Benkahla, A., & Barkallah, I. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-297 · Cited by 71
Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria
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Tasakis, R. N., Samaras, G., Jamison, A., Lee, M., Paulus, A., Whitehouse, G., Verkoczy, L., Papavasiliou, F. N., & Diaz, M. (2021) · PLOS ONE · doi:10.1371/journal.pone.0255169 · Cited by 26
Detecting Interspecific Positive Selection Using Convolutional Neural Networks
West, C., Walker, C. R., Arasti, S., Vasilev, V., Xu, X., De Maio, N., & Goldman, N. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf154 · Cited by 1
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Metadata
- Authors
- Wong, W. S. W., Yang, Z., Goldman, N., & Nielsen, R.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-10-01
- Volume
- 168
- Issue
- 2
- Pages
- 1041-1051
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2152076818
- Cited by
- 598
- References
- 4
- FWCI
- 23.24
- Type
- journal article
- Language
- en
- Open access
- closed
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