Detecting individual sites subject to episodic diversifying selection

PLoS Genetics

Volumn 8, Issue 7, 2012, Pages

  Murrell, Ben ^a,b   Wertheim, Joel O ^c   Moola, Sasha ^b   Weighill, Thomas ^b   Scheffler, Konrad ^b,d   Kosakovsky Pond, Sergei L ^d  

^a SOUTH AFRICAN MEDICAL RESEARCH COUNCIL   (South Africa)

^b STELLENBOSCH UNIVERSITY   (South Africa)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; RHODOPSIN;

ARTICLE; ARTIODACTYLA; BIOLOGICAL MODEL; CONTROLLED STUDY; DIVERSIFYING SELECTION; EMPIRICAL RESEARCH; EVOLUTIONARY ADAPTATION; GENETIC MODEL; JAPANESE ENCEPHALITIS VIRUS; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; SEQUENCE ANALYSIS; SIMULATION;

AMINO ACIDS; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, THEORETICAL; OPEN READING FRAMES; PHYLOGENY; RHODOPSIN; SELECTION, GENETIC; VERTEBRATES;

EID: 84864605220     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002764     Document Type: Article

References (38)

1. Muse SV, Gaut BS, (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715-724.
2. Goldman N, Yang Z, (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-36.
3. Delport W, Scheffler K, Seoighe C, (2009) Models of coding sequence evolution. Brief Bioinform 10: 97-109.
4. Anisimova M, Kosiol C, (2009) Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 26: 255-271.
5. Hughes AL, Nei M, (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-70.
6. Bonhoeffer S, Holmes EC, Nowak MA, (1995) Causes of HIV diversity. Nature 376: 125.
7. Messier W, Stewart CB, (1997) Episodic adaptive evolution of primate lysozymes. Nature 385: 151-4.
8. Kimura M, (1968) Evolutionary rate at the molecular level. Nature 217: 624-6.
9. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170 doi:10.1371/journal.pbio.0030170.
10. Nielsen R, Yang Z, (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-36.
11. Sawyer SL, Wu LI, Emerman M, Malik HS, (2005) Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci U S A 102: 2832-7.
12. Brault AC, Huang CYH, Langevin SA, Kinney RM, Bowen RA, et al. (2007) A single positively selected West Nile viral mutation confers increased virogenesis in American crows. Nat Genet 39: 1162-6.
13. Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP, (2004) Modeling the site-specific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences of the United States of America 101: 12957-12962.
14. Delport W, Scheffler K, Seoighe C, (2008) Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS Pathog 4: e1000242 doi:10.1371/journal.ppat.1000242.
15. Seoighe C, Ketwaroo F, Pillay V, Scheffler K, Wood N, et al. (2007) A model of directional selection applied to the evolution of drug resistance in HIV-1. Mol Biol Evol 24: 1025-31.
16. Kosakovsky Pond SL, Poon AFY, Leigh Brown AJ, Frost SDW, (2008) A maximum likelihood method for detecting directional evolution in protein sequences and its application to inuenza A virus. Mol Biol Evol 25: 1809-24.
17. Yang Z, dos Reis M, (2011) Statistical properties of the branch-site test of positive selection. Mol Biol Evol 28: 1217-28.
18. Yokoyama S, Tada T, Zhang H, Britt L, (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A 105: 13480-5.
19. Chen J, Sun Y, (2011) Variation in the analysis of positively selected sites using nonsynonymous/synonymous rate ratios: an example using inuenza virus. PLoS ONE 6: e19996 doi:10.1371/journal.pone.0019996.
20. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SDW, Delport W, et al. (2011) A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol 28: 3033-3043.
21. Kosakovsky Pond S, Delport W, Muse SV, Scheffler K, (2010) Correcting the bias of empirical frequency parameter estimators in codon models. PLoS ONE 5: e11230 doi:10.1371/journal.pone.0011230.
22. Felsenstein J, (1981) Evolutionary trees from DNA-sequences - a maximum-likelihood approach. J Mol Evol 17: 368-376.
23. Yang Z, (2000) Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human inuenza virus A. Journal of Molecular Evolution 51: 423-432.
24. Kosakovsky Pond SL, Frost SDW, (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22: 1208-1222.
25. Wertheim JO, Kosakovsky Pond SL, (2011) Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol.
26. Pond SK, Muse SV, (2005) Site-to-site variation of synonymous substitution rates. Mol Biol Evol 22: 2375-85.
27. Self SG, Liang KY, (1987) Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests Under Nonstandard Conditions. J Am Stat Assoc 82: 605-310.
28. Yang ZH, Nielsen R, Goldman N, Pedersen AMK, (2000) Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites. Genetics 155: 431-449.
29. Nozawa M, Suzuki Y, Nei M, (2009) Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A 106: 6700-5.
30. Pond SLK, Scheffler K, Gravenor MB, Poon AFY, Frost SDW, (2010) Evolutionary fingerprinting of genes. Mol Biol Evol 27: 520-36.
31. Wu KP, Wu CW, Tsao YP, Kuo TW, Lou YC, et al. (2003) Structural basis of a avivirus recognized by its neutralizing antibody: solution structure of the domain III of the Japanese encephalitis virus envelope protein. J Biol Chem 278: 46007-13.
32. Gangwar RS, Shil P, Cherian SS, Gore MM, (2011) Delineation of an epitope on domain I of Japanese encephalitis virus Envelope glycoprotein using monoclonal antibodies. Virus Res 158: 179-87.
33. Tanaka T, Nei M, (1989) Positive darwinian selection observed at the variable-region genes of immunoglobulins. Mol Biol Evol 6: 447-59.
34. Harmsen M, Ruuls R, Nijman I, Niewold T, Frenken L, et al. (2000) Llama heavy-chain V regions consist of at least four distinct subfamilies revealing novel sequence features. Molecular Immunology 37: 579-590.
35. Su C, Nguyen VK, Nei M, (2002) Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids. Mol Biol Evol 19: 205-15.
36. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
37. Tuffley C, Steel M, (1998) Modeling the covarion hypothesis of nucleotide substitution. Mathematical biosciences 147: 63-91.
38. McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-4.