Variation in the pattern of nucleotide substitution across sites

Journal of Molecular Evolution

Volumn 48, Issue 1, 1999, Pages 86-93

  Huelsenbeck, John P ^a   Nielsen, Rasmus ^b,c  

^a Smithsonian Museum Support Center   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Likelihood ratio testing; Maximum likelihood; Molecular evolution; Molecular systematics; Phylogeny

Indexed keywords

ARTICLE; GENE EXPRESSION; GENE STRUCTURE; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN EXPRESSION;

ANIMALS; CODON; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; POINT MUTATION; PSEUDOGENES; VARIATION (GENETICS);

EID: 0032923454     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006448     Document Type: Article

References (27)

1. Churchill GA, von Haeseler A, Navidi WC (1992) Sample size for a phylogenetic inference. Mol Biol Evol 9:753-769
2. Cummings MP, Otto SP, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12: 814-822
3. Farris JS (1969) A successive approximations approach to character weighting. Syst Zool 18:374-385
4. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368-376
5. Fishman GS (1996) Monte Carlo. Springer-Verlag, New York
6. Golding GB (1983) Estimates of DNA and protein sequence divergence: An examination of some assumptions. Mol Biol Evol 1:125-142
7. Goldman N (1993) Statistical tests of models of DNA substitution. J Mol Evol 36:182-198
8. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736
9. Goloboff PA (1993) Estimating character weights during tree searches. Cladistics 9:83-91
10. Gu X, Fu Y-X, Li W-H (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 12:546-557
11. Hasegawa M, Yano T, Kishino H (1984) A new molecular clock of mitochondrial DNA and the evolution of Hominoids. Proc Japan Acad Ser B 60:95-98
12. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
13. Jin L, Nei M (1990) Limitations of the evolutionary parsimony method of phylogeny analysis. Mol Biol Evol 7:82-102
14. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86-93
15. Miyamoto MM, Slightom JL, Goodman M (1987) Phylogenetic relationships of humans and African apes as ascertained from DNA sequences (7.1 kilobase pairs) of the ψη-globin region. Science 238:369-373
16. Muse SV, Gaut S (1994) A likelihood approach for comparing synonymous and nonsynonymous substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715-724
17. Reeves JH (1992) Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J Mol Evol 35:17-31
18. Sidow A, Nguyen T, Speed TP (1992) Estimating the fraction of invariable codons with a capture-recapture method. J Mol Evol 35: 253-260
19. Swofford DL, Olsen GP, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Montz C, Mable BK (eds) Molecular systematics, 2nd ed. Sinauer, Sunderland, MA, pp 407-514
20. Tavaré S (1986) Some probabilistic and statistical problems on the analysis of DNA sequences. Lect Math Life Sci 17:57-86
21. Waddell PJ, Penny D (1996) Evolutionary trees of apes and humans from DNA sequences. In: Lock AJ, Peters CR (eds) Handbook of symbolic evolution. Clarendon Press, Oxford, pp 53-73
22. Wakeley J (1994) Substitution rate variation among sites and the estimation of transition bias. Mol Biol Evol 11:436-442
23. Yang Z (1993) Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10:1396-1401
24. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314
25. Yang Z (1996a) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 11:367-372
26. Yang Z (1996b) Maximum likelihood models for combined analyses of multiple sequence data. J Mol Evol 42:587-596
27. Yang Z, Goldman N, Friday AE (1994) Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Mol Biol Evol 11:316-324