Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs

Genes and Genetic Systems

Volumn 75, Issue 2, 2000, Pages 79-92

  Sumida, Masayuki ^a   Kaneda, Hideki ^b   Kato, Yoji ^a   Kanamori, Yasushi ^a   Yonekawa, Hiromichi ^b   Nishioka, Midori ^a,c  

^a HIROSHIMA UNIVERSITY   (Japan)

^b TOKYO METROPOLITAN INSTITUTE OF MEDICAL SCIENCE   (Japan)

^c HIROSHIMA INTERNATIONAL UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; FROG; GENE LOCATION; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC VARIABILITY; JAPAN; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS;

ANIMALS; ANURA; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, MITOCHONDRIAL; GENE REARRANGEMENT; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; POLYMERASE CHAIN REACTION; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT;

EID: 0034174325     PISSN: 13417568     EISSN: None     Source Type: Journal    
DOI: 10.1266/ggs.75.79     Document Type: Article

References (75)

1. Aquadro, C. F., and Greenberg, B. D. (1983) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103, 287-312.
2. Brown, W. M. (1985) The mitochondrial genome of animals. In: Molecular Evolutionary Genetics (ed.: R. J. MacIntyre), pp. 95-130. Plenum Press, New York.
3. Brown, W. M., George, M. Jr., and Wilson, A. C. (1979) Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76, 1967-1971.
4. Brown, W. M., Prager, E. M., Wang, A., and Wilson, A. C. (1982) Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol. 18, 225-239.
5. Brown, G. G., Gadaleta, G., Pepe, G., Saccone, C., and Sbisà. E. (1986) Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192, 503-511.
6. Chang, D. D., and Clayton, D. A. (1985) Priming human mitochondrial DNA replication occurs at the light-strand promoter. Proc. Natl. Acad. Sci. USA 82, 351-355.
7. Clayton, D. A. (1992) Transcription and replication of animal mitochondrial DNAs. In: Mitochondrial Genomes (eds.; D. R. Wolstenholme, and K. W. Jeon), pp. 217-232. Academic Press, New York.
8. Cope, E. D. (1868) An examination of the Reptilia and Batrachia obtained by the Orton expedition to Equador and the upper Amazon, with notes on other species. Proc. Acad. Nat. Sci. Phila. 1868, 96-140.
9. Crews, S., Ojala, D., Posakony, J., Nishiguchi, J., and Attardi, G. (1979) Nucleotide sequence of a region of human mitochondrial DNA containing the precisely identified origin of replication. Nature 277, 192-198.
10. Davis, L. G., Dibner, M. D., and Battey, J. F. (1986) Basic Methods in Molecular Biology. Elsevier Science Publ., New York.
11. Doda, J. N., Wright, C. T., and Clayton, D. A. (1981) Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA 78, 6116-6120.
12. Dunon-Bluteau, D., and Brun. G. (1986) The secondary structures of the Xenopus laevis and human mitochondrial small ribosomal subunit RNA are similar. FEBS Lett. 198, 333-338.
13. Dunon-Bluteau, D., and Brun, G. (1987) Mapping at the nucleotide level of Xenopus laevis mitochondrial D-loop H strand: Structural features of the 3' region. Biochem. Intern. 14, 643-657.
14. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Pakage) Version 3.5c. Univ. Washington Press, Seattle.
15. Foran, L. A., Hixson, J. E., and Brown, W. M. (1989) Similarities of ape and human sequences that regulate mitochondrial DNA transcription and their DNA synthesis. Nucleic Acids Res. 17, 5841-5861.
16. García-Paris, M., Alcobendas, M., and Alberch, P. (1998) Influence of the Guadalquivir River Basin on mitochondrial DNA evolution of Salamandra salamandra (Caudata, Salamandridae) from southern Spain. Copeia 1998, 173-176.
17. Giorgi, C. D., Martiradonna, A., Lanave, C., and Saccone, C. (1996) Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: Conserved features of the echinoid mitochondrial genome. Mol. Phylogenet. Evol. 5, 323-332.
18. Härlid, A., Janke, A., and Arnason, U. (1997) The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds. Mol. Biol. Evol. 14, 754-761.
19. Hay, J. M., Ruvinsky, I., Hedges, S. B., and Maxson, L. R. (1995) Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12, 928-937.
20. Hedges, S. B., and Maxson, L. R. (1993) A molecular perspective on lissamphibian phylogeny. Herpetol. Monogr. 7, 27-42.
21. Hedges, S. B., Bezy, R. L., and Maxson, L. R. (1991) Phylogenetic relationships and biogeography of xantusiid lizards inferred from mitochondrial DNA sequences. Mol. Biol. Evol. 8, 767-780.
22. Hedges, S. B., Nussbaum, R. A., and Maxson, L. R. (1993) Caecilian phylogeny and biogeography inferred from mitochondrial DNA sequences of the 12S rRNA and 16S rRNA genes (Amphibia, Gymnophiona). Herpetol. Monogr. 7, 64-76.
