Detecting excess radical replacements in phylogenetic trees

Gene

Volumn 319, Issue 1-2, 2003, Pages 127-135

  Pupko, Tal ^a   Sharan, Roded ^b   Hasegawa, Masami ^c   Shamir, Ron ^a   Graur, Dan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

^c INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

Author keywords

Carbonic anhydrase I; Chemical distance; Class I major histocompatibility complex glycoproteins; Dermaseptin related peptides; Maximum likelihood; Molecular evolution; Positive Darwinian selection

Indexed keywords

CARBONATE DEHYDRATASE I; GLYCOPROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

AMINO ACID SUBSTITUTION; CONFERENCE PAPER; GENETIC LINKAGE; GENETIC MODEL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR GENETICS; MOLECULAR PHYLOGENY; PHYLOGENETIC TREE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE; TAXONOMY;

DARWINIA;

EID: 0242321236     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00802-3     Document Type: Conference Paper

References (39)

1. Adachi J., Hasegawa M. MOLPHY: Programs for Molecular Phylogenetics Based on Maximum Likelihood, Version 2.3. 1996;Institute of Statistical Mathematics, Tokyo, Japan.
2. Dagan T., Talmor Y., Graur D. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol. Biol. Evol. 19:2002;1022-1025.
3. Duda T., Vanhoye D., Nicolas P. Roles of diversifying selection and coordinated evolution in the evolution of amphibian antimicrobial peptides. Mol. Biol. Evol. 19:2002;858-864.
4. Fay J., Wu C.-I. The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11:2001;642-646.
5. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
6. Grantham R. Amino acid difference formula to help explain protein evolution. Science. 185:1974;862-864.
7. Halanych K., Robinson T. Multiple substitutions affect the phylogenetic utility of cytochrome b and 12S rDNA data: examining a rapid radiation in Leporid (Lagomorpha) evolution. J. Mol. Evol. 48:1999;369-379.
8. Huelsenbeck J., Rannala B., Masly J. Accommodating phylogenetic uncertainty in evolutionary studies. Science. 288:2000;2349-2350.
9. Hughes A. Adaptive Evolution of Genes and Genomes. 1999;Oxford Univ. Press, New York.
10. Hughes A., Hughes M. Adaptive evolution in the rat olfactory receptor gene family. J. Mol. Evol. 36:1993;249-254.
11. Hughes A., Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 335:1988;167-170.
12. Hughes A., Yeager M. Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32:1998;415-435.
13. Hughes A., Ota T., Nei M. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major- histocompatibility-complex molecules. Mol. Biol. Evol. 7:1990;515-524.
14. Jones D., Taylor W., Thornton J. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:1992;275-282.
15. Kimura M. The Neutral Theory of Molecular Evolution. 1983;Cambridge Univ. Press, Cambridge.
16. Kishino H., Miyata T., Hasegawa M. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:1990;151-160.
17. Lee Y., Ota T., Vacquier V. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12:1995;231-238.
18. Lie P., Goldman N. Models of molecular evolution and phylogeny. Genome Res. 8:1998;1233-1244.
19. Miyata T., Miyazawa S., Yasunaga T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:1979;219-236.
20. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:1986;418-426.
21. Parham P., Lomen C., Lawlor D., Ways J., Holmes N., Coppin H., Salter R., Won A., Ennis P. Nature of polymorphism in HLA-A, -B, and -C molecules. Proc. Natl. Acad. Sci. U. S. A. 85:1988;4005-4009.
22. Pupko T., Pe'er L., Shamir R., Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol. 17:2000;890-896.
23. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
24. Seibert S., Howell C., Hughes M., Hughes A. Natural selection on the gag, pol, and env genes of human inummodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 12:1995;803-813.
25. Sneath P. Relations between chemical structure and biological activity in peptides. J. Theor. Biol. 12:1966;157-195.
26. Stewart C., Wilson A. Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters. Cold Spring Harbor Symp. Quant. Biol. 52:1987;891-899.
27. Swanson W., Yang Z., Wollner M., Aquadro C. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. U. S. A. 98:2001;2509-2514.
28. Swofford D., Olsen G., Waddell P., Hillis D. Phylogenetic inference. Hillis D., Moritz C., Mable B. Molecular Systematics. 2nd ed. 1995;407-514 Sinauer, Sunderland, MA.
29. Thorne J., Goldman N., Jones D. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:1996;666-673.
30. Wang H., Dopazo J., Carazo J. Self-organizing tree growing network for classifying amino acids. Bioinformatics. 14:1998;376-377.
31. Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1993;1396-1401.
32. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:1994;306-314.
33. Yang Z. Among-site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 11:1996;367-372.
34. Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51:2000;423-432.
35. Yang Z., Bielawski J. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:2000;496-503.
36. Yang Z., Kumar S., Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics. 141:1995;1641-1650.
37. Zhang J., Kumar S. Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14:1997;527-536.
38. Zhang J., Kumar S., Nei M. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol. Biol. Evol. 14:1997;1335-1338.
39. Zhang J., Rosenberg H., Nei M. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. U. S. A. 95:1998;3708-3713.