Molecular evolution and phylogenetic utility of the Polyubiquitin locus in mammals and higher vertebrates

Molecular Phylogenetics and Evolution

Volumn 6, Issue 2, 1996, Pages 259-269

  Vrana, Paul B ^a,b,c   Wheeler, Ward C ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b Columbia University ^*  (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA; VERTEBRATA;

BIOPOLYMER; DNA; POLYUBIQUITIN; UBIQUITIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CLASSIFICATION; CODON; GENETIC VARIABILITY; GENETICS; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BIOPOLYMERS; CODON; DNA; EVOLUTION, MOLECULAR; HUMANS; MAMMALS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; POLYUBIQUITIN; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; UBIQUITINS; VARIATION (GENETICS); VERTEBRATES;

EID: 0030253236     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1996.0075     Document Type: Article

References (24)

1. Allard, M. W., Ellsworth, D. L., and Honeycutt, R. L. (1991). The production of single-stranded DNA suitable for sequencing using the polymerase chain reaction. BioTechniques 10: 24-26.
2. D'Onofrio, G., Mouchiroud, D., Aïssani, B., Gautier, C., and Bernardi, G. (1991). Correlations between the compositional properties of human genes, codon usage, and amino acid compositions of proteins. J. Mol. Evol. 32: 504-510.
3. Ellsworth, D. L., Hewett-Emmett, D., and Li, W. H. (1994). Evolution of base composition in the insulin and insulin-like growth factors genes. Mol. Biol. Evol. 11: 875-885.
4. Finley, D., and Varshavsky, A. (1985). The ubiquitin system: Functions and mechanisms. Trends Biochem. Sci. 10: 343-347.
5. Hedges, S. B., Moberg, K. D., and Maxson, L. R. (1990). Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol. Biol. Evol. 7: 607-633.
6. Le, H. L. V., Lecointre, G., and Perasso, R. (1993). A 28S rRNA-based phylogeny of the Gnathostomes: First steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylogenet. Evol. 2: 31-51.
7. Maisey, J. G. (1986). Heads and tails: A chordate phylogeny. Cladistics 2: 201-256.
8. Mita, K., Ichimura, S., and Nenoi, M. (1991). Essential factors determining codon usage in ubiquitin genes. J. Mol. Evol. 33: 216-225.
9. Müller, W. E. G., Schröder, H. C., Müller, I. M., and Gamulin, V. (1994). Phylogenetic relationship of ubiquitin repeats in the polyubiquitin gene from the marine sponge Geodia cydonium. J. Mol. Evol. 39: 369-377.
10. Nemer, M., Rondinelli, E., Infante, D., and Infante, A. A. (1991). Polyubiquitin RNA characteristics and conditional induction in sea urchin embryos. Dev. Biol. 145: 255-265.
11. Novacek, M. J. (1992). Mammalian phylogeny: Shaking the tree. Nature 356: 121-125.
12. Özkaynak, E., Finley, D., Soloman, M. J., and Varshavsky, A. (1987). The yeast ubiquitin genes: A family of natural gene fusions. EMBO J. 6: 1429-1439.
13. Rechsteiner, M. (1991). Natural substrates of the ubiquitin proteolytic pathway. Cell 66: 615-618.
14. Richard, I., and Beckman, J. S. (1995). How neutral are synonymous codon mutations? Nature Genet. 10: 259.
15. Sharp, P. M., and Li, W-H. (1987a). Molecular evolution of ubiquitin genes. Trends Ecol. Evol. 2: 328-332.
16. Sharp, P. M., and Li, W-H. (1987b). Ubiquitin genes as a paradigm of concerted evolution of tandem repeats. J. Mol. Evol. 25: 58-64.
17. Sharp, P. M., and Matassi, G. (1994). Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4: 851-860.
18. Swofford, D. L. (1993). "PAUP Users Manual Version 3.1.1," Illinois Natural History Survey, Champaign, IL.
19. Tan, Y., Bishoff, S. T., and Riley, M. A. (1993). Ubiquitins revisited: Further examples of within- and between-locus concerted evolution. Mol. Phylogenet. Evol. 2: 351-360.
20. Vijay-Kumar, S., Bugg, C. E., Wilkinson, K. D., and Cook, W. J. (1985). Three-dimensionsl structure of ubiquitin at 2,8 resolution. Proc. Natl. Acad. Sci. USA 82: 3582-3585.
21. Vrana, P. B., Milinkovitch, M. C., Powell, J. R., and Wheeler, W. C. (1994). Higher level relationships of the arctoid carnivora based on sequence data and total evidence. Mol. Phylogenet. Evol. 3: 47-58.
22. Wheeler, W. C., Cartwright, P., andHayashi, C. Y. (1993). Arthropod phylogeny: A combined approach. Cladistics 9: 1-39.
23. Wolfe, K. (1991). Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
24. Wray, C. G., and DeSalle, R. (1994). Phylogenetic utility of ubiquitin DNA sequence from 3 marine protist lineages. Mol. Marine Biol. Biotech. 3: 13-22.