23. Hoelzel, A. R., Hancock, J. M., and Dover, G. A. (1991) Evolution of the cetacean mitochondrial D-loop region. Mol. Biol. Evol. 8, 475-493.
24. Irwin, D. M., Kocher, T. D., and Wilson, A. C. (1991) Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144.
25. Kawamura, T. (1962) On the names of some Japanese frogs. J. Sci. Hiroshima Univ., Ser. B, Div. 1, 20, 181-193.
26. Kim, K. S., Lee, S. E., Jeong, H. W., and Ha, J. H. (1998) The complete nucleotide sequence of the domestic dog (Canis familiaris) mitochondrial genome. Mol. Phylogenet. Evol. 10, 210-220.
27. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
28. Kobel, H. R., Barandun, B., and Thiebaud, Ch. H. (1998) Mitochondrial rDNA phylogeny in Xenopus. Herpetol. Jour. 8, 13-17.
29. Lee, H.-I., Yang, D.-E., Kim, Y.-R., Lee, H., Lee, J.-E., Yang, S.-Y., and Lee, H.-Y. (1999) Genetic variation of the mitochondrial cytochrome b sequence in Korean Rana rugosa (Amphibia; Ranidae). Korean J. Biol. Sci. 3, 89-96.
30. Lopez, J. V., Cevario, S., and O'Brien, S. J. (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33, 229-246.
31. Macey, J. R., Larson, A., Ananjeva, N. B., Fang, Z., and Papenfuss, T. J. (1997) Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14, 91-104.
32. Macey, J. R., Schultell, J. A., Larson, A., Fang, Z., Wang, Y., Tuniyev, B. S., and Papenfuss, T. J. (1998) Phylogenetic relationships of toads in the Bufo bufo species group from the Eastern Escarpment of the Tibetan plateau: a case of vicariance and dispersal. Mol. Phylogenet. Evol. 9, 80-87.
33. Martin, A. P., Nayor, G. J. P., and Palumbi, S. R. (1992) Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357, 153-155.
34. Matsui, M., and Hikida, T. (1985) Tomoptera porosa Cope, 1868, a senior synonym of Rana brevipoda Ito, 1941 (Ranidae). J. Herpetol. 19, 423-425.
35. Moritz, C., Dowling, T. E., and Brown, W. M. (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18, 269-292.
36. Moritz, C., Schneider, C. J., and Wake, D. B. (1992) Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41, 273-291.
37. Moriya, K. (1954) Studies on the five races of the Japanese pond frog, Rana nigromaulata Hallowell. I. Differences in the morphological characters. J. Sci. Hiroshima Univ., Ser. B, Div. 1, 15, 1-21.
38. Moriya, K. (1960a) Studies on the five races of the Japanese pond frog, Rana nigromaulata Hallowell. II. Differences in characters of development. J. Sci. Hiroshima Univ., Ser. B, Div. 1, 18, 109-124.
39. Moriya, K. (1960b) Studies on the five races of the Japanese pond frog, Rana nigromaulata Hallowell. III. Sterility in interracial hybrids. J. Sci. Hiroshima Univ., Ser. B, Div. 1, 18, 125-156.
40. Nei, M. (1975) Molecular Population Genetics and Evolution. North-Holland, Amsterdam.
41. Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
42. Nishioka, M., Ueda, H., and Sumida, M. (1981) Genetic variation of five enzymes in Japanese pond frogs. Sci. Rep. Lab. Amphibian Biol., Hiroshima Univ. 5, 107-153.
43. Nishioka, M., Sumida, M., and Ohtani, H. (1992) Differentiation of 70 populations in the Rana nigromaculata group by the method of electrophoretic analyses. Sci. Rep. Lab. Amphibian Biol., Hiroshima Univ. 11, 1-70.
44. Nishioka, M., and Sumida, M. (1992) Biochemical differentiation of pond frogs distributed in the Palearctic region. Sci. Rep. Lab. Amphibian Biol., Hiroshima Univ. 11, 71-108.
45. Rand, D. M. (1993) Endotherms, ectotherms, and mitochondrial genome-size variation. J. Mol. Evol. 37, 281-295.
46. Rand, D. M. (1994) Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9, 125-131.
47. Rand, D. M., and Harrison, R. G. (1989) Molecular population genetics of mtDNA size variation in crickets. Genetics 121, 551-559.
48. Richards, C. M., and Moore, W. S. (1996) A phylogeny for the African treefrog family Hyperoliidae based on mitochondrial rDNA. Mol. Phylogenet. Evol. 5, 522-532.
49. Richards, C. M., and Moore, W. S. (1998) A molecular phylogenetic study of the old world treefrog family Rhacophoridae. Herpetol. Jour. 8, 41-46.
50. Roe, B. A., Ma, D.-P., Wilson, R. K., and Wong, F.-H. (1985) The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260, 9759-9774.
51. Ruvinsky, I., and Maxson, L. R. (1996) Phylogenetic relationships among bufonid frogs (Anura: Neobatrachia) inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 5, 533-547.
52. Saccone, C., Attimonelli, M., and Sbisà, E. (1987) Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA. J. Mol. Evol. 26, 205-211.
