pANT: A Method for the Pairwise Assessment of Nonfunctionalization Times of Processed Pseudogenes

Molecular Biology and Evolution

Volumn 20, Issue 11, 2003, Pages 1876-1880

  Fleishman, Sarel J ^a   Dagan, Tal ^a   Graur, Dan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Computational method; Galactosyltransferase; Molecular evolution; Nonfunctionalization; Pseudogenes; Substitution rates

Indexed keywords

ALPHA 1,3 GALACTOSYLTRANSFERASE; GALACTOSYLTRANSFERASE; NUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CODON; GENE SEQUENCE; HUMAN; MOLECULAR EVOLUTION; MONKEY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PAIRWISE ASSESSMENT OF NONFUNCTIONALIZATION TIMES; PALEONTOLOGY; PROBABILITY; PSEUDOGENE; SEQUENCE HOMOLOGY; STATISTICAL MODEL; TAXONOMY;

ANIMALS; CALIBRATION; CEBIDAE; CERCOPITHECIDAE; EVOLUTION, MOLECULAR; GALACTOSYLTRANSFERASES; GENETICS; MODELS, GENETIC; MODELS, STATISTICAL; TIME FACTORS;

CERCOPITHECIDAE; PLATYRRHINI;

EID: 0242582365     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg202     Document Type: Article

References (17)

1. Boyce, W. E., and R. C. Diprima. 1977. Elementary differential equations. Wiley, New York.
2. Galili, U., and K. Swanson. 1991. Gene sequences suggest inactivation of α-1,3-galactosyltransferase in catarrhines after the divergence of apes from monkeys. Proc. Natl. Acad. Sci. USA 88:7401-7404.
3. Gojobori, T., W. H. Li, and D. Graur. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18:360-369.
4. Goodman, M., C. A. Porter, J. Czelusniak, S. L. Page, H. Schneider, J. Shoshani, G. Gunnell, and C. P. Groves. 1998. Towards a phylogenetic classification of primates based on DNA evidence complemented by fossil data. Mol. Phyl. Evol. 9:585-598.
5. Graur, D., and W. H. Li. 1999. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, Mass.
6. Joziasse, D. H., J. H. Shaper, E. W. Jabs, and N. L. Shaper. 1991. Characterization of an α-1,3-galactosyltransferase homologue on human chromosome 12 that is organized as a processed pseudogene. J. Biol. Chem. 266:6991-6998.
7. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-32 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
8. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
9. Koike, C., J. J. Fung, D. A. Geller, R. Kannagi, T. Libert, P. Luppi, I. Nakashima, J. Profozich, W. Rudert, S. B. Sharma, T. E. Starzl, and M. Trucco. 2002. Molecular basis of evolutionary loss of the α -1,3-galactosyltransferase genes in higher primates. J. Biol. Chem. 277:10114-10120.
10. Li, W. H., T. Gojobori, and M. Nei. 1981. Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239.
11. Miyata, T., and T. Yasunaga. 1981. Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history. Proc. Natl. Acad. Sci. U.S.A. 78:450-453.
12. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
13. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press, New York.
14. Ophir, R. 1999. The contribution of mutational factors and functional constraints to the molecular evolution of murids and humans. Doctoral thesis, Tel-Aviv University.
15. Shaul, S., and D. Graur. 2002. Playing chicken (Gallus gallus): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points. Gene 300:59-61.
16. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
17. Zhang, Z., P. Harrison, and M. Gerstein. 2002. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res. 12:1466-1482.