Substitution rates of organelle and nuclear genes in sharks: Implicating metabolic rate (again)

Molecular Biology and Evolution

Volumn 16, Issue 7, 1999, Pages 996-1002

  Martin, Andrew P ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Nuclear; Nucleotide substitution; Organelle; Sharks

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

AEROBIC METABOLISM; ARTICLE; DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; GENE MUTATION; GENE REPLICATION; GENE TARGETING; GERM LINE; METABOLIC RATE; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; SHARK;

CHONDRICHTHYES; MAMMALIA;

EID: 0033007378     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026189     Document Type: Article

References (56)

1. ADACHI, J., Y. CAO, and M. HASEGAWA. 1993. Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J. Mol. Evol. 36:270-281.
2. AGARWAL, S., and R. S. SOHAL. 1994. DNA oxidative damage and life expectancy in houseflies. Proc. Natl. Acad. Sci. USA 91:12332-12335.
3. AVISE, J. C., B. W. BOWEN, T. LAMB, A. B. MEYLAN, and E. BERMINGHAM. 1992. Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines. Mol. Biol. Evol. 9:457-473.
4. BERNARDI, G., and G. BERNARDI. 1986. Compositional constraints and genome evolution. J. Mol. Evol. 24:1-11.
5. BLEIWEISS, R. 1998. Relative-rate tests and biological causes of molecular evolution in hummingbirds. Mol. Biol. Evol. 15:481-491.
6. BRIDGES, B. A. 1997. DNA turnover and mutation in resting cells. Bioessays 19:347-352.
7. BRITTEN, R. J. 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231:1393-1398.
8. BROMHAM, L., A. RAMBAUT, and P. H. HARVEY. 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43:610-621.
9. CAILLIET, G. M., and D. W. BEDFORD. 1983. The biology of three pelagic sharks from California waters, and their emerging fisheries: a review. Calif. COFI Rep. 24:57-69.
10. CHARLESWORTH, B. 1993 More mutations in males? Curr. Biol. 3:466-467.
11. CLARK, A. G., L. WANG, and T. HULLEBERG. 1995. Spontaneous mutation rate of modifiers of metabolism in Drosophila. Genetics 139:767-779.
12. COMPAGNO, L. V. J. 1984. FAO species catalog sharks of the world. Vol. 1. FAO Fish. Synop. 125:1-249.
13. CORTOPASSI, G. A., and E. WANG. 1996. There is substantial agreement among interspecies estimates of DNA repair activity. Mech. Ageing Dev. 91:211-218.
14. CROTEAU, D. L., and V. A. BOHR. 1997. Repair of oxidative damage to nuclear and mitochondrial DNA in mammalian cells. J. Biol. Chem. 272:25409-25412.
15. DAWSON, K. J. 1998. Evolutionarily stable mutation rates. J. Theor. Biol. 194:143-157.
16. FARRIS, J. S., M. KALLERSJO, A. KLUGEM, and C. BULT. 1995. Testing significance of incongruence. Cladistics 10:315-319.
17. GILLESPIE, J. H. 1991. The causes of molecular evolution. Oxford University Press, N.Y.
18. HASEGAWA, M., H. KISHINO, and T. YANO. 1985. Dating the human-ape splitting by a molecular clock. J. Mol. Evol. 22: 160-174.
19. HELBOCK, H. J., K. B. BECKMAN, M. K. SHIGENAGA, P. B. WALTER, A. A. WOODALL, H. C. YEO, and B. N. AMES. 1998. DNA oxidation matters: the HPLC-electrochemical detection assay of 8-oxo-deoxyguanosine and 8-oxo-guanine. Proc. Natl. Acad. Sci. USA 95:288-293.
20. HUELSENBECK, J. P., and B. RANNALA. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.
21. HURST, L. D., and H. ELLEGREN. 1998. Sex biases in the mutation rate. Trends Genet. 14:446-452.
22. KOCHER, T. D., and K. L. CARLETON. 1997. Base substitution in fish mitochondrial DNA.: patterns and rates. Pp. 13-24 in T. D. KOCHER and C. A STEPIEN, eds. Molecular systematics of fishes. Academic Press, New York.
23. KOHNE, D. E. 1970. Evolution of higher-organism DNA. Q. Rev. Biophys. 33:327-375.
24. KONARZEWSKI, M., and J. DIAMOND. 1995. Evolution of basal metabolic rate and organ masses in laboratory mice. Evolution 49:1239-1248.
25. LI, W.-H. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
26. LIU, K.-M., P.-J. CHIANG, and C.-T. CHEN. 1998. Age and growth estimates of the bigeye thresher shark, Alopias superciliosus, in northeastern Taiwan waters. Fish. Bull. 96: 482-491.
27. LOEB, L. A., and K. C. CHENG. 1990. Errors in DNA synthesis: a source of spontaneous mutations. Mutat. Res. 238:297-304.
28. MARTIN, A. P. 1995. Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. Mol. Biol. Evol. 12:1124-1131.
29. MARTIN, A. P., G. J. P. NAYLOR, and S. R. PALUMBI. 1992. Rate of mitochondrial DNA evolution is slow in sharks compared to mammals. Nature 357:153-155.