53. Saccone, C., Pesole, G., and Sbisà, E. (1991) The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33, 83-91
54. Saitou, N., and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
55. Shaffer, H. B., and McKnight, M. L. (1996) The polytypic species revisited: Genetic differentiation and molecular phylogenetic of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex. Evolution 50, 417-433.
56. Shields, G. F., and Wilson, A. C. (1987) Calibration of mitochondrial DNA evolution in geese. J. Mol. Biol. 24, 212-217.
57. Sumida, M. (1980) Electrophoretic study on the hemoglobin of Japanese pond frogs. Sci. Rep. Lab. Amphibian Biol., Hiroshima Univ. 4, 239-248.
58. Sumida, M. (1997) Inheritance of mitochondrial DNAs and allzymes in the female hybrid lineages of two Japanese pond frog species. Zool. Sci. 14, 277-286.
59. Sumida, M., and Ogata, M. (1998) Intraspecific differentiation in the Japanese brown frog Rana japonica inferred from mitochondrial DNA sequences of the cytochrome b gene. Zool. Sci. 15, 989-1001.
60. Sumida, M., Ogata, M., Kaneda, H., and Yonekawa, H. (1998) Evolutionary relationships among Japanese pond frogs inferred from mitochondrial DNA sequences of cytochrome b and 12S ribosomal RNA genes. Genes Genet. Syst. 73, 121-133.
61. Sumida, M., Ogata, M., and Nishioka, M. (2000) Molecular phylogenetic relationships of pond frogs distributed in the Palearctic region inferred from DNA sequences of mitochondrial 12S ribosomal RNA and cytochrome b genes. Mol. Phylogenet. Evol. 13, in press.
62. Tanaka, T., Matsui, M., and Takenaka, O. (1994) Estimation of phylogenetic relationships among Japanese brown frogs from mitochondrial cytochrome b gene (Amphibia, Anura). Zool. Sci. 11, 753-757.
63. Tanaka, T., Matsui, M., and Takenaka, O. (1996) Phylogenetic relationships of Japanese brown frogs (Rana: Ranidae) assessed by mitochondrial cytochrome b gene sequences. Biochem. Syst. Ecol. 24, 299-307.
64. Tanaka, T., Matsui, M., and Takenaka, O. (1998) Local population differentiation and phylogenetic relationships of Russian brown frog, Rana amurensis inferred by mitochondrial cytochrome b gene sequences (Amphibia, Ranidae). Jpn. J. Herpetol. 17, 91-97.
65. Tanaka-Ueno, T., Matsui, M., Chen, S.-L., Takenaka, O., and Ohta, H. (1998a) Phylogenetic relationships of brown frogs from Taiwan and Japan assessed by mitochondrial cytochrome 6 gene sequences (Rana: Ranidae). Zool. Sci. 15, 283-288.
66. Tanaka-Ueno, T., Matsui, M., Sato, T., Takenaka, S., and Takenaka, O. (1998b) Phylogenetic relationships of brown frogs with 24 chromosomes from Far East Russia and Hokkaido assessed by mitochondrial cytochrome b gene sequences (Rana: Ranidae). Zool. Sci. 15, 289-294.
67. Titus, T. A., and Larson, A. (1995) A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 44, 125-151.
68. Tsuda, K., Kikkawa, Y., Yonekawa, H., and Tanabe, Y. (1997) Extensive interbreeding occurred among multiple matriarchal ancestors during the domestication of dogs: evidence from inter-and intraspecies polymorphisms in the D-loop region of mitochondrial DNA between dogs and wolves. Genes Genet. Syst. 72, 229-238.
69. Wilkinson, G. S., and Chapman, A. M. (1991) Length and sequence variation in evening bat D-loop mtDNA. Genetics 128, 607-617.
70. Wilson, A. C., Cann, R. C., Carr, S. M., George, M. Jr., Gyllensten, U. B., Helm-Bychowski, K., Higuchi, R. C., Palumbi, S. R., Prager, E. M., Sage, R. D., and Stoneking, M. (1985) Mitochondrial DNA and two perspective on evolutionary genetics. Biol. J. Linnean Soc. 26, 375-400.
71. Wolstenholme, D. R. (1992) Animal mitochondrial DNA: structure and evolution. In: Mitochondrial Genomes (eds.: D. R. Wolstenholme, and K. W. Jeon), pp. 173-216. Academic Press, New York.
72. Wong, J. F. H., Ma, D. P., Wilson, R. K., and Roe, B. A. (1983) DNA sequence of the Xenopus laevis mitochondrial heavy and light strand replication origins and flanking tRNA genes. Nucleic Acid Res. 11, 4977-4995.
73. Xu, X., Janke, A., and Arnason, U. (1996) The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationships among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea). Mol. Biol. Evol. 13, 1167-1173.
74. Yang, Y.-J., Lin, Y.-S., Wu, J.-L., and Hui, C.-F. (1994) Variation in mitochondrial DNA and population structure of the Taipei treefrog Rhacophorus taipeianus in Taiwan. Mol. Ecol. 3, 219-228.
75. Yoneyama, Y. (1987) The nucleotide sequences of the heavy and light strand replication origins of the Rana catesbeiana mitochondrial genome. J. Nippon Med. Sch. 54, 429-440.