Erratum: An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes (Molecular Biology and Evolution (2012) 29:5 (1297-1300) DOI: 10.1093/molbev/msr311);An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes

Molecular Biology and Evolution

Volumn 29, Issue 5, 2012, Pages 1297-1300

  Weadick, Cameron J ^a   Chang, Belinda S W ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

Clade model; Codon substitution model; DN dS; Gene family evolution; Maximum likelihood; Nonsynonymous to synonymous substitution rate ratio

Indexed keywords

RHODOPSIN; RIBONUCLEASE;

ARTICLE; CLADISTICS; CODON; EVOLUTION; GENETIC VARIABILITY; MOLECULAR MODEL; NONHUMAN; PROTEIN FUNCTION; SIMULATION;

MAMMALIA; PRIMATES;

EID: 84862892391     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss127     Document Type: Erratum

References (14)

1. Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol. 26:255-271.
2. Bielawski JP, Yang Z. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol. 59:121-132. (Pubitemid 38858437)
3. Chang BSW, Du J, Weadick CJW, Muller J, Bickelmann C, Yu DD, Morrow JM. Forthcoming. The future of codon models in studies of molecular function: ancestral reconstruction, and clade models of functional divergence. In: Cannarozii GM, Schneider A, editors. Codon evolution: mechanisms and models. Oxford: Oxford University Press.
4. Dean AM, Thornton JW. 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet. 8:675-688. (Pubitemid 47281989)
5. Dyer KD, Rosenberg HF. 2006. The RNase a superfamily: generation of diversity and innate host defense. Mol Divers. 10:585-597. (Pubitemid 44885235)
6. Forsberg R, Christiansen FB. 2003. A codon-based model of hostspecific selection in parasites, with an application to the influenza A virus. Mol Biol Evol. 20:1252-1259. (Pubitemid 36961243)
7. Goldman N, Whelan S. 2000. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol Biol Evol. 17:975-978. (Pubitemid 30346557)
8. Nei M, Suzuki Y, Nozawa M. 2010. The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet. 11:265-289.
9. Teeling EC. 2009. Hear, hear: the convergent evolution of echolocation in bats? Trends Ecol Evol. 24:351-354.
10. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)
11. Yang Z, dos Reis M. 2011. Statistical properties of the branch-site test of positive selection. Mol Biol Evol. 28:1217-1228.
12. Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449. (Pubitemid 30257141)
13. Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22:1107-1118. (Pubitemid 40471423)
14. Zhao H, Ru B, Teeling EC, Faulkes CG, Zhang S, Rossiter SJ. 2009. Rhodopsin molecular evolution in mammals inhabiting low light environments. PLoS One 4:e8326.