30. MARTIN, A. P., and S. P. PALUMBI. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90:4087-4091.
31. MARTIN, G. M., C. E. OGBURN, L. M. COLGIN, A. M. GOWN, S. D. EDLAND, and R. J. MONNAT JR. 1996. Somatic mutations are frequent and increase with age in human kidney epithelial cells. Hum. Mol. Genet. 5:215-221.
32. MASON, J. M., R. VALENCIA, R. C. WOODRUFF, and S. ZIMMERING. 1985. Genetic drift and seasonal variation in spontaneous mutation frequencies in Drosophila. Environ. Mutagen. 7:663-676.
33. MINDELL, D. P., A. KNIGHT, C. BAER, and C. J. HUDDLESTON. 1996. Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypotheses. Mol. Biol. Evol. 13:422-436.
34. MIYATA, T., H. HAYASHIDA, K. KUMA, K. MITSUYASU, and T. YASUNAGA. 1987. Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harb. Symp. Quant. Biol. 52:863-867.
35. MOOERS, A. O., and P. H. HARVEY. 1994. Metabolic rate, generation time, and the rate of molecular evolution. Mol. Phylogenet. Evol. 3:344-350.
36. MULLER-WEEKS, S. B. MASTRAN, and S. CARADONNA. 1998. The nuclear isoform of the highly conserved human uracil-DNA glycosylase is an Mr 36,000 phosphoprotein. J. Biol. Chem. 273:21909-21917.
37. NAGELHUS, T. A., G. SLUPPHAUG, T. LINDMO, and H. E. KROKAN. 1995. Cell cycle regulation and subcellular localization of the major human uracil-DNA glycosylase. Exp. Cell Res. 220:292-297.
38. NARAYANAN, L., J. A. FRITZELL, S. M. BAKER, R. M. LISKAY, and P. M. GLAZER. 1997. Elevated levels of mutation in multiple tissues of mice deficient in the DNA mismatch repair gene Pms2. Proc. Natl. Acad. Sci. USA 94:3122-3127.
39. NAYLOR, G. J. P., A. P. MARTIN, E. MATTISON, and W. M. BROWN. 1997. The inter-relationships of lamniform sharks: testing phylogenetic hypotheses with sequence data. Pp. 199-218 in T. D. KOCHER and C. STEPIEN, eds. Molecular systematics of fishes. Academic Press, New York.
40. NOTHEL, H. 1987. Adaptation of Drosophila melanogaster populations to high mutation pressure: evolutionary adjustment of mutation rates. Proc. Natl. Acad. Sci. USA 84: 1045-1049.
41. NUNN, G. B., and S. E. STANLEY. 1998. Body size effects and rates of cytochrome b evolution in tube-nosed seabirds. Mol. Biol. Evol. 15:1360-1371.
42. PINZ, K. G., and D. F. BOGENHAGEN. 1998. Efficient repair of abasic sites in DNA by mitochondrial enzymes. Mol. Cell. Biol. 18:1257-1265.
43. RAND, D. M. 1994. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9:125-131.
44. REZNICK, D. N., F. G. SHAW, F. H. RODD, and R. G. SHAW. 1997. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science 275:1934-1937.
45. RICHTER, C., J.-W. PARK, and B. N. AMES. 1988. Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc. Natl. Acad. Sci. USA 85:6465-6467.
46. RYOJI, M., H. KATAYAMA, H. FUSAMAE, A. MATSUDA, F. SAKAI, and H. UTANO. 1996. Repair of DNA damage in a mitochondrial lysate of Xenopus laevis oocytes. Nucleic Acids Res. 24:4057-4062.
47. SHARP, P. M., and W.-H. LI. 1989. On the rate of DNA sequence evolution in Drosophila. J. Mol. Evol. 28:398-405.
48. SIMPSON, A. J. 1997. The natural somatic mutation frequency and human carcinogenesis. Adv. Cancer Res. 71:209-240.
49. SWOFFORD, D. S. 1998. PAUP: phylogenetic analysis using parsimony. Version 4.0*b. Sinauer, Sunderland, Mass.
50. TAKAO, M., H. ABURATANI, K. KOBAJASHI, and A. YASUI. 1998. Mitochondrial targeting of human DNA glycosylases for repair of oxidative DNA damage. Nucleic Acids Res. 26:2917-2922.
51. THOMAS, W. K., and A. C. WILSON. 1991. Mode and tempo of molecular evolution in the nematode caenorhabditis: cytochrome oxidase II and calmodulin sequences. Genetics 128: 269-279.
52. THYAGARAJAN, B., R. A. PADUA, and C. CAMPBELL. 1996. Mammalian mitochondria possess homologous DNA recombination activity. J. Biol. Chem. 271:27536-27543.
53. VAWTER, L., and W. M. BROWN. 1986. Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science 234:194-196.
54. WAGNER, J. R., C.-C. HU, and B. N. AMES. 1992. Endogenous oxidative damage of deoxycytidine in DNA. Proc. Natl. Acad. Sci. USA 89:3380-3384.
55. WANG, D. Y.-C., S. KUMAR, and S. B. HEDGES. 1999. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond. B Biol. Sci. 266:163-171.
56. WOODRUFF, R. C., J. N. THOMPSON JR., M. A. SEEGER, and W. E. SPIVEY. 1984. Variation in spontaneous mutation and repair in natural population lines of Drosophila melanogaster. Heredity 53:223-